Index (SMRT View)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

AboutDialog - Class in com.pacbio.secondary.vis.gui.dialogs: Application about dialog
AboutDialog(Frame, VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.AboutDialog
abs_max_coverage - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
ABS_MAX_DETAILS_MAX_COVERAGE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
ABS_MAX_DETAILS_VIEW_DYNAMIC_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
ABS_MAX_DETAILS_VIEW_FIXED_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
ABS_MIN_SCREEN_WIDTH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
ABS_MIN_SCREN__HEIGHT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
AbstractCellEditor - Class in com.pacbio.secondary.vis.gui.control.treetable: Abstract cell editor
AbstractCellEditor() - Constructor for class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor
AbstractTreeTableModel - Class in com.pacbio.secondary.vis.gui.control.treetable: An abstract implementation of the TreeTableModel interface, handling the list of listeners.
AbstractTreeTableModel(Object) - Constructor for class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
AbstractTreeTableModel() - Constructor for class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
accept(File) - Method in class com.pacbio.secondary.vis.common.utils.filefilter.FileFilterGeneric
accept(File, String) - Method in class com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterDirectory
accept(File, String) - Method in class com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterGeneric
accept(File, String) - Method in class com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterMultipleExtensions
accept(IntervalTreeVisitor) - Method in class com.pacbio.secondary.vis.data.interval.IntervalTree: Recursively applies for each node the given visitor.
accept(int, IntervalTreeVisitor) - Method in class com.pacbio.secondary.vis.data.interval.IntervalTreeNode
acceptDockingAction(DockingActionEvent) - Method in interface pub.vlsolutions.swing.docking.event.DockingActionListener: Invoked before a docking action is processed, to give a chance to the listener to react to it and cancel it if needed.
acceptDrag(Shape) - Method in class pub.vlsolutions.swing.docking.event.DockDragEvent: Used by a DockDropReceiver to indicate that the drag operation is accepted (mouse is over a droppable zone).
acceptDrop() - Method in class pub.vlsolutions.swing.docking.event.DockDropEvent: shortcut for acceptDrop(true).
acceptDrop(boolean) - Method in class pub.vlsolutions.swing.docking.event.DockDropEvent: notifies the event manager that docking is accepted.
acceptNewDataAndClear(GenomicViewDetailsData, Interval, WsResults, String) - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage
acceptNewDataAndClear(GenomicViewDetailsData, int, Interval, String) - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage
acceptNewDataAndClear(GenomicViewDetailsData, int, Interval, String) - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage
acceptOverwriteExistingLocalFile(Component, String) - Static method in class com.pacbio.secondary.vis.common.utils.FileUtils
acceptOverwriteExistingServerFile(VioletApp, String, String) - Static method in class com.pacbio.secondary.vis.common.utils.FileUtils
action - Variable in class pub.vlsolutions.swing.docking.event.DockEvent: The action corresponding to the drag and drop gesture (actions can be seen as allowed docking gestures)
action - Variable in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton: The action triggered when the clicks on the icon
ACTION_ADD_DOCKABLE - Static variable in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Field associated to an addDockable action
ACTION_CLOSE - Static variable in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Field associated to a closing action
ACTION_CREATE_TAB - Static variable in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Field associated to a createTab action
ACTION_SPLIT_COMPONENT - Static variable in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Field associated to a split component action
ACTION_SPLIT_DOCKABLE - Static variable in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Field associated to a split dockable action
ACTION_SPLIT_DOCKABLE_CONTAINER - Static variable in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Field associated to a multipurpose (API internals) splut container action
ACTION_STATE_CHANGE - Static variable in class pub.vlsolutions.swing.docking.event.DockingActionEvent: A multipurpose action used to describe maximize, hide and detach actions
actionFileAddTracksFromServer() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO
actionFileExportAsGraphics() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO
actionFileExportDataAsGFF() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO
actionFileNew() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionFileOpenData() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO
actionFileOpenJobFromServer() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO
actionFilePrint() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO
actionFilePrinterSettings() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO
actionFileRemoveTrack() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO
actionFileSaveSession() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO
actionGoToLocation() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionInstallSMRTView() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionLayout(String) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionMagnification(String) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions: set magnification of active view
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.control.VioletToolBarTest
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.AboutDialog
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx: This is called when users click on a check box
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.PrintOptionsDialog.myActionListener
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.PropertiesDialog
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel
actionPerformed(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor: Handles events from the editor button and from the dialog's OK button.
actionProgramOptions() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionSessionProperties() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO: Show file properties
actionToggleFilterAnnotationsByVariants(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionToggleKinetics(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionToggleLinkPanels(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionToggleLockRegionGenomicRange(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionToggleRetrieveDetailedAnnotations(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionToggleShowMapQV(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionToggleShowQV(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionToggleShowReads(ActionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
actionViewInsertions(String) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
active - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
ACTIVE_TITLE_BACKGROUND - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
ACTIVE_TITLE_FOREGROUND - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
actual_genomic_end - Variable in class com.pacbio.secondary.vis.io.indexer.indexinfo.FileIndexInfo
actual_genomic_start - Variable in class com.pacbio.secondary.vis.io.indexer.indexinfo.FileIndexInfo
add(byte) - Method in class com.pacbio.secondary.vis.common.collection.ByteArrayList: Appends the specified element to the end of this list.
add(int, byte) - Method in class com.pacbio.secondary.vis.common.collection.ByteArrayList: Inserts the specified element at the specified position in this list.
add(T) - Method in class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet
add(T) - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet
add(Marker) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection: Adds a marker to the collection
add(Marker) - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage
add(AutoHideButton) - Method in class pub.vlsolutions.swing.docking.AutoHideButtonPanel: Adds a new AutoHideButton.
add(Component, Object) - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer: Overriden to track component constraints
add(JToolBar) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanel: Adds a new toolbar respecting the given positionning constraints.
add(JToolBar, int) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanel: Adds a new JToolBar to the Panel at the given row.
add(VLToolBar, ToolBarConstraints) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanel: Adds a new toolbar respecting the given positionning constraints.
add(Component) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar: Overriden to track AbstractButton added
add(AbstractButton) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar: Adds a new button to this toolbar
add(JButton) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar: Adds a new button to this toolbar
add_return(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse: Auto generated add method for the array for convenience
add_return(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse: Auto generated add method for the array for convenience
add_return(VisServiceStub.WsFileInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse: Auto generated add method for the array for convenience
add_return(VisServiceStub.WsTrackInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse: Auto generated add method for the array for convenience
addAnimationListener(AnimationListener) - Method in class pub.vlsolutions.swing.docking.animation.ComponentAnimator: Adds a new listener to the animator
addBaseModInfo(StringBuffer, Marker, String, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
addButtons(ActionListener) - Method in class com.pacbio.secondary.vis.gui.control.VioletToolBar
addCellEditorListener(CellEditorListener) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor
addChangeListener(ChangeListener) - Method in class com.pacbio.secondary.vis.common.collection.ChangeNotifier
addChangeListener(ChangeListener) - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel
addChangeListener(ChangeListener) - Method in interface com.pacbio.secondary.vis.gui.evt.IChangeNotifier: All listeners have to be notified when this object changes.
addContigSummaryInfo(DeNovoContigInfo) - Method in class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage: Called by summary parser
addDataSetFromModelToSlots(VariableResolutionDataModel) - Method in class com.pacbio.secondary.vis.data.session.DataStorage
addDefaultBand(String, int, int, int, int) - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB
addDesktop(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockingContext: Adds a desktop to this context
addDesktop(WSDesktop) - Method in class pub.vlsolutions.swing.docking.ws.Workspace: Adds a new desktop to this workspace
addDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Adds a dockable in the docking desktop.
addDockable(Dockable, RelativeDockablePosition) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Adds a dockable in the docking desktop, and tries to respect the relative positionning provided.
addDockable(CompoundDockable, Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Adds a dockable inside a compound dockable.
addDockable(Dockable, int) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane: Adds a new tab respecting the presentation and constraints of the component.
addDockable(Dockable, int) - Method in interface pub.vlsolutions.swing.docking.TabbedDockableContainer: Adds a dockable to the given index tab.
addDockable(WSDockKey) - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop: Adds the first dockable to this desktop.
addDockable(WSDockKey, WSDockKey) - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop: Adds a dockable into a compound dockable
addDockableSelectionListener(DockableSelectionListener) - Method in class pub.vlsolutions.swing.docking.DockingContext: Adds a new DockableSelectionListener to this desktop.
addDockableSelectionListener(DockableSelectionListener) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Adds a new DockableSelectionListener to this desktop.
addDockableStateChangeListener(DockableStateChangeListener) - Method in class pub.vlsolutions.swing.docking.DockingContext: Adds a new DockableStateChangeListener to this desktop.
addDockableStateChangeListener(DockableStateChangeListener) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Adds a new DockableStateChangeListener to this desktop.
addDockableStateWillChangeListener(DockableStateWillChangeListener) - Method in class pub.vlsolutions.swing.docking.DockingContext: Adds a new DockableStateWillChangeListener to this desktop.
addDockableStateWillChangeListener(DockableStateWillChangeListener) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Adds a new DockableStateWillChangeListener to this desktop.
addDockingActionListener(DockingActionListener) - Method in class pub.vlsolutions.swing.docking.DockingContext
addDockingActionListener(DockingActionListener) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Adds a new DockingActionListener to this desktop.
addDockingDesktopListeners() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
addExperienceIndexMetrics(long, long, double) - Method in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics: adds one new metrics data point
addExtension(String) - Method in class com.pacbio.secondary.vis.common.utils.filefilter.FileFilterGeneric: Adds an extension to this filter.
addFileInfoToTracks(List<WsTrackInfo>, String, String, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.MetadataInfoParser
addFilterItemsToLayout() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase: creates optional ui filter elements
addGeneHtmlTooltip(GenomicViewEvents, StringBuffer, Marker, NumberFormat, boolean) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: gene tooltip
addGenesTrackInfo(GenomicViewEvents, StringBuffer, NumberFormat) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
addGenomicRangeToDetailsViewDataRequestsQueue(Interval, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
addGenomicRangeToDetailsViewDataRequestsQueue(Interval, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
addGenomicRangeToDetailsViewIPDConsensusRequestQueue(Interval) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
addGenomicRangeToDetailsViewReferenceRequestQueue(Interval) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
addHiddenDockable(Dockable, RelativeDockablePosition) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Registers and add a dockable on an auto-hide border.
addHiddenDockable(WSDockKey, RelativeDockablePosition) - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop: Adds a new dockable (and stores its return-to-docked position)
addImportedFileInfo(File, DataFileInfo.eFileType) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper
addLayoutComponent(Component, Object) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout
addLayoutComponent(String, Component) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout
addLayoutComponent(Component, Object) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout
addLayoutComponent(String, Component) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout
addLayoutComponent(Component, Object) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout
addLayoutComponent(String, Component) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout
addLayoutComponent(Component, Object) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout
addLayoutComponent(String, Component) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout
addM_contigs_info_array(VisServiceStub.WsContigInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated add method for the array for convenience
addM_tracks_info_array(VisServiceStub.WsTrackInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo: Auto generated add method for the array for convenience
addMarkerCollectionHtmlTooltip(GenomicViewEvents, StringBuffer, MarkerCollection, NumberFormat, boolean) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: track tooltip
addMarkerHtmlTooltip(GenomicViewEvents, StringBuffer, Marker, MarkerCollection, NumberFormat, boolean) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: marker tooltip
addMetrics(StringBuffer, String, String, String, int, long, long, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex
addModel(IVariableResolutionDataModelServer) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger
addModel(IVariableResolutionDataModelServer) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
addNewPushpin(VioletApp, String, byte[]) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage
addNewPushpinInteractive(Component, VioletApp) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage
addPropertyChangeListener(PropertyChangeListener) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy: Hook for property change notification
addPropertyChangeListener(String, PropertyChangeListener) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy: Hook for property change notification
addPropertyChangeListener(PropertyChangeListener) - Method in class pub.vlsolutions.swing.docking.DockKey: Hook for property change notification
addReadHtmlTooltip(GenomicViewDetails, StringBuffer, Marker, NumberFormat, boolean) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: read tooltip
addReadsInfo(GenomicViewEvents, StringBuffer, NumberFormat) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
addReferenceKinetogramInfo(GenomicViewEvents, StringBuffer, NumberFormat) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
addRequest(DetailsDataRequest) - Method in class com.pacbio.secondary.vis.data.queue.DetailsDataRequestsQueue
addROI() - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog
AddRow(String) - Method in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfoCalculator
addSaveButtonToTabbedPane() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase: Deprecated.
addSelectionChangedListener(ChangeListener) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
addSelectionListener() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase: When selection changes, call notification function with both view and model.
addSeparator() - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI
addSeparator() - Method in class pub.vlsolutions.swing.toolbars.VLToolBar: Adds a new separator to this toolbar
addSubRead(WsRead) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure: add more sub-reads
addToTabbedGroup(Dockable, Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Registers a dockable as belonging to a tab group.
addToTabbedGroup(WSDockKey, WSDockKey) - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop: Registers a dockable as belonging to a tab group.
addTrackDataToViewAndUpdateLayout(MarkerCollection, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData: Adds a marker set to a track MarkerCollection.
addTrackInfo(TrackDataInfo) - Method in class com.pacbio.secondary.vis.data.session.tracks.TracksDataInfoList
addTreeModelListener(TreeModelListener) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
addURLToHistoryAndGoto(URL) - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserEditorPane
addWorkDone(JobInfo) - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkDoneQueue
addWorkToDo(JobInfo, boolean) - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkToDoQueue
adjustForQV(Color, double) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants: QV is adjusted by darkening...
AlignedTabbedPaneUI - Class in com.pacbio.secondary.vis.gui.dialogs
AlignedTabbedPaneUI() - Constructor for class com.pacbio.secondary.vis.gui.dialogs.AlignedTabbedPaneUI
AlignmentConstants - Class in com.pacbio.secondary.vis.io.hdf.constants: Constants used by aligned data pairs
AlignmentConstants() - Constructor for class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants
AlignmentIndexTable - Class in com.pacbio.secondary.vis.io.hdf.data: Simple extension class to store Alignement Index table data.
AlignmentIndexTable(long, long, Object) - Constructor for class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Public constructor
aln_index_label - Variable in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo
alpha_fill - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
alpha_fill_low - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
ALWAYS_ADD_MAIN_SAMPLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
always_show_mem_stats_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
ALWAYS_SHOW_MEM_STATS_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
alwaysShowMemoryInfo - Variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
analyzeSingleContigDataFile(String, String, int, long, long, HDFServiceExperienceIndex.ExperienceIndexMetrics) - Method in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex
ancestorListener - Variable in class pub.vlsolutions.swing.docking.ui.DockViewUI: Ancestor listener used to install different borders depending on the usage of the dock view (docked, maximized, tabbed).
ANCHOR_BOTTOM - Static variable in class pub.vlsolutions.swing.docking.AnchorConstraints: Field describing a dockable anchored to the BOTTOM border of its ancestor container
ANCHOR_LEFT - Static variable in class pub.vlsolutions.swing.docking.AnchorConstraints: Field describing a dockable anchored to the LEFT border of its ancestor container
ANCHOR_RIGHT - Static variable in class pub.vlsolutions.swing.docking.AnchorConstraints: Field describing a dockable anchored to the RIGHT border of its ancestor container
ANCHOR_TOP - Static variable in class pub.vlsolutions.swing.docking.AnchorConstraints: Field describing a dockable anchored to the TOP border of its ancestor container
AnchorConstraints - Class in pub.vlsolutions.swing.docking: A constraint used to specify how a dockable is tied (anchored) to its containing parent .
AnchorConstraints(int) - Constructor for class pub.vlsolutions.swing.docking.AnchorConstraints: Constructor for an immutable contraints
AnchorManager - Class in pub.vlsolutions.swing.docking: A helper class used to specify and enforce constraints within a container (DockingPanel or CompoundDockingPanel).
AnchorManager(DockingContext, Container) - Constructor for class pub.vlsolutions.swing.docking.AnchorManager: Constructs a new AnchorManager responsible for a container (desktop or compound)
animation(AnimationEvent) - Method in interface pub.vlsolutions.swing.docking.animation.AnimationListener: This method is invoked when the animation state change.
ANIMATION_END - Static variable in class pub.vlsolutions.swing.docking.animation.AnimationEvent: state identifying the end of an animation
ANIMATION_FRAME - Static variable in class pub.vlsolutions.swing.docking.animation.AnimationEvent: state identifying a change in the animation (the component has changed of bounds)
ANIMATION_START - Static variable in class pub.vlsolutions.swing.docking.animation.AnimationEvent: state identifying the beginning of an animation
AnimationEvent - Class in pub.vlsolutions.swing.docking.animation: An Event describing the state of an animation
AnimationEvent(Component, int) - Constructor for class pub.vlsolutions.swing.docking.animation.AnimationEvent: Event Constructor.
AnimationListener - Interface in pub.vlsolutions.swing.docking.animation: The AnimationListener interface is used to notify listeners about the state of an animation process (animation start and end).
ann - Variable in class com.pacbio.secondary.vis.svc.server.data.WsRead
ANNOTATED_READS_MAX_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
ANNOTATED_READS_WITH_BASES - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
ANNOTATED_READS_WITH_BASES - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants
ANNOTATED_READS_WITH_NO_METRICS - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
ANNOTATED_READS_WITH_PW - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
ANNOTATED_READS_WITH_PW - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants
ANNOTATED_READS_WITH_QV - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
ANNOTATED_READS_WITH_QV - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants
ANNOTATED_READS_WITH_RAW_IPD - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
ANNOTATED_READS_WITH_RAW_IPD - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants
ANNOTATIONS_1_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs
ANNOTATIONS_2_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs
app - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase
app - Variable in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog
app - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
app - Variable in class com.pacbio.secondary.vis.io.importer.ImportDataHelper
APP_INFO_PANEL_FONT_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
app_options - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper
app_options - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase
APP_SHOW_WHATS_NEW_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
app_type - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase
appendImageInfo(GenomicViewEvents, StringBuffer, String, int, int, String) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
appendMsg(String) - Static method in class com.pacbio.secondary.vis.io.hdf.file.bash5.BaseH5FileBase
AppendRowToTable(String, String, StringBuffer) - Method in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex
apply(DockingContext) - Method in class pub.vlsolutions.swing.docking.ws.Workspace: Applies this workspace to the given docking context (this is equivalent as loading a workspace file from DockingContext.readXML() : it removes every dockable from the context and associated desktops, and clears their dockable states, then it reloads the dockables as specified by this workspace layout.
applyWorkspace() - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceButton: Invoked when the button is pressed : applies the workspace to the associated context
applyWorkspace() - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem: Invoked when the button is pressed : applies the workspace to the associated context
appVisualFilter - Variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
areGroupsCompatible(DockGroup, DockGroup) - Static method in class pub.vlsolutions.swing.docking.DockGroup: convenience method to check compatibility between groups
args - Variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
arm - Variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand
ARM_BOTH - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Arm
ARM_P - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Arm
ARM_Q - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Arm
ArrayConstants - Class in com.pacbio.secondary.vis.common.utils.constants
ArrayConstants() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.ArrayConstants
ASCIIFileIndexInfo - Class in com.pacbio.secondary.vis.io.indexer.indexinfo
ASCIIFileIndexInfo(int, long, long) - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.ASCIIFileIndexInfo
ASCIIFileIndexInfo() - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.ASCIIFileIndexInfo: de-serialization only
ASCIIFileIndexInfo(long, long) - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.ASCIIFileIndexInfo
assembleReads(WsResults, int, List<WsRead>, boolean, boolean, long, int, long, long, long) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder: analyze and pile-up reads, create structure info and results metadata
assembleReadsWithGappedInsertions() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect: Creates pseudo-reads with added gaps so we can construct and view an MSA
assembleResultsWithoutStructures(ArrayList<Marker>, int) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
assembleResultsWithoutStructures(WsResults, List<WsRead>, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler
assembleResultsWithStructures(WsResults, List<WsRead>, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler: Full assembly of results with graphic structures
AUTO_IDEO_BAND_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
AUTO_IDEO_MAX_NUM_BANDS - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
AUTO_IDEO_NUM_BANDS - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
autofitLabelWidth(Graphics, String) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: changes string to display enough chars to fit to label width
AutoHideBorderLayout - Class in pub.vlsolutions.swing.docking: A Layout Manager for auto-hide borders.
AutoHideBorderLayout(boolean) - Constructor for class pub.vlsolutions.swing.docking.AutoHideBorderLayout: Constructs a new Layout.
AutoHideBorderLayout(boolean, int) - Constructor for class pub.vlsolutions.swing.docking.AutoHideBorderLayout: Constructs a new Layout.
AutoHideButton - Class in pub.vlsolutions.swing.docking: The button used to show Dockables in auto-hide borders.
AutoHideButton() - Constructor for class pub.vlsolutions.swing.docking.AutoHideButton
AutoHideButtonPanel - Class in pub.vlsolutions.swing.docking: A Swing panel used as a toolbar for autohide buttons.
AutoHideButtonPanel(AutoHideExpandPanel, int) - Constructor for class pub.vlsolutions.swing.docking.AutoHideButtonPanel: Constructs a new AutoHideButtonPanel, with a shared expandPanel, and for a specified border zone.
AutoHideButtonPanelUI - Class in pub.vlsolutions.swing.docking.ui: The UI associated with the AutoHideButtonPanel.
AutoHideButtonPanelUI() - Constructor for class pub.vlsolutions.swing.docking.ui.AutoHideButtonPanelUI
AutoHideButtonUI - Class in pub.vlsolutions.swing.docking.ui: The UI delegate for AutoHideButtons.
AutoHideButtonUI() - Constructor for class pub.vlsolutions.swing.docking.ui.AutoHideButtonUI
AutoHideExpandPanel - Class in pub.vlsolutions.swing.docking: A component used to show the currently expanded view.
AutoHideExpandPanel() - Constructor for class pub.vlsolutions.swing.docking.AutoHideExpandPanel
AutoHideExpandPanelUI - Class in pub.vlsolutions.swing.docking.ui: The UI delegate for the AutoHideExpandPanel component.
AutoHideExpandPanelUI() - Constructor for class pub.vlsolutions.swing.docking.ui.AutoHideExpandPanelUI
AutoHidePolicy - Class in pub.vlsolutions.swing.docking: This class holds preferences on default autohiding behaviour.
AutoHidePolicy.ExpandMode - Enum in pub.vlsolutions.swing.docking: A set of constants for expanding a button on rollover, or on click
avg_reads_per_slice() - Method in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo
avg_row_lenght - Variable in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo
AxisUtils - Class in com.pacbio.secondary.vis.gui.draw.utils
AxisUtils() - Constructor for class com.pacbio.secondary.vis.gui.draw.utils.AxisUtils

B

BackgroundPainter - Interface in pub.vlsolutions.swing.toolbars: An interface implemented by objects which can paint toolbar backgrounds.
band - Variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand
bandsPalette - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
Base64Utils - Class in com.pacbio.secondary.vis.common.utils: A very fast and memory efficient class to encode and decode to and from BASE64 in full accordance with RFC 2045.

On Windows XP sp1 with 1.4.2_04 and later ;), this encoder and decoder is about 10 times faster on small arrays (10 - 1000 bytes) and 2-3 times as fast on larger arrays (10000 - 1000000 bytes) compared to sun.misc.Encoder()/Decoder().

On byte arrays the encoder is about 20% faster than Jakarta Commons Base64 Codec for encode and about 50% faster for decoding large arrays.
Base64Utils() - Constructor for class com.pacbio.secondary.vis.common.utils.Base64Utils
BASE_DELETION - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures
BASE_LEFT_INSERTION - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures
BASE_MATCH - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures
BASE_POS_INSERTION - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures
BASE_RIGHT_INSERTION - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures
BASE_SVN - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures
BaseDataModel - Class in com.pacbio.secondary.vis.data.base
BaseDataModel(BaseDataModel.eDataType, int) - Constructor for class com.pacbio.secondary.vis.data.base.BaseDataModel
BaseDataModel.eDataType - Enum in com.pacbio.secondary.vis.data.base
BaseDataRecord - Class in com.pacbio.secondary.vis.data.base
BaseDataRecord() - Constructor for class com.pacbio.secondary.vis.data.base.BaseDataRecord
BaseH5FileBase - Class in com.pacbio.secondary.vis.io.hdf.file.bash5
BaseH5FileBase(File, int, int) - Constructor for class com.pacbio.secondary.vis.io.hdf.file.bash5.BaseH5FileBase
BASEMOD_BASE_ID_MASK - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_MOTIF_ID_MASK - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_NUM_SUMMARY_METRICS - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_TYPE_4MC - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_TYPE_5MC - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_TYPE_6MA - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_TYPE_MASK - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_TYPE_MODIFIED - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_TYPE_MOTIF - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_TYPE_UNKNOWN - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_TYPES_LABELS - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMOD_TYPES_TAGS - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
baseModID(float) - Static method in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
basemods - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
basemods_enabled - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase
basemods_filter_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
basemods_filter_threshold - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
basemods_map - Variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
BASEMODS_OPTIONS - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
basemods_options_cb - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
baseqv_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
BaseRangeToXExtent(double) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: Transforms the basepair extent pos to x-width of the canvas.
bases - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
BaseToXCoord(long) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: Transforms the basepair location pos to x-coordinates of the canvas.
BaseToYCoord(long) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: Transforms the basepair location pos to y-coordinates of the canvas.
bCircular - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
bContinue - Variable in class com.pacbio.secondary.vis.svc.server.threads.VisWorkSenderThread
bDetails - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
bDone - Variable in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper
bDone - Variable in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper
bDone - Variable in class com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper
bDone - Variable in class com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper
beginPoint - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
beginSelection(Point) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
bFitRegionViewToWindowHeight - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
bFitToWindow - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
bGZipped - Variable in class com.pacbio.secondary.vis.io.importer.DataFileInfo
bHorizontal - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
binarySearchLastOccurrence(int[], int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase: Extend binary search to return index of last occurrence of key if sorted array contains multiple key instances.
bInspection - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
BITMASK_RESULTS_MAX_COVERAGE - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
BITMASK_RESULTS_METRICS - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
BITMASK_RESULTS_MISC - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
BITMASK_RESULTS_READS - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
BITMASK_RESULTS_STRUCTURES - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
borderDist(long) - Method in class com.pacbio.secondary.vis.data.interval.Interval
borderPanes - Variable in class pub.vlsolutions.swing.docking.DockingDesktop: array containing the border panes
BorderSplitter - Class in pub.vlsolutions.swing.docking: An utility class used to delegate the border drag/drop scanning for docking ( since the same code is used in many DockDropReceivers).
BorderSplitter(Component) - Constructor for class pub.vlsolutions.swing.docking.BorderSplitter
BOTTOM - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition: convenience field referencing the BOTTOM border of the DockingDesktop
BOTTOM_CENTER - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition: convenience field referencing the CENTER part of the BOTTOM border of the DockingDesktop
BOTTOM_LEFT - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition: convenience field referencing the TOP-RIGHT corner of the DockingDesktop
BOTTOM_PANEL - Static variable in class pub.vlsolutions.swing.toolbars.ToolBarPanelBorder
BOTTOM_RIGHT - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition: convenience field referencing the TOP-RIGHT corner of the DockingDesktop
bottomBorderPane - Variable in class pub.vlsolutions.swing.docking.DockingDesktop: panel used to display autohide buttons
bottomMarkerBounds - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
bottomPileUpBounds - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
bottomReferenceBounds - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
brighter(Color, double) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
browser_panel - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
browseReference(String) - Method in class com.pacbio.secondary.vis.gui.dialogs.OpenRemoteDataHelper: browse reference.info.xml
btn_inset - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
buildCacheFileName(String, int, int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer
buildContigIndexFileName(String) - Method in class com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer
buildIndexFileName(String) - Method in class com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer
buildPathAfterLastTab(Rectangle, Rectangle) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane: Creates a general path suitable for showing tab insertion after the last tab
buildPathForCurrentTab(Rectangle, Rectangle) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane: Creates a general path suitable for showing tab insertion before the currentTab
buildPathForTab(Rectangle) - Method in class pub.vlsolutions.swing.docking.DockView: Create a path used to display the drag shape of a tab container
buildSequence(String, int, String, long, long) - Method in class com.pacbio.secondary.vis.io.fasta.FastaFileReader
buildStats(int, long, long) - Method in class com.pacbio.secondary.vis.io.fasta.FastaFileReader
buildStats(int, long, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures
button - Variable in class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor
ByteArrayList - Class in com.pacbio.secondary.vis.common.collection: ArrayList of byte primitives.
ByteArrayList(byte[]) - Constructor for class com.pacbio.secondary.vis.common.collection.ByteArrayList: Constructs a list containing the elements of the specified array.

C

CACHE_DIRECTORY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
calcRequiredGapsForRead(ReadInfo, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect: count total gaps to add to this read
calcSize() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
calculateInsertionExtent() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect: two pass to determine insertion range and start-stop ref coordinates
calculateInsertionInfo() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect: Determines insertion genomic range and start-stop coordinates
cancel() - Method in class com.pacbio.secondary.vis.data.session.timer.SessionDataTimer: stops timer
cancel() - Method in class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog
cancel() - Method in class com.pacbio.secondary.vis.smrtcloud.CloudTimer: stops timer
cancel() - Method in class pub.vlsolutions.swing.docking.animation.ComponentAnimator: Cancels the animation (the component is not reset to its initial location/size)
CANCEL - Static variable in class pub.vlsolutions.swing.docking.DockingSelectorDialog: Closing state of the dialog when the user has selected the cancel option
cancel() - Method in class pub.vlsolutions.swing.docking.event.DockableStateWillChangeEvent: Refuse the change of dockable state.
cancelCellEditing() - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor
cancelDrag() - Method in interface pub.vlsolutions.swing.docking.DragControler
canDrawIPDConsensus() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData: can painters draw consensus ipd based on current graphic layout?
canDrawIPDConsensus() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
canUseMouseInfo() - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: Returns whether we can use the secured and 1.5 MouseInfo class
cdna_enabled - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase
center(long) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails: Scroll to the given basepair (such that the position is centered)
center(long) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents: Scroll to the given basepair (such that the position is centered)
center_location - Variable in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog
center_pos - Variable in class com.pacbio.secondary.vis.data.db.MotifData
centerFrame(Frame) - Static method in class com.pacbio.secondary.vis.common.utils.GUIUtils
changeDNAFontSize(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
changeDNAFontSize(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
changeDNAFontSize(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
changeIPDConsensusHeight(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
changeIPDConsensusHeight(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
changeIPDConsensusHeight(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
ChangeNotifier - Class in com.pacbio.secondary.vis.common.collection
ChangeNotifier() - Constructor for class com.pacbio.secondary.vis.common.collection.ChangeNotifier
changeNotifier - Variable in class com.pacbio.secondary.vis.data.base.BaseDataModel
changeTrackSize(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
changeTrackSize(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
changeTrackSize(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion
children - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFileNode
children - Variable in class com.pacbio.secondary.vis.data.interval.IntervalTreeNode
CHIMERIC_STANDARD_THRESHOLD - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler
CHIMERIC_STROBE_THRESHOLD - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler
choose(int, int) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility
chromosome - Variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand
ChromosomeBand - Class in com.pacbio.secondary.vis.data.chromosomeband: Encapsulates a chromosomal Band identifier (e.g.
ChromosomeBand() - Constructor for class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand
ChromosomeBand(String) - Constructor for class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand
chromosomes_panel - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
chromosomes_scroller - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
chromosomes_views - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
chunk_size - Variable in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo
CIRCULAR_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
circular_scroller - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
circular_view - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
CIRCULAR_VIEW_PANEL_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
CIRCULAR_VIEW_PANEL_TOOLTIP - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
clear() - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet
clear() - Method in class com.pacbio.secondary.vis.data.db.GeneDB: Creates a new set of empty IntervalTrees.
clear(boolean) - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB: Creates a new set of empty IntervalTrees.
clear() - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure
clear() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection
clear() - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage
clear() - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage
clear() - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage
clear() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
clear() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger
clear() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
clear(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
clear() - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
clear() - Method in class pub.vlsolutions.swing.docking.AnchorManager: Cleanup for this manager : removes references and listeners
clear() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel: Clears the state of this expand panel.
clear() - Method in class pub.vlsolutions.swing.docking.DockingDesktop: removes every dockables from this desktop
clear() - Method in class pub.vlsolutions.swing.docking.ws.Workspace: Removes the contained desktops
clear() - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop: removes all information stored into this desktop, which becomes ready to be reused.
clearAllDetailsData() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
clearAllSlots() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
clearDataSet(H5ScalarDS) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Clears memory held by the dataset, such as data buffer
clearMarkers(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData: Removes all markers from this ideogram.
clearMarkersFromAllViews(boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
clearSelections() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
CLIENT_PROGRAM_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
clientData - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler
clientData - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler
clipReadsTo(int, int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResults: used to clip reads for msa/insertions view
clipReadTo(int, int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead: assumes length > 0
clone() - Method in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Overriden clone method
clone() - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon
close(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingContext: Close this dockable
close(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Disposes the dockable container of this dockable.
close_text - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
closeAction - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab
closeAllDockablesInTab(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Convenience method to close all dockables of the tabbedContainer containing "base" (including the base dockable).
closeAllOtherDockablesInTab(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Convenience method to close all dockables of a TabbedDockableContainer except one.
closePopUp() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab: This method is invoked to hide the pop-up that could still be visible (To avoid a visible pop-up for an invisible component)
closePopUp() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: This method is invoked to hide the pop-up that could still be visible (To avoid a visible pop-up for an invisible component)
closeSmartIcon - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab
CloudTimer - Class in com.pacbio.secondary.vis.smrtcloud: helper class containing an instance of timer used to check on smrtcloud data status the timer is created as a daemon thread
CloudTimer(VioletApp) - Constructor for class com.pacbio.secondary.vis.smrtcloud.CloudTimer
CloudUtils - Class in com.pacbio.secondary.vis.smrtcloud: This class provides utilities for dealing with smrtcloud environment
CloudUtils() - Constructor for class com.pacbio.secondary.vis.smrtcloud.CloudUtils
CMD_LINE_ANNOTATION - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_CIRCULAR - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_CLOUD - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_CUR_SESSION - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_CUR_WORKSPACE - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_DATA - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_DESKTOP - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_GROUPS - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_HOST_URL - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_JNLP_SERVICE - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_JOB_METADATA - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_OPTIONS - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_OPTIONS_SEPARATOR - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_REFERENCE - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_SAMPLE - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_SEPARATOR - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_SESSION_TAG - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_SUMMARY_ONLY - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_TEMPLATE - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_TEST_BROWSER - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_TRACKS - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_USER - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_VIS_PORT - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
CMD_LINE_WORKSPACE_TAG - Static variable in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
cmd_options - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase
CMDLINE_HOSTNAME - Static variable in class com.pacbio.secondary.vis.update.UpdaterUtils
CMDLINE_HTTPPORT - Static variable in class com.pacbio.secondary.vis.update.UpdaterUtils
CMDLINE_VERBOSE - Static variable in class com.pacbio.secondary.vis.update.UpdaterUtils
CMPH5_AIDX_ALIGNMENT_READ_START - Static variable in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable
CMPH5_AIDX_STROBE_NUMBER - Static variable in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable
CMPH5_FWD_IPD_OFFSET - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants
CMPH5_REV_IPD_OFFSET - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants
CMPH5_VERSION_1_1_MARKER - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants
CMPH5_VERSION_1_2_MARKER - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants
CMPH5_VERSION_1_3_MARKER - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants
CMPH5_VERSION_2_0_MARKER - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants
CMPH5Constants - Class in com.pacbio.secondary.vis.io.hdf.constants: Constants used in PacBio cmp.h5 files
CMPH5Constants() - Constructor for class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants
CMPH5File - Class in com.pacbio.secondary.vis.io.hdf.file.cmph5: Base class for accessing cmp.h5 files
CMPH5File(File, int, int) - Constructor for class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5File
CMPH5FileBase - Class in com.pacbio.secondary.vis.io.hdf.file.cmph5
CMPH5FileBase(File, int, int) - Constructor for class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase
CMPH5FileData - Class in com.pacbio.secondary.vis.io.hdf.file.cmph5: This class wraps high level access to lazy data storage
CMPH5FileData(File, int, int) - Constructor for class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileData
CMPH5ReadGroupInfo - Class in com.pacbio.secondary.vis.io.hdf.referenceinfo: Encapsulates concept of cmp.h5's read groups metadata storage
CMPH5ReadGroupInfo(String[], int[], boolean) - Constructor for class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo
CMPH5ReferenceInfo - Class in com.pacbio.secondary.vis.io.hdf.referenceinfo: Encapsulates concept of cmp.h5's reference metadata storage
CMPH5ReferenceInfo(String, String, int) - Constructor for class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo
cNames - Static variable in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
cNames - Static variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
COARSE_MODE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
COL_COV_METRICS_AVG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COL_COV_METRICS_MINMAX - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COL_COV_NUM_GAPS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COL_QV_METRICS_AVG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COL_QV_METRICS_MINMAX - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COL_VAR_METRICS_MAX - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
collapse() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel: Collapse the expand panel (making it unvisible)
collectGarbage() - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils
COLOR_ABOUT_DIALOG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_BASE_MODS_EVENTS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_BASE_MODS_HEATMAP - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_BASE_MODS_IPDRATIO - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_BASE_MODS_LOW_CV - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_BASE_MODS_MID_CV - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_CLEAR_PAINTBUFFER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_CONTIG_LABELS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_ACEN - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_1 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_10 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_11 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_12 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_13 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_14 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_15 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_16 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_17 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_18 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_19 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_2 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_20 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_4 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_5 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_6 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_7 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_8 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_FISH_9 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_GNEG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_GPOS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_GVAR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_STALK - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DENSITY_UNKNOWN - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DNA_SEQUENCE_LETTER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_GENES - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_GENES_SELECTED - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_SELECTED_BARS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_STRUCTURES - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_TRACK - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_TRACK_BKG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_TRACK_BKG_ALT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_TRACK_DIVIDER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_TRACK_INSERTION_BKG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_TRACK_LEGEND_AREA_BKG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_TRACK_LEGEND_BKG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_TRACK_LEGEND_TEXT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_DRAW_TRACK_SELECTED_BKG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_FILL_STRUCTURES - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_FILL_STRUCTURES_2 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_FULL_REFERENCE_SEQUENCE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
color_info - Variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
COLOR_PANEL_AXIS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_PANEL_AXIS_HIGHLIGHT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_PANEL_AXIS_HIGHLIGHT_LOCKED - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_PANEL_BKG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_PANEL_BORDER_NORMAL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_PANEL_BORDER_SELECTED - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_PASTEL_REFERENCE_SEQUENCE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_REFERENCE_SEQUENCE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_REFERENCE_TRACK - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_SELECTED_RANGE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_SHADOWBOX_DNA_SEQUENCE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_SOFT_ORANGE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_SPLITTER_BKG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_SUMMARY_TRACK_GRADIENT_END - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_SUMMARY_TRACK_GRADIENT_START - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_TABBED_PANEL_HEADERS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_TABLE_PANEL_HEADER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_TITLED_BORDER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_TRACKS_HEADER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_UNCLOSED_END_TRACK - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_UNKNOWN_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_VIEW_BKG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_WHOLE_GENOME_VIEW_BKG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
COLOR_WHOLE_GENOME_VIEW_LABEL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
colorChooser - Variable in class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor
ColorConstants - Class in com.pacbio.secondary.vis.common.utils.constants
ColorConstants() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
ColorEditor - Class in com.pacbio.secondary.vis.gui.table.renderer
ColorEditor() - Constructor for class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor
ColorPalette - Class in com.pacbio.secondary.vis.common.utils.constants: Rainbow colors palette for kinetics
ColorPalette() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
ColorRenderer - Class in com.pacbio.secondary.vis.gui.table.renderer
ColorRenderer(boolean) - Constructor for class com.pacbio.secondary.vis.gui.table.renderer.ColorRenderer
column_names - Variable in class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage
column_names - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
column_names - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval
column_names - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelTrack
column_names_multicontig - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
column_names_singlecontig - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
columns - Variable in class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip
com.pacbio.secondary.vis.common.collection - package com.pacbio.secondary.vis.common.collection: Specialized collection classes
com.pacbio.secondary.vis.common.utils - package com.pacbio.secondary.vis.common.utils: Client/Server common utilities
com.pacbio.secondary.vis.common.utils.constants - package com.pacbio.secondary.vis.common.utils.constants: Client/Server common constants
com.pacbio.secondary.vis.common.utils.exception - package com.pacbio.secondary.vis.common.utils.exception: Specialized exception handlers
com.pacbio.secondary.vis.common.utils.filefilter - package com.pacbio.secondary.vis.common.utils.filefilter: Filters used for file open/save dialogs
com.pacbio.secondary.vis.data.base - package com.pacbio.secondary.vis.data.base: Base genomic data model
com.pacbio.secondary.vis.data.chromosomeband - package com.pacbio.secondary.vis.data.chromosomeband: Chromosomal band abstraction
com.pacbio.secondary.vis.data.contig - package com.pacbio.secondary.vis.data.contig: Single, contiguous reference (contig)
com.pacbio.secondary.vis.data.db - package com.pacbio.secondary.vis.data.db: Ideogram and genes collections support
com.pacbio.secondary.vis.data.filesystem - package com.pacbio.secondary.vis.data.filesystem: Abstraction layer for local and remote filesystem access
com.pacbio.secondary.vis.data.gene - package com.pacbio.secondary.vis.data.gene: Gene abstraction
com.pacbio.secondary.vis.data.graph - package com.pacbio.secondary.vis.data.graph: Graphic structures
com.pacbio.secondary.vis.data.interval - package com.pacbio.secondary.vis.data.interval: Support for genomic interval
com.pacbio.secondary.vis.data.locus - package com.pacbio.secondary.vis.data.locus: Support for genomic locus
com.pacbio.secondary.vis.data.marker - package com.pacbio.secondary.vis.data.marker: Marker data model
com.pacbio.secondary.vis.data.queue - package com.pacbio.secondary.vis.data.queue: Client/Server data requests utilities
com.pacbio.secondary.vis.data.read - package com.pacbio.secondary.vis.data.read: Genomic read data model
com.pacbio.secondary.vis.data.session - package com.pacbio.secondary.vis.data.session: Client side user session data models
com.pacbio.secondary.vis.data.session.options - package com.pacbio.secondary.vis.data.session.options: Client side user options
com.pacbio.secondary.vis.data.session.timer - package com.pacbio.secondary.vis.data.session.timer: Timer and timer task for restoring user session
com.pacbio.secondary.vis.data.session.tracks - package com.pacbio.secondary.vis.data.session.tracks: Tracks data model
com.pacbio.secondary.vis.data.table.model - package com.pacbio.secondary.vis.data.table.model: Genomic tables data models
com.pacbio.secondary.vis.data.variableresolution.model - package com.pacbio.secondary.vis.data.variableresolution.model: Variable resolution data models
com.pacbio.secondary.vis.data.variableresolution.model.gff - package com.pacbio.secondary.vis.data.variableresolution.model.gff: GFF3 variable resolution data model
com.pacbio.secondary.vis.data.variableresolution.record - package com.pacbio.secondary.vis.data.variableresolution.record: Variable resolution record data model
com.pacbio.secondary.vis.data.xmlinfo - package com.pacbio.secondary.vis.data.xmlinfo: XML metadata files data models
com.pacbio.secondary.vis.gui.app - package com.pacbio.secondary.vis.gui.app: Main application classes, support local, remote, webstart based deployment
com.pacbio.secondary.vis.gui.control - package com.pacbio.secondary.vis.gui.control: Specialized gui controls
com.pacbio.secondary.vis.gui.control.treetable - package com.pacbio.secondary.vis.gui.control.treetable: TreeTable control
com.pacbio.secondary.vis.gui.desktop - package com.pacbio.secondary.vis.gui.desktop: Support for dockable windows based desktop
com.pacbio.secondary.vis.gui.dialogs - package com.pacbio.secondary.vis.gui.dialogs: Application dialogs
com.pacbio.secondary.vis.gui.draw.print - package com.pacbio.secondary.vis.gui.draw.print: Print support
com.pacbio.secondary.vis.gui.draw.track - package com.pacbio.secondary.vis.gui.draw.track: Track Abstraction
com.pacbio.secondary.vis.gui.draw.utils - package com.pacbio.secondary.vis.gui.draw.utils: Drawing utilities
com.pacbio.secondary.vis.gui.draw.views - package com.pacbio.secondary.vis.gui.draw.views: Genomic views
com.pacbio.secondary.vis.gui.evt - package com.pacbio.secondary.vis.gui.evt: Specialized event handlers
com.pacbio.secondary.vis.gui.frame - package com.pacbio.secondary.vis.gui.frame: Client application main frame
com.pacbio.secondary.vis.gui.panels - package com.pacbio.secondary.vis.gui.panels: Specialized dockable genomic panels
com.pacbio.secondary.vis.gui.panels.base - package com.pacbio.secondary.vis.gui.panels.base: Generic dockable genomic panels
com.pacbio.secondary.vis.gui.table - package com.pacbio.secondary.vis.gui.table: Genomic data tables
com.pacbio.secondary.vis.gui.table.renderer - package com.pacbio.secondary.vis.gui.table.renderer: Specialized table renderers for genomic information
com.pacbio.secondary.vis.io.epipro - package com.pacbio.secondary.vis.io.epipro: Parser for epipro/unmapped reads data
com.pacbio.secondary.vis.io.export - package com.pacbio.secondary.vis.io.export: GFF3 export support
com.pacbio.secondary.vis.io.fasta - package com.pacbio.secondary.vis.io.fasta: FASTA reader support
com.pacbio.secondary.vis.io.gff - package com.pacbio.secondary.vis.io.gff: GFF3 reader support
com.pacbio.secondary.vis.io.gff.modifications - package com.pacbio.secondary.vis.io.gff.modifications: GFF3 Base Modifications Info support
com.pacbio.secondary.vis.io.gff.summary - package com.pacbio.secondary.vis.io.gff.summary: GFF3 Summary Info support
com.pacbio.secondary.vis.io.gff.variants - package com.pacbio.secondary.vis.io.gff.variants: GFF3 variants support
com.pacbio.secondary.vis.io.hdf.constants - package com.pacbio.secondary.vis.io.hdf.constants: Constants definitions for hdf and cmp.h5 libraries
com.pacbio.secondary.vis.io.hdf.data - package com.pacbio.secondary.vis.io.hdf.data: Data models for cmp.h5 file based data representation
com.pacbio.secondary.vis.io.hdf.exception - package com.pacbio.secondary.vis.io.hdf.exception: Exception specialization for hdf library
com.pacbio.secondary.vis.io.hdf.file.bash5 - package com.pacbio.secondary.vis.io.hdf.file.bash5: Support for reading/writing of bas.h5 and bax.h5 files
com.pacbio.secondary.vis.io.hdf.file.cmph5 - package com.pacbio.secondary.vis.io.hdf.file.cmph5: Support for reading/writing of cmp.h5 files
com.pacbio.secondary.vis.io.hdf.file.hdf5 - package com.pacbio.secondary.vis.io.hdf.file.hdf5: Support for reading/writing of HDF5 files
com.pacbio.secondary.vis.io.hdf.hyperslabinfo - package com.pacbio.secondary.vis.io.hdf.hyperslabinfo: Hdf5 hyperslab data model
com.pacbio.secondary.vis.io.hdf.referenceinfo - package com.pacbio.secondary.vis.io.hdf.referenceinfo: Cmp.h5 reference groups data model
com.pacbio.secondary.vis.io.hdf.streaming - package com.pacbio.secondary.vis.io.hdf.streaming: Support for callback-based, asynchronous data streaming
com.pacbio.secondary.vis.io.hdf.test - package com.pacbio.secondary.vis.io.hdf.test: Hdf library test suite
com.pacbio.secondary.vis.io.importer - package com.pacbio.secondary.vis.io.importer: Local and remote data files import support
com.pacbio.secondary.vis.io.indexer.fasta - package com.pacbio.secondary.vis.io.indexer.fasta: FASTA indexer
com.pacbio.secondary.vis.io.indexer.gff - package com.pacbio.secondary.vis.io.indexer.gff: GFF indexer
com.pacbio.secondary.vis.io.indexer.gff.metadata - package com.pacbio.secondary.vis.io.indexer.gff.metadata: GFF3 metadata info
com.pacbio.secondary.vis.io.indexer.indexinfo - package com.pacbio.secondary.vis.io.indexer.indexinfo: Generic ASCII files indexer
com.pacbio.secondary.vis.io.indexer.text - package com.pacbio.secondary.vis.io.indexer.text: Text files indexer
com.pacbio.secondary.vis.io.motifs - package com.pacbio.secondary.vis.io.motifs: Parser for Motifs files
com.pacbio.secondary.vis.io.ucsc.gtf.reader - package com.pacbio.secondary.vis.io.ucsc.gtf.reader: Parser for UCSC generated gtf (gene transfer format) files
com.pacbio.secondary.vis.io.update - package com.pacbio.secondary.vis.io.update: Support for interactive data updates after user preferences changes
com.pacbio.secondary.vis.io.vcf - package com.pacbio.secondary.vis.io.vcf: Parser for VCF (variants) files
com.pacbio.secondary.vis.smrtcloud - package com.pacbio.secondary.vis.smrtcloud: SMRT Cloud deployment support
com.pacbio.secondary.vis.svc.hdf.client - package com.pacbio.secondary.vis.svc.hdf.client: HDFService client support
com.pacbio.secondary.vis.svc.hdf.client.auto - package com.pacbio.secondary.vis.svc.hdf.client.auto: HDFService stubs
com.pacbio.secondary.vis.svc.server - package com.pacbio.secondary.vis.svc.server: SMRTView web services
com.pacbio.secondary.vis.svc.server.data - package com.pacbio.secondary.vis.svc.server.data: Server side data models
com.pacbio.secondary.vis.svc.server.data.parser - package com.pacbio.secondary.vis.svc.server.data.parser: Server side data and metadata parsers
com.pacbio.secondary.vis.svc.server.hdf - package com.pacbio.secondary.vis.svc.server.hdf: HDFService utils
com.pacbio.secondary.vis.svc.server.jnlp - package com.pacbio.secondary.vis.svc.server.jnlp: JNLPService utilities
com.pacbio.secondary.vis.svc.server.test - package com.pacbio.secondary.vis.svc.server.test: Local tests for smrt view web services
com.pacbio.secondary.vis.svc.server.threads - package com.pacbio.secondary.vis.svc.server.threads: Parallel processing support
com.pacbio.secondary.vis.svc.server.utils - package com.pacbio.secondary.vis.svc.server.utils: Utilities for web services
com.pacbio.secondary.vis.svc.vis.client - package com.pacbio.secondary.vis.svc.vis.client: VisService client support
com.pacbio.secondary.vis.svc.vis.client.auto - package com.pacbio.secondary.vis.svc.vis.client.auto: VisService stubs
com.pacbio.secondary.vis.update - package com.pacbio.secondary.vis.update: Smrtview updating utilities
CommandLineOptions - Class in com.pacbio.secondary.vis.data.session.options
CommandLineOptions(String[]) - Constructor for class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
comp - Variable in class pub.vlsolutions.swing.docking.animation.ComponentAnimator: The animated component
comparator() - Method in class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet
comparator() - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet
compare(Marker, Marker) - Method in class com.pacbio.secondary.vis.data.marker.MarkerComparator: Used for kinetics drawing code artifact removal
compare(WsRead, WsRead) - Method in class com.pacbio.secondary.vis.svc.server.data.KineticsComparator
compare(WsRead, WsRead) - Method in class com.pacbio.secondary.vis.svc.server.data.RStartComparator
compare(WsRead, WsRead) - Method in class com.pacbio.secondary.vis.svc.server.data.StrandComparator
compareElementsAt(int, int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.MergeSort
compareForGenomicLocation(Marker, Marker) - Method in class com.pacbio.secondary.vis.data.marker.MarkerComparator: not used
compareold(WsRead, WsRead) - Method in class com.pacbio.secondary.vis.svc.server.data.StrandComparator
compareTo(SweepLineIterator<T>.CutLine) - Method in class com.pacbio.secondary.vis.common.collection.SweepLineIterator.CutLine
compareTo(BaseDataRecord) - Method in class com.pacbio.secondary.vis.data.base.BaseDataRecord
compareTo(DeNovoContigInfo) - Method in class com.pacbio.secondary.vis.data.contig.DeNovoContigInfo
compareTo(Interval) - Method in class com.pacbio.secondary.vis.data.interval.Interval
compareTo(Locus) - Method in class com.pacbio.secondary.vis.data.locus.Locus
compareTo(Marker) - Method in class com.pacbio.secondary.vis.data.marker.Marker
compareTo(VariableValuesDataRecord) - Method in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesDataRecord
compareTo(WholeGenomePanel.CtgInfo) - Method in class com.pacbio.secondary.vis.gui.panels.WholeGenomePanel.CtgInfo
compareTo(WsContigInfo) - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo
compareTo(WsIntervalSvc) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc
compareTo(WsRead) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
compareTo(GenomicDataStructures.WsReadStructure) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure
compareTo(DockableState) - Method in class pub.vlsolutions.swing.docking.DockableState: Comparable interface, used to sort components by name order.
ComponentAnimator - Class in pub.vlsolutions.swing.docking.animation: Utility class used to perform move/resize animation for awt/swing components.
ComponentAnimator(Component, Rectangle, Rectangle, float, AnimationListener) - Constructor for class pub.vlsolutions.swing.docking.animation.ComponentAnimator: Single-shot animator (use another ComponentAnimator for a new animation).
ComponentAnimator(Component, Rectangle, Rectangle, float) - Constructor for class pub.vlsolutions.swing.docking.animation.ComponentAnimator: Reusable component animator.
componentHidden(ComponentEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges
componentMoved(ComponentEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges
componentResized(ComponentEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges: Called when window is resized Also called from docking splitters
componentShown(ComponentEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges
CompoundDockable - Class in pub.vlsolutions.swing.docking: Describes a Dockable that can contain sub-dockables.
CompoundDockable(DockKey) - Constructor for class pub.vlsolutions.swing.docking.CompoundDockable: Constructs a new CompoundDockable with a given key
CompoundDockingPanel - Class in pub.vlsolutions.swing.docking: A specialized container used to nest dockables inside that sub-part of the desktop.
CompoundDockingPanel(CompoundDockable) - Constructor for class pub.vlsolutions.swing.docking.CompoundDockingPanel: Constructs a new CompoundDockingPanel, for a given dockable
conf_filter_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
conf_filter_threshold - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
CONFIGURATION_FILE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
CONFIGURATION_FOLDER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
configureAttachButton(JButton) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: installs the icons and tooltip suitable for an attach button
configureButton(AbstractButton) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar: This method is invoked upon adding a button to the toolbar.
configureButtons(DockViewTitleBar) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: Update the buttons to track state changes (for example, the maximize button can become "restore" when the view is maximized.
configureCloseButton() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab
configureCloseButton() - Method in class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab
configureCloseButton(JButton) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: installs the icons and tooltip suitable for a close button
configureCommonButtons(JButton, JButton, JButton) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx
configureDockButton(JButton) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: installs the icons and tooltip suitable for a dock button
configureFloatButton() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab
configureFloatButton() - Method in class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab
configureFloatButton(JButton) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: installs the icons and tooltip suitable for a float button
configureHelpButton(JButton) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: installs the icons and tooltip suitable for the help button
configureHideButton() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab
configureHideButton() - Method in class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab
configureHideButton(JButton) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: installs the icons and tooltip suitable for a hide button
configureMaximizeButton() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab
configureMaximizeButton() - Method in class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab
configureMaximizeButton(JButton) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: installs the icons and tooltip suitable for a maximize button
configureRestoreButton(JButton) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: installs the icons and tooltip suitable for a restore button.
configureSortButton(JToggleButton) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI: installs the icons and tooltip suitable for the sort button
CONFIRM - Static variable in class pub.vlsolutions.swing.docking.DockingSelectorDialog: Closing state of the dialog when the user has selected the confirm option
ConsensusCallsTable - Class in com.pacbio.secondary.vis.io.hdf.data: Stores data for consensus calls.
ConsensusCallsTable(Object) - Constructor for class com.pacbio.secondary.vis.io.hdf.data.ConsensusCallsTable
contains(Object) - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet
contains(Interval) - Method in class com.pacbio.secondary.vis.data.interval.Interval
contains(Locus) - Method in class com.pacbio.secondary.vis.data.locus.Locus
contains(Interval) - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage: custom method to check if requested visible interval is available takes into account that visible range can start from 0, while coordinates are 1-based
containsValue(long) - Method in class com.pacbio.secondary.vis.data.interval.Interval
content - Variable in class com.pacbio.secondary.vis.data.interval.IntervalTreeNode
CONTEXT_SENSITIVE_HELP_BASE - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
ContextHelpUtils - Class in com.pacbio.secondary.vis.common.utils
ContextHelpUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
contig - Variable in class com.pacbio.secondary.vis.data.locus.Locus
contig - Variable in class com.pacbio.secondary.vis.io.indexer.indexinfo.ASCIIFileIndexInfo
contig_column_index - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
contig_end - Variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
contig_full_names - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
CONTIG_ID - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest
contig_ids - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
contig_info - Variable in class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage
contig_length - Variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
contig_length - Variable in class com.pacbio.secondary.vis.data.contig.ContigInfo
contig_names - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
contig_start - Variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
ContigInfo - Class in com.pacbio.secondary.vis.data.contig
ContigInfo() - Constructor for class com.pacbio.secondary.vis.data.contig.ContigInfo
contigLength - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
contigs_info - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
copy() - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon: Creates a shalow copy of this icon
copyAsMarkerCollectionArray() - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer
copyAsMarkerCollectionArray() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel: Creates copy of a variableresolution model as a MarkerCollection array.
copyResults(WsResults, List<WsRead>, List<RawRead>, float, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder: copy as basic array from arraylist
copyResults(WsResults, List<WsRead>) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder
copyWsRead(String, int, int, String, byte[], byte[], int, int) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
cov_filter_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
cov_filter_threshold - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
coverage_filter_value - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
createAndLoadDataStorage(boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp
createAndShowGUI() - Method in class com.pacbio.secondary.vis.gui.app.VioletApp
createAttachTabAction(Dockable, DockingDesktop) - Static method in class pub.vlsolutions.swing.docking.TabbedContainerActions: returns an action suitable for attaching a dockable contained in a floating tab.
createAutoHideExpandPanel() - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Creates the autohide expand panel to be used in this desktop.
createBaseModsTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx
createCircularViewPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createCloseAction(Dockable, DockingDesktop) - Static method in class pub.vlsolutions.swing.docking.TabbedContainerActions: returns an action suitable for closing a dockable contained in a tab.
createCloseAllAction(Dockable, DockingDesktop) - Static method in class pub.vlsolutions.swing.docking.TabbedContainerActions: returns an action suitable for closing every dockable contained in a tab.
createCloseAllOtherAction(Dockable, DockingDesktop) - Static method in class pub.vlsolutions.swing.docking.TabbedContainerActions: returns an action suitable for closing every dockable contained in a tab excepted the current one.
createCmdOptionsFromRemoteDataSelection(String[]) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp
createCommonButtons() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx
createDefaultContainer(boolean, boolean, boolean, boolean) - Static method in class pub.vlsolutions.swing.toolbars.ToolBarContainer: Creates a default ToolBarContainer with preinstalled toolbar panels on the borders with the LEADING alignment.
createDefaultContainer(boolean, boolean, boolean, boolean, int) - Static method in class pub.vlsolutions.swing.toolbars.ToolBarContainer: Creates a default ToolBarContainer with preinstalled toolbar panels on the borders with the specified alignment The value of the alignment argument must be one of FlowLayout.LEFT, FlowLayout.RIGHT, FlowLayout.CENTER, FlowLayout.LEADING, or FlowLayout.TRAILING.
createDefaultDivider() - Method in class pub.vlsolutions.swing.docking.ui.DockingSplitPaneUI: Creates the default divider.
createDeNovoTableViewPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createDesktopImage() - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils: Create a BufferedImage of the desktop
createDetailsTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx
createDetailsViewPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createDockableContainer(Dockable, DockableContainerFactory.ParentType) - Method in class pub.vlsolutions.swing.docking.DefaultDockableContainerFactory: Returns the component used to modify the expand panel size when expanded from the top.
createDockableContainer(Dockable, DockableContainerFactory.ParentType) - Method in class pub.vlsolutions.swing.docking.DockableContainerFactory: This method is called by the DockingDesktop whenever a dockable is inserted in its containment hierachy.
createDockableContainer(Dockable, boolean) - Method in class pub.vlsolutions.swing.docking.DockableContainerFactory: Deprecated.
use the other createDockableContainer method (#createDockableContainer(Dockable, int)
createDockableContainer(Dockable, DockableContainerFactory.ParentType) - Method in class pub.vlsolutions.swing.docking.TabFactory
createDockableDesktop() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createDockableWholeGenomeScrollPanel(int) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createDockingGUIFramework() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createDockingGUIFramework() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameDesktop
createDockingGUIFramework() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameSummary
createDragControler(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DragControlerFactory
createEmptyDataset(String, H5Group, H5Datatype, long[], long[]) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Creates empty scalar dataset of specific type.
createEpiProReadsTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx
createFileMenu() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
createFilesListFromDataInfo(ProgressDialog) - Method in class com.pacbio.secondary.vis.data.session.DataStorage
createFilesListFromJobMetaDataInfo(ProgressDialog, CommandLineOptions) - Method in class com.pacbio.secondary.vis.data.session.DataStorage
createFilledDataset(String, H5Group, H5Datatype, long[], long[], Object) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Creates scalar dataset of specific type.
createFilter() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase
createFloatingDockableContainer(Window) - Method in class pub.vlsolutions.swing.docking.DefaultDockableContainerFactory: This method is called when a dockable is detached from the DockingDesktop and put in the FLOATING state.
createFloatingDockableContainer(Window) - Method in class pub.vlsolutions.swing.docking.DockableContainerFactory: This method is called when a dockable is detached from the DockingDesktop and put in the FLOATING state.
createFloatingDockableContainer(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Creates a floating JDialog to be used with this dockable.
createFloatingDockableContainer(TabbedDockableContainer) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Creates a floating JDialog to be used for a whole TabbedDockableContainer.
createFloatTabAction(Dockable, DockingDesktop) - Static method in class pub.vlsolutions.swing.docking.TabbedContainerActions: returns an action suitable for floating (detach) a dockable contained in a tab.
createFromRawRead(WsRead, RawRead, float, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures: must report right or left insertion...
createFromRawReadWithInsertions(WsRead, RawRead, float, int, long) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures: report insertion at position...
createGenericTableViewPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createGraphLinesStructure(GenomicDataStructures.WsReadStructure[], int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler: Strobe reads as graphic lines
createGraphLinksStructure(GenomicDataStructures.WsReadStructure[], int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler: CCS reads as graphic links
createGraphNodesStructure(GenomicDataStructures.WsReadStructure[], int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler: Strobe reads as graphic nodes
createGraphStructure(WsResults, GenomicDataStructures.WsReadStructure[], int, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler: Creates annotated graph structure from data
createGroup(String, H5Group) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Creates a new group under a parent group
createHelpMenu() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
createHideTabAction(Dockable, DockingDesktop) - Static method in class pub.vlsolutions.swing.docking.TabbedContainerActions: returns an action suitable for hiding a dockable contained in a tab.
createImage(JComponent) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils: Create a BufferedImage for Swing components.
createImage(JComponent, Rectangle) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils: Create a BufferedImage for Swing components.
createImage(Component) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils: Create a BufferedImage for AWT components.
createImage(Rectangle) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils: Create a BufferedImage from a rectangular region on the screen.
createLayout() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog
createListeners() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog: Add all listeners
createListeners() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameDesktop
createListeners() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameSummary
createMatrix(int, int) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility
createMaximizeTabAction(Dockable, DockingDesktop) - Static method in class pub.vlsolutions.swing.docking.TabbedContainerActions: returns an action suitable for maximizing a dockable contained in a tab.
createMenuBar() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
createMenuBar() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameDesktop: desktop menu has all entries disabled except open job data, exit and help items
createNewJNLPFromOldVersion(String, String) - Method in class com.pacbio.secondary.vis.update.SMRTViewUpdater
createPopupMenu() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog: export graphs/print menu items
createPopupMenu() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
createPopupMenu() - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel: create table browser popup menu
createPopupMenu() - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel: create table browser popup menu
createPopupMenu() - Method in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel: create table browser popup menu
createProgramOptionsTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx
createQVTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx
createRegionViewPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createRootPane() - Method in class com.pacbio.secondary.vis.gui.dialogs.SMRTViewDialog
createSelectionInfoPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createStatusbar() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
createStructuresTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx
createTab(Dockable, Dockable, int) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Adds a view in a tab, or create it if it doesn't exist.
createTab(Dockable, Dockable, int, boolean) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Add a view in a tab, or create it if it doesn't exist.
createTab(WSDockKey, WSDockKey, int) - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop: Creates a tab containing baseTab and newTab (if baseTab is already into a Tab, then newTab will just be added at the "order" position.
createTabbedDockableContainer() - Method in class pub.vlsolutions.swing.docking.DefaultDockableContainerFactory: Returns the container used for tabbed docking.
createTabbedDockableContainer() - Method in class pub.vlsolutions.swing.docking.DockableContainerFactory: This method is called when a tab insertion is requested by the DockingDesktop.
createTabbedPanel() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx: Any change in the order of tabs should be reflected in the help constants,
createTabHeader() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab
createTabHeader() - Method in class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab
createTable() - Method in class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog
createTable() - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel
createTimer() - Method in class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog
createTitleBar() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel: creates the shared title bar for all expanded panels
createTitleBar() - Method in class pub.vlsolutions.swing.docking.DefaultDockableContainerFactory: This implementation of the factory method return a default DockViewTitleBar object.
createTitleBar() - Method in class pub.vlsolutions.swing.docking.DockableContainerFactory: This method is invoked when a dockable container needs to install a title bar.
createTitlePanel() - Method in class pub.vlsolutions.swing.docking.FloatingDialog: Creates the component used as a header to drag the window
createToolbar() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
createToolbar() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameDesktop: desktop toolbar has all buttons disabled except open job data
createToolbar() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameSummary: desktop toolbar has all buttons disabled except open job data
createToolbarOld() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameDesktop: desktop toolbar has all buttons disabled except open job data
createToolsMenu() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
createToolTip() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
createToolTip() - Method in class com.pacbio.secondary.vis.gui.table.GenomicTableBase
createUI(JComponent) - Static method in class com.pacbio.secondary.vis.gui.dialogs.AlignedTabbedPaneUI
createUI(JComponent) - Static method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonPanelUI
createUI(JComponent) - Static method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonUI: Creates a new DockingSplitPaneUI instance
createUI(JComponent) - Static method in class pub.vlsolutions.swing.docking.ui.AutoHideExpandPanelUI
createUI(JComponent) - Static method in class pub.vlsolutions.swing.docking.ui.DetachedDockViewUI: Creates a UI for the given component (shared instance)
createUI(JComponent) - Static method in class pub.vlsolutions.swing.docking.ui.DockingSplitPaneUI: Creates a new DockingSplitPaneUI instance
createUI(JComponent) - Static method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI
createUI(JComponent) - Static method in class pub.vlsolutions.swing.docking.ui.DockViewUI
createUI(JComponent) - Static method in class pub.vlsolutions.swing.toolbars.ToolBarGripperUI
createUnknownContigInfo(int) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
createVariantsTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx
createView() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog
createViewMenu() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
createWebBrowserPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createWholeGenomePanel(VioletFrameActions, GenomicViewSingleContig[]) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
createWindowMenu() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
CS_DEFAULT_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_DENOVO_GENOME_PANEL_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_DENOVO_TABLE_PANEL_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_DESKTOP_MODE_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_DETAILS_PANEL_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_MOTIFS_SUMMARY_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_OPEN_REMOTE_DATA_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_PREF_CDNA_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_PREF_DETAILS_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_PREF_EPIPRO_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_PREF_GENERAL_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_PREF_KINETICS_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_PREF_QV_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_PREF_STRUCTURE_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_PREF_VARIANTS_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_REGION_PANEL_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_SELECTION_PANEL_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_TABLE_BROWSER_PANEL_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_VIEW_INSERTIONS_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_WEB_BROWSER_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_WHATS_NEW_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
CS_WHOLE_GENOME_PANEL_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils
ctg - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
cTypes - Static variable in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
cTypes - Static variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
current_view - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval
current_view - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelTrack
currentColor - Variable in class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor
currentContig - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper
currentMainFrameContig - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
currentViewContig - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

D

d270DegreeAngle - Static variable in class com.pacbio.secondary.vis.common.utils.constants.MathConstants
d315DegreeAngle - Static variable in class com.pacbio.secondary.vis.common.utils.constants.MathConstants
d90DegreeAngle - Static variable in class com.pacbio.secondary.vis.common.utils.constants.MathConstants
d_temp - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelBase
darker(Color, double) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
DASHED_LINE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
data - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
data - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
data - Variable in class com.pacbio.secondary.vis.io.hdf.data.UCharMatrixArray
data - Variable in class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray
data_helper - Variable in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog
data_loaded - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase
data_on_demand_queue - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
data_on_demand_timer - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
data_request_queue - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
data_storage - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase
data_table - Variable in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel
data_type - Variable in class com.pacbio.secondary.vis.data.base.BaseDataModel
data_type - Variable in class com.pacbio.secondary.vis.data.marker.MarkerCollection
DataFileInfo - Class in com.pacbio.secondary.vis.io.importer
DataFileInfo(String, VioletApp) - Constructor for class com.pacbio.secondary.vis.io.importer.DataFileInfo: Open and analyze file to find out what type it is and if it requires sub-sampling Called by background (from server) loader
DataFileInfo(File, VioletApp) - Constructor for class com.pacbio.secondary.vis.io.importer.DataFileInfo
DataFileInfo.eFileType - Enum in com.pacbio.secondary.vis.io.importer
DataHandlerToByteArray(DataHandler) - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils
DataStorage - Class in com.pacbio.secondary.vis.data.session
DataStorage(VioletApp) - Constructor for class com.pacbio.secondary.vis.data.session.DataStorage
DataStorageBase - Class in com.pacbio.secondary.vis.data.session
DataStorageBase(VioletApp) - Constructor for class com.pacbio.secondary.vis.data.session.DataStorageBase
decode(char[]) - Static method in class com.pacbio.secondary.vis.common.utils.Base64Utils: Decodes a BASE64 encoded char array.
decode(byte[]) - Static method in class com.pacbio.secondary.vis.common.utils.Base64Utils: Decodes a BASE64 encoded byte array.
decode(String) - Static method in class com.pacbio.secondary.vis.common.utils.Base64Utils: Decodes a BASE64 encoded String.
DEFAULT_BASE_MODS_FILTER_THRESHOLD - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
default_border_width - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
DEFAULT_DETAILS_COARSE_MODE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
DEFAULT_DETAILS_MAX_COVERAGE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
DEFAULT_DETAILS_VIEW_DYNAMIC_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
DEFAULT_DETAILS_VIEW_FIXED_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
DEFAULT_DETAILS_VIEW_LIMITING_MODE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
DEFAULT_DNA_FONT_HEIGTH - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DEFAULT_DNA_LETTER_TRACK_PIXELS - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
default_feature_size - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
default_height_top_axis - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
DEFAULT_HOME_URL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
default_ideogram_height - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
default_ideogram_label_width - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
default_ideogram_width - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
DEFAULT_IO_BLOCK_TRANSFER_SIZE - Static variable in class com.pacbio.secondary.vis.svc.server.utils.ServiceUtils
DEFAULT_IPD_CONSENSUS_TRACK_HEIGHT - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DEFAULT_KINETICS_PALETTE_SCALING - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
DEFAULT_LANE_OFFSET_PIXELS - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DEFAULT_LANE_OFFSET_PIXELS_GRAPHS - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DEFAULT_LAYOUT_FILE_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
default_left_info_width - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
DEFAULT_PROJECT_EXTENSION - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
DEFAULT_ROIS_EXTENSION - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
DEFAULT_TEST_DATAFILE - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex
default_tracks_height - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
default_tracks_width - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
DEFAULT_USER_DATA_DIRECTORY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
DEFAULT_VIEW_HEIGHT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
default_view_height - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
DEFAULT_VIEW_WIDTH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
default_view_width - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
DEFAULT_WEB_SEARCH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
default_workspace_layout - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
default_y_bottom_ideogram - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
default_y_top_ideogram - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
DefaultDockableContainerFactory - Class in pub.vlsolutions.swing.docking: Default implementation of the DockableContainerFactory.
DefaultDockableContainerFactory() - Constructor for class pub.vlsolutions.swing.docking.DefaultDockableContainerFactory
defaultIcon - Variable in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton: the default icon (enabled/visible)
delay - Static variable in class com.pacbio.secondary.vis.data.session.timer.SessionDataTimer
delay - Static variable in class com.pacbio.secondary.vis.smrtcloud.CloudTimer
delegateDrag() - Method in class pub.vlsolutions.swing.docking.event.DockDragEvent: Rejects the drag, but allows the docking system to search for othet drop receiver in ancestors.
DENOVO_GENOME_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
denovo_model - Variable in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel
DENOVO_REF_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
denovo_summary - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase
denovo_table - Variable in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel
denovo_table_panel - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
DENOVO_TABLE_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
DENOVO_TABLE_PANEL_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
DENOVO_TABLE_PANEL_TOOLTIP - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
DeNovoContigInfo - Class in com.pacbio.secondary.vis.data.contig: Class holds summary info for one contig.
DeNovoContigInfo(String, String, int, double[]) - Constructor for class com.pacbio.secondary.vis.data.contig.DeNovoContigInfo
DeNovoSummaryParser - Class in com.pacbio.secondary.vis.svc.server.data.parser: This class reads a summary file and generates virtual reference info for a DeNovo experiment
DeNovoSummaryParser(String, String) - Constructor for class com.pacbio.secondary.vis.svc.server.data.parser.DeNovoSummaryParser
DeNovoSummaryStorage - Class in com.pacbio.secondary.vis.data.session
DeNovoSummaryStorage() - Constructor for class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage
DeNovoTablePanel - Class in com.pacbio.secondary.vis.gui.panels: Specialized table panel for denovo experiments
DeNovoTablePanel(VioletApp, String, String, String, boolean) - Constructor for class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel
DeNovoTablePanel.DeNovoTablePanelMouseListener - Class in com.pacbio.secondary.vis.gui.panels
DeNovoTablePanel.DeNovoTablePanelMouseListener() - Constructor for class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel.DeNovoTablePanelMouseListener
density - Variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand
DENSITY_ACEN - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C1 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C10 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C11 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C12 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C13 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C14 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C15 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C16 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C17 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C18 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C19 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C2 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C20 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C3 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C4 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C5 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C6 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C7 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C8 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_C9 - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_FIRST - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_GNEG - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_GPOS - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_GVAR - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_LAST - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_STALK - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
DENSITY_UNKNOWN - Static variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: Types
description - Variable in class com.pacbio.secondary.vis.common.utils.filefilter.FileFilterGeneric
desktop - Variable in class pub.vlsolutions.swing.docking.DockTabbedPane
desktop - Variable in class pub.vlsolutions.swing.docking.DockView: the desktop managing this view
desktop - Variable in class pub.vlsolutions.swing.docking.event.DockEvent: The docking desktop which is the destination of the drag and drop gesture
desktop - Variable in class pub.vlsolutions.swing.docking.FloatingDialog
DESKTOP_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
DesktopApp - Class in com.pacbio.secondary.vis.gui.app
DesktopApp(String[]) - Constructor for class com.pacbio.secondary.vis.gui.app.DesktopApp
detach() - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer
detach() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel
detach() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger
detach() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
DetachedDockView - Class in pub.vlsolutions.swing.docking: A DockView suitable for detached dockables (in their own window).
DetachedDockView(Dockable) - Constructor for class pub.vlsolutions.swing.docking.DetachedDockView
DetachedDockViewUI - Class in pub.vlsolutions.swing.docking.ui: The UI of the "detached" (floating) dockview.
DetachedDockViewUI() - Constructor for class pub.vlsolutions.swing.docking.ui.DetachedDockViewUI
details_close_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
details_coarse_mode - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
details_data - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
details_help_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
details_interval - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper
DETAILS_METRICS_MODE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
details_metrics_mode - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
details_options - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper
details_options - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
DETAILS_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
details_range_mode - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
details_save_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
details_scroller - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
details_tab - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
details_tracks_height - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper
details_view - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
details_view_coarse_cb - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
details_view_dynamic_range - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
details_view_fixed_range - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
DETAILS_VIEW_LIMITING_MODE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
details_view_max_coverage - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
DETAILS_VIEW_PANEL_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
DETAILS_VIEW_PANEL_TOOLTIP - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
details_view_range_mode_cb - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
details_view_separator - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DetailsDataRequest - Class in com.pacbio.secondary.vis.data.queue
DetailsDataRequest(Locus) - Constructor for class com.pacbio.secondary.vis.data.queue.DetailsDataRequest
DetailsDataRequest() - Constructor for class com.pacbio.secondary.vis.data.queue.DetailsDataRequest
DetailsDataRequestsQueue - Class in com.pacbio.secondary.vis.data.queue
DetailsDataRequestsQueue() - Constructor for class com.pacbio.secondary.vis.data.queue.DetailsDataRequestsQueue
DetailsOptions - Class in com.pacbio.secondary.vis.data.session.options
DetailsOptions(JComponent) - Constructor for class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DetailsOptions() - Constructor for class com.pacbio.secondary.vis.data.session.options.DetailsOptions: de-serialization only
DetailsStorage - Class in com.pacbio.secondary.vis.data.session
DetailsStorage() - Constructor for class com.pacbio.secondary.vis.data.session.DetailsStorage
dialog - Variable in class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor
dim_ideogramview - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
dims - Variable in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo
dims - Variable in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo
dir - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFile
directPaintAll(Graphics2D) - Method in class com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper
directPaintGenomeView(Graphics2D) - Method in class com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper
directPaintSingleView(GenomicViewDraw, Graphics2D) - Method in class com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper
disabledIcon - Variable in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton: the icon for the disabled effect
displayResult(String) - Method in class com.pacbio.secondary.vis.gui.control.VioletToolBarTest
displayURL(String) - Static method in class com.pacbio.secondary.vis.common.utils.WebBrowserUtils: Display a file in the system browser.
dispose() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5File: this method must be called after using the file
dispose() - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: this method must be called after using the file
dispose(FloatingDockableContainer) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: disposes a detached dockable, regardless of its type (frame or dialog)
disposeDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.SMRTViewDialog
distance(long) - Method in class com.pacbio.secondary.vis.data.interval.Interval
DNA_BASE_LETTER_EXTRA_PADDING - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DNA_BASE_RECTANGLE_EXTRA_PADDING - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
dna_char_height - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
dna_char_width - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DNA_COLOR_0 - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
DNA_COLOR_1 - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
DNA_COLOR_2 - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
DNA_COLOR_3 - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
dna_colors_panel - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
dna_font - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DNA_LETTER_TRACK_PADDING - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
DNAColorsOptionsPane - Class in com.pacbio.secondary.vis.gui.dialogs: Options panel for DNA annotations
DNAColorsOptionsPane(TableModelListener, int) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.DNAColorsOptionsPane
doAsyncGetAnnotatedResults(String, int, long, long, int, Object) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper: Gets high resolution, fully annotated reads
doASyncGetConsensusSequence(String, String, int, long, long, Object) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper: Gets consensus sequence from cmp.h5
doASyncGetFastaSequence(String, String, int, long, long, Object) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doASyncGetFileBytes(String, Object) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doASyncGetGZippedFileBytes(String, Object) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doASyncGetIPDConsensus(String, String, int, long, long, Object) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper: Gets IPD consensus from cmp.h5
Dockable - Interface in pub.vlsolutions.swing.docking: Interface describing a component (AWT/Swing) that can be managed by the DockingDesktop.
dockable - Variable in class pub.vlsolutions.swing.docking.DockView: the dockable managed by this view
DockableActionCustomizer - Class in pub.vlsolutions.swing.docking: An objet that can provide actions relative to a dockable.
DockableActionCustomizer() - Constructor for class pub.vlsolutions.swing.docking.DockableActionCustomizer: Default constructor
DockableContainer - Interface in pub.vlsolutions.swing.docking: A DockableContainer is the base interface of GUI components used to display Dockable components.
DockableContainerFactory - Class in pub.vlsolutions.swing.docking: An abstract factory used by the DockingDesktop to create instance of Dockable containers.
DockableContainerFactory() - Constructor for class pub.vlsolutions.swing.docking.DockableContainerFactory
DockableContainerFactory.ParentType - Enum in pub.vlsolutions.swing.docking
DockableDragSource - Interface in pub.vlsolutions.swing.docking: An interface implemented by visual components used for drag and drop operations on a DockableContainer.
DockablePaneBase - Class in com.pacbio.secondary.vis.gui.panels.base
DockablePaneBase() - Constructor for class com.pacbio.secondary.vis.gui.panels.base.DockablePaneBase
DockablePanel - Class in pub.vlsolutions.swing.docking: A basic implementation of Dockable.
DockablePanel() - Constructor for class pub.vlsolutions.swing.docking.DockablePanel
DockablePanel(Component, DockKey) - Constructor for class pub.vlsolutions.swing.docking.DockablePanel
DockableResolver - Interface in pub.vlsolutions.swing.docking: An interface used to find a dockable (when read from an input stream like XML) when the only information given is its DockKey id.
DockableScrollPaneBase - Class in com.pacbio.secondary.vis.gui.panels.base
DockableScrollPaneBase(String, String, String, String, Component, int, int) - Constructor for class com.pacbio.secondary.vis.gui.panels.base.DockableScrollPaneBase
DockableSelectionEvent - Class in pub.vlsolutions.swing.docking.event: An event for tracking selection changes of dockables.
DockableSelectionEvent(Dockable) - Constructor for class pub.vlsolutions.swing.docking.event.DockableSelectionEvent
DockableSelectionListener - Interface in pub.vlsolutions.swing.docking.event: This interface describes a listener for dockable selection changes.
DockableState - Class in pub.vlsolutions.swing.docking: General information about the current state of a dockable component.
DockableState() - Constructor for class pub.vlsolutions.swing.docking.DockableState
DockableState(DockingDesktop, Dockable, DockableState.Location) - Constructor for class pub.vlsolutions.swing.docking.DockableState
DockableState(DockingDesktop, Dockable, DockableState.Location, RelativeDockablePosition) - Constructor for class pub.vlsolutions.swing.docking.DockableState
DockableState(DockableState, RelativeDockablePosition) - Constructor for class pub.vlsolutions.swing.docking.DockableState: Creates a dockable state based on an existing state, with another relative positionning
DockableState.Location - Enum in pub.vlsolutions.swing.docking: Possible locations of a dockable
dockableStateChanged(DockableStateChangeEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges: dockable windows docked/hidden or tabbed
dockableStateChanged(DockableStateChangeEvent) - Method in interface pub.vlsolutions.swing.docking.event.DockableStateChangeListener: this method will be called after a dockable component has changed of state (closed, hidden, docked)
DockableStateChangeEvent - Class in pub.vlsolutions.swing.docking.event: An event triggered after a change of dockable state.
DockableStateChangeEvent(DockableState, DockableState) - Constructor for class pub.vlsolutions.swing.docking.event.DockableStateChangeEvent
DockableStateChangeListener - Interface in pub.vlsolutions.swing.docking.event: Interface implemented by classes that need to be notified of a state change of a dockable.
dockableStates - Variable in class pub.vlsolutions.swing.docking.DockingContext: inner state of the dockables
dockableStateWillChange(DockableStateWillChangeEvent) - Method in interface pub.vlsolutions.swing.docking.event.DockableStateWillChangeListener: invoked before a dockable state change.
DockableStateWillChangeEvent - Class in pub.vlsolutions.swing.docking.event: An event triggered before a change of dockable state.
DockableStateWillChangeEvent(DockableState, DockableState) - Constructor for class pub.vlsolutions.swing.docking.event.DockableStateWillChangeEvent
DockableStateWillChangeListener - Interface in pub.vlsolutions.swing.docking.event: Interface implemented by classes that need to be notified of a state change of a dockable before it is processed.
DockableStoreButton - Class in pub.vlsolutions.swing.docking: A Button that can be used to store a dockable (for example to allow moving a dockable between two workspaces).
DockableStoreButton(String) - Constructor for class pub.vlsolutions.swing.docking.DockableStoreButton
DockableStoreButton() - Constructor for class pub.vlsolutions.swing.docking.DockableStoreButton
DockDragEvent - Class in pub.vlsolutions.swing.docking.event: An event describing a drag operation occuring for docking purpose.
DockDragEvent(DockingDesktop, DockableDragSource, MouseEvent) - Constructor for class pub.vlsolutions.swing.docking.event.DockDragEvent: Creates an event based on a drag source and a mouse event.
DockDropEvent - Class in pub.vlsolutions.swing.docking.event: An event send to a dockDropReceiver to complete a drop operation
DockDropEvent(DockingDesktop, DockableDragSource, MouseEvent) - Constructor for class pub.vlsolutions.swing.docking.event.DockDropEvent
DockDropReceiver - Interface in pub.vlsolutions.swing.docking: An interface implemented by components that can accept docking action with mouse drag and drop.
DockEvent - Class in pub.vlsolutions.swing.docking.event: Abstract superclass of drag and drop docking events.
DockEvent(DockingDesktop, DockableDragSource, MouseEvent) - Constructor for class pub.vlsolutions.swing.docking.event.DockEvent: Constructor for dock events.
DockGroup - Class in pub.vlsolutions.swing.docking: This class describes a logical group of Dockables.
DockGroup(String) - Constructor for class pub.vlsolutions.swing.docking.DockGroup: Constructs a new dockgroup with a given name.
DockGroup(String, DockGroup) - Constructor for class pub.vlsolutions.swing.docking.DockGroup: Constructs a new dockgroup with a given name and a parent group.
docking_desktop - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
DockingActionAddDockableEvent - Class in pub.vlsolutions.swing.docking.event: A DockingActionEvent describing the first insertion of a dockable either inside a desktop docking panel (main panel) or into a compoundDockable (nested) container.
DockingActionAddDockableEvent(DockingDesktop, Dockable, DockableState.Location, DockableState.Location, Container) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionAddDockableEvent: Constructor for a DockingActionAddDockableEvent
DockingActionCloseEvent - Class in pub.vlsolutions.swing.docking.event: A DockingActionEvent describing the closing of a dockable
DockingActionCloseEvent(DockingDesktop, Dockable, DockableState.Location) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionCloseEvent
DockingActionCreateTabEvent - Class in pub.vlsolutions.swing.docking.event: A DockingActionEvent describing a tab insertion (or movement).
DockingActionCreateTabEvent(DockingDesktop, Dockable, DockableState.Location, DockableState.Location, Dockable, int) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionCreateTabEvent
DockingActionDockableEvent - Class in pub.vlsolutions.swing.docking.event: A DockingActionEvent involving a single dockable as source of the action.
DockingActionDockableEvent(DockingDesktop, Dockable, DockableState.Location, DockableState.Location, int) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionDockableEvent
DockingActionEvent - Class in pub.vlsolutions.swing.docking.event: An abstract event class describing a docking action.
DockingActionEvent(DockingDesktop, DockableState.Location, DockableState.Location, int) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionEvent: Constructs a new DockingActionEvent
DockingActionListener - Interface in pub.vlsolutions.swing.docking.event: A listener to docking actions.
dockingActionPerformed(DockingActionEvent) - Method in interface pub.vlsolutions.swing.docking.event.DockingActionListener: Invoked once a docking action has been performed.
DockingActionSimpleStateChangeEvent - Class in pub.vlsolutions.swing.docking.event: An event describing a basic state change.
DockingActionSimpleStateChangeEvent(DockingDesktop, Dockable, DockableState.Location, DockableState.Location) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionSimpleStateChangeEvent: Constructs a new event
DockingActionSplitComponentEvent - Class in pub.vlsolutions.swing.docking.event: A DockingActionEvent describing a split action (from a base component (splitcontainer, tab...)).
DockingActionSplitComponentEvent(DockingDesktop, Dockable, DockableState.Location, DockableState.Location, Component, DockingConstants.Split, float) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionSplitComponentEvent: Constructs a new event
DockingActionSplitComponentEvent(DockingDesktop, Dockable, DockableState.Location, DockableState.Location, Component, DockingConstants.Split, float, float) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionSplitComponentEvent: Constructs a new event.
DockingActionSplitDockableContainerEvent - Class in pub.vlsolutions.swing.docking.event: A split event : split a base component in two, and puts a dockable container in the other split position.
DockingActionSplitDockableContainerEvent(DockingDesktop, DockableState.Location, DockableState.Location, Component, Container, DockingConstants.Split, float) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableContainerEvent: Constructs a new event
DockingActionSplitDockableEvent - Class in pub.vlsolutions.swing.docking.event: A DockingActionEvent describing a split action (from a base dockable).
DockingActionSplitDockableEvent(DockingDesktop, Dockable, DockableState.Location, DockableState.Location, Dockable, DockingConstants.Split, float) - Constructor for class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableEvent: Constructs a new event
DockingBorderLayout - Class in pub.vlsolutions.swing.docking: A layout adapted to autohide panels.
DockingBorderLayout() - Constructor for class pub.vlsolutions.swing.docking.DockingBorderLayout
DockingConstants - Class in pub.vlsolutions.swing.docking: Constants used by the DockingDesktop to position Dockables.
DockingConstants() - Constructor for class pub.vlsolutions.swing.docking.DockingConstants
DockingConstants.Hide - Class in pub.vlsolutions.swing.docking: Typesafe enumeration describing an auto-hide operation on the DockingDesktop.
DockingConstants.Split - Class in pub.vlsolutions.swing.docking: Typesafe enumeration describing a split operation on the DockingDesktop.
DockingContext - Class in pub.vlsolutions.swing.docking: A context that can be shared by multiple docking desktops.
DockingContext() - Constructor for class pub.vlsolutions.swing.docking.DockingContext: Constructs a new DockingContext
DockingDesktop - Class in pub.vlsolutions.swing.docking: The DockingDesktop is the main class of the VLDocking Framework.
DockingDesktop() - Constructor for class pub.vlsolutions.swing.docking.DockingDesktop: Constructs a DockingDesktop with a default name (suitable for single-desktop applications).
DockingDesktop(String) - Constructor for class pub.vlsolutions.swing.docking.DockingDesktop: Constructs a DockingDesktop with a given name (suitable for multiple-desktop applications).
DockingDesktop(String, DockingContext) - Constructor for class pub.vlsolutions.swing.docking.DockingDesktop: Constructs a DockingDesktop with a given name (suitable for multiple-desktop applications).
dockingPanel - Variable in class pub.vlsolutions.swing.docking.DockingDesktop: main central container for dockables
DockingPanel - Class in pub.vlsolutions.swing.docking: This class is responsible for the containment of a Dockable component.
DockingPanel() - Constructor for class pub.vlsolutions.swing.docking.DockingPanel: Javabeans constructor
DockingPreferences - Class in pub.vlsolutions.swing.docking: This is the centralized settings repository for managing docking look and feel.
DockingSelectorDialog - Class in pub.vlsolutions.swing.docking: A Helper class providing information about the visibility of user components.
DockingSelectorDialog() - Constructor for class pub.vlsolutions.swing.docking.DockingSelectorDialog: Default constructor.
DockingSelectorDialog(Dialog) - Constructor for class pub.vlsolutions.swing.docking.DockingSelectorDialog: Constructor for Dialog parent window.
DockingSelectorDialog(Frame) - Constructor for class pub.vlsolutions.swing.docking.DockingSelectorDialog: Constructor for Frame parent window.
DockingSplitPaneUI - Class in pub.vlsolutions.swing.docking.ui: A specific UI for removing border effects of the JSplitPanes used for docking.
DockingSplitPaneUI() - Constructor for class pub.vlsolutions.swing.docking.ui.DockingSplitPaneUI
DockingUISettings - Class in pub.vlsolutions.swing.docking.ui: Central class to manage Look and feel settings for the docking framework.
DockingUISettings() - Constructor for class pub.vlsolutions.swing.docking.ui.DockingUISettings
DockingUtilities - Class in pub.vlsolutions.swing.docking: Utility class implementing search/replace algorithms used by the framework.
DockKey - Class in pub.vlsolutions.swing.docking: Provides a unique identification for a Dockable and runtime properties, like icon, name, tooltip, preferred audohide-zone...
DockKey() - Constructor for class pub.vlsolutions.swing.docking.DockKey: JavaBeans constructor : If used, also think to set the dockKey property.
DockKey(String) - Constructor for class pub.vlsolutions.swing.docking.DockKey: Constructs a DockKey with dockKey (unique key) and name set to the same value
DockKey(String, String) - Constructor for class pub.vlsolutions.swing.docking.DockKey: Constructs a DockKey with dockKey (unique key) and a displayed name
DockKey(String, String, String) - Constructor for class pub.vlsolutions.swing.docking.DockKey: Constructs a DockKey with dockKey (unique key), a displayed name and a tooltip
DockKey(String, String, String, Icon) - Constructor for class pub.vlsolutions.swing.docking.DockKey: Constructs a DockKey with dockKey (unique key), a displayed name, a tooltip and an icon.
DockKey(String, String, String, Icon, DockingConstants.Hide) - Constructor for class pub.vlsolutions.swing.docking.DockKey: Constructs a DockKey with dockKey (unique key), a displayed name, a tooltip, an icon and a default autohide border.
DockTabbedPane - Class in pub.vlsolutions.swing.docking: A JTabbedPane customized for integration with the docking framework.
DockTabbedPane() - Constructor for class pub.vlsolutions.swing.docking.DockTabbedPane
DockView - Class in pub.vlsolutions.swing.docking: DefaultImplementation of the SingleDockableContainer.
DockView() - Constructor for class pub.vlsolutions.swing.docking.DockView: Constructs an empty DockView.
DockView(Dockable) - Constructor for class pub.vlsolutions.swing.docking.DockView: Constructs a new DockView for the given dockable.
DockView(Dockable, boolean) - Constructor for class pub.vlsolutions.swing.docking.DockView: Constructs a new DockView for the given dockable.
DockViewAsTab - Class in pub.vlsolutions.swing.docking: This component is used to display single dockables like if they were in a tabbed pane.
DockViewAsTab(Dockable) - Constructor for class pub.vlsolutions.swing.docking.DockViewAsTab
DockViewAsTab.TabHeader - Class in pub.vlsolutions.swing.docking
DockViewAsTab.TabHeader() - Constructor for class pub.vlsolutions.swing.docking.DockViewAsTab.TabHeader
DockViewTitleBar - Class in pub.vlsolutions.swing.docking: A title bar, associated to a DockView (container of a single user component).
DockViewTitleBar() - Constructor for class pub.vlsolutions.swing.docking.DockViewTitleBar: Constructs an empty title bar (no dockable yet associated).
DockViewTitleBar(Dockable) - Constructor for class pub.vlsolutions.swing.docking.DockViewTitleBar: Constructs a title bar for the specified dockable.
DockViewTitleBarUI - Class in pub.vlsolutions.swing.docking.ui: A UI for the DockViewTitleBar.
DockViewTitleBarUI(DockViewTitleBar) - Constructor for class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI
DockViewUI - Class in pub.vlsolutions.swing.docking.ui: This is the UI delegate for the DockView class.
DockViewUI() - Constructor for class pub.vlsolutions.swing.docking.ui.DockViewUI
doFullUIUpdate() - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper
doInBackground() - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper
doInBackground() - Method in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper
doInBackground() - Method in class com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper.ThreadHelper
doInBackground() - Method in class com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper.ThreadHelper
doIt() - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper
doIt() - Method in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper
doIt() - Method in class com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper.ThreadHelper
doIt() - Method in class com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper.ThreadHelper
doLoadDataInBackgroundFromInputStream(InputStream, TrackDataInfo) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper
doLoadDataInteractivelyFromFile(File) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper
done() - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper
done() - Method in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper
done() - Method in class com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper.ThreadHelper
done() - Method in class com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper.ThreadHelper
doneStreamingData() - Method in class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer: this method is called at the end of data transfer after all data has been read.
doneStreamingData() - Method in class com.pacbio.secondary.vis.io.hdf.streaming.UCharStreamingDataConsumer: override if need opportunity for additional cleanup
doneStreamingData() - Method in class com.pacbio.secondary.vis.io.hdf.streaming.UIntStreamingDataConsumer: this method is called at the end of data transfer after all data has been read.
doSyncGetAnnotatedInsertions(String, String, int, long, long, int) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper
doSyncGetAnnotatedResults(String, String, int, long, long, int) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper
doSyncGetConsensusSequence(String, String, int, long, long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper: Gets consensus sequence from cmp.h5
doSyncGetDefaultDirectory() - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncGetDirectoryList(String, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncGetFastaSequence(String, String, int, long, long) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncGetFileBytes(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncGetFileHeader(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper
doSyncGetFilesInformation(String, String, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncGetGZippedFileBytes(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncGetIPDConsensus(String, String, int, long, long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper: Gets IPD consensus sequence from cmp.h5
doSyncGetJobmetadataInfoFromURL(String, int) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncGetReferenceInfoFromURL(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncGetServiceExperienceIndex() - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper
doSyncGetServiceInfo() - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper
doSyncGetServiceInfo() - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncGetTemplateInfoFromURL(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
doSyncPutFileBytes(String, DataHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
DOTTED_LINE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
DragControler - Interface in pub.vlsolutions.swing.docking: This interface defines the features required for a drag controler.
DragControlerFactory - Class in pub.vlsolutions.swing.docking: A Basic factory providing a lightweight and heavyweight implementation of the DragControler interface
DragControlerFactory() - Constructor for class pub.vlsolutions.swing.docking.DragControlerFactory
DragControlerGlassPane - Class in pub.vlsolutions.swing.docking: A glasspane use to paint drag / drop shape on top of the desktop
DRAW_MIN_BASE_MOD_WIDTH - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
DRAW_MODS_SUMMARY - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
DRAW_PANEL_ICONS - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
drawAlleleShape(Graphics2D, Marker, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil: Draw a variant using two colors scheme from allele results
drawAxisHeaderlabel(Graphics, double, int, int, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawBackgroundSelections(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: draw marker lines and selected profile lines
drawBackgroundSelections(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: draw marker lines and selected profile lines
drawBackgroundSelections(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect: draw header area and reference sequence outline
drawBaseMod(Graphics, int, int, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil: uses triangles at top/bottom for strand
drawBaseModShape(Graphics, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
drawBaseModShapeDna(Graphics, int, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
drawBaseModUnmodified(Graphics, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
drawCircularText(Graphics2D, String, Point, double, double, double) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil: Draw text on a circular curve, one character at a time
drawCircularViewToGraphicsContext(Graphics2D) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular
drawCircularViewToPaintBuffer(Graphics2D) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular
drawCrossLines(Graphics, boolean, boolean, int, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: draw cross line if the ends are cut
drawDetailsLegend(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawEpiProFoldedRead(Graphics, Marker, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsDraw
drawEpiProIdeogram(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawEpiProUnfoldedReadMappedCoord(Graphics, Marker, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsDraw
drawEpiProUnfoldedReadSubreadCoord(Graphics, Marker, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsDraw
drawEpiProUnfoldedReadSubreadCoordOrg(Graphics, Marker, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsDraw: Deprecated.
drawFilledRoundRectangle(Graphics, int, int, int, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
drawFilledStrandedRect(Graphics, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
drawFilteredTrack(Graphics, List<Marker>, MarkerCollection, ArrayList<Integer>, VariableResolutionDataSet) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawFilteredTracks(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawForegroundSelections(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawForegroundSelections(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawForegroundSelections(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
drawGene(Graphics, Marker, boolean, Color) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
drawGene(Graphics, Marker, boolean, Color) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: Draws a gene into the graphic context
drawGene(Graphics, Marker, boolean, Color) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: Draws a gene into the graphic context
drawGenes(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
drawGenes(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: Paints the gene markers into the given Graphics device.
drawGenomicViewDoubleBuffered(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular: Main draw function for class
drawGenomicViewDoubleBuffered(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: Main draw function for class
drawGenomicViewDoubleBuffered(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
drawGenomicViewToGraphicsContext(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
drawGenomicViewToGraphicsContext(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawGenomicViewToGraphicsContext(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawGenomicViewToGraphicsContext(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: Paints the ideogram into the given graphical context.
drawGenomicViewToGraphicsContext(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
drawGenomicViewToPaintBuffer(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawGraphStructures(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails: draws various types of graphs
drawHeaderFooter(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
drawHeaderFooter(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawHeaderFooter(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawHeaderFooter(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
drawHorizontalAxisDetails(Graphics, GenomicViewDraw) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.AxisUtils
drawHorizontalAxisDetailsInspect(Graphics, GenomicViewInspect) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.AxisUtils
drawHorizontalAxisRegion(Graphics, GenomicViewDraw) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.AxisUtils
drawHorizontalTracksHeader(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawHorizontalTracksHeader(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawHorizontalTracksHeader(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: Draws the labels for each track
drawHorizontalTracksHeader(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
drawIdeogram(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
drawIdeogram(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawIdeogram(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawInfoLabel(Graphics, String, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawInfoLabelJustified(Graphics, String, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: draw label into info area
drawInspectTickmark(Graphics, GenomicViewInspect, NumberFormat, long, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.AxisUtils: draws vertical labels for axis values
drawIPDConsensusPlot(Graphics, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawIPDConsensusRevRefAndBases(Graphics, char[], int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawKineticsLegendToDeviceContext(Graphics, int, int, int, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails: Draw kinetics palette in legend area *****version for dual palette for kinetics
drawLabelWithOffsetAndWidth(Graphics, String, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawLabelWithoutCollision(Graphics, String, Color, int, int, int, Rectangle, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawLineStructures(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails: draws graphic structures created for strobes as lines
drawLinkStructures(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails: draws graphic structures created for standard reads
drawMapQVLegendToDeviceContext(Graphics, int, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails: Draw mapqv palette in legend area
drawMarker(Graphics, Marker, int, Rectangle, Color, boolean, Color) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
drawMarker(Graphics, Marker, int, Rectangle, Color, boolean, Color) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: Draws a single marker.
drawMarkerHorizontal(Graphics, Marker, ArrayList<Integer>, Rectangle, Color, boolean, Color) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: Draws a single marker.
drawMarkerInterval(Graphics, Marker, int, Rectangle, boolean, Color) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawMarkerInterval(Graphics, Marker, int, Rectangle, boolean, Color) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawMarkers(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
drawMarkers(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawMarkers(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawMarkersLegend(Graphics, VariableResolutionDataSet, Rectangle) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawMinMaxIPDRatioLabel(Graphics, double, double, int, int, double, String, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawMinMaxLabel(Graphics, double, double, int, int, double, String, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawMinSizeMarker(Graphics, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
drawModification(Graphics, Marker, int, Rectangle) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawModification(Graphics, Marker, ArrayList<Integer>, Rectangle, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawModificationInterval(Graphics2D, Marker, int, Rectangle, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawModificationInterval(Graphics2D, Marker, int, Rectangle, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawModificationsLegend(Graphics2D, VariableResolutionDataSet, Rectangle) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: draw legend for motifs/mods track
drawModificationSummaryHeatmap(Graphics2D, Marker, int, int, int, int, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawModificationSummaryHistogram(Graphics2D, Marker, int, int, int, int, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawMotifLegend(Graphics2D, String, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: draws a single motif string up to max x coordinate
drawMultipleHorizontalAxis(Graphics, GenomicViewDraw, int[], NumberFormat, long, String) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.AxisUtils
drawNodeStructures(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails: draws all graphic structures for strobes as rectangles
drawOutlinedStrandedRect(Graphics, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
drawRangeSelection(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawRangeSelection(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawReadFiltered(Graphics, List<Marker>, Marker, int, boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawReadKinetic(Graphics, Marker, int, boolean, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawReadKinetic(Graphics, Marker, int, boolean, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
drawReadLengthLegendToDeviceContext(Graphics, int, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails: Draw read length palette in legend area
drawReadsFiltered(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawReadShape(Graphics, Marker, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsDraw
drawReadsKinetics(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawReadsUnfiltered(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawReadUnfiltered(Graphics, Marker, int, boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawReadUnfiltered(Graphics, Marker, int, boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
drawReferenceBases(Graphics, char[], int, int, int, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawReferenceBasesOutline(Graphics, char[], int, int, int, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawReferenceSequence(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawReferenceSequence(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
drawReferenceSequenceOutline(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawRotatedLabel(String, Graphics, Color, int, int, double) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawRoundRectangle(Graphics, int, int, int, int, int, int, int, int, boolean, boolean, boolean, boolean) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
drawStructureLegend(Graphics, int, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails: Draw legend for structure graphs
drawSubReads() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawSummary(Graphics, Marker, int, Color, double, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: Draws coverage info for one coverage slot (marker)
drawSummaryInterval(Graphics, int, Marker, boolean, Color, double, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawSummaryLegends(Graphics, VariableResolutionDataSet, int, Rectangle, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: draws summary legends
drawSummaryRegion(Graphics2D, Shape, int[], int[], Color, Color) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawSummaryTracks(Graphics2D, List<Marker>, ArrayList<Integer>, Color, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawTargetInDetailsView() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect: draw selection in region panel
drawTest(Graphics2D) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular
drawTrackMetricLabel(Graphics, int, int, double, String) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawTruncatedEndsOfLink(Graphics, int, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawTruncatedEndsOfRead(Graphics, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
drawUnFilteredTracks(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawVariant(Graphics, Marker, int, Rectangle) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawVariant(Graphics, Marker, ArrayList<Integer>, Rectangle, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawVariantInterval(Graphics2D, Marker, int, Rectangle, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
drawVariantInterval(Graphics2D, Marker, int, Rectangle, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawVariantIntervalOrg(Graphics2D, Marker, int, Rectangle, VariableResolutionDataSetValues) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawVariantShape(Graphics2D, int, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
drawVariantsLegend(Graphics2D, VariableResolutionDataSet, Rectangle) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
drawVariantsLegendOrg(Graphics, Rectangle) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal: draw legend for variants track
dropRemove(DockableDragSource) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Removes a visible dockable : called from a drag and drop operation.
duration - Variable in class pub.vlsolutions.swing.docking.animation.ComponentAnimator: the animation duration in seconds
dynamic_range_label - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

E

EDIT - Static variable in class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor
editorPane - Variable in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel
elapsed - Variable in class pub.vlsolutions.swing.docking.animation.ComponentAnimator: time elapsed since the beginnig of animation
ENABLE_EPIPRO - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
enable_filter - Variable in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase
enable_graph_structure - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
ENABLE_GRAPH_STRUCTURE_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
ENABLE_VARIANTS_VCF - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
encodeToChar(byte[], boolean) - Static method in class com.pacbio.secondary.vis.common.utils.Base64Utils: Encodes a raw byte array into a BASE64 char[] representation i accordance with RFC 2045.
encodeToString(byte[], boolean) - Static method in class com.pacbio.secondary.vis.common.utils.Base64Utils: Encodes a raw byte array into a BASE64 String representation i accordance with RFC 2045.
end - Variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo
end - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
end_first_insertion - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
end_insertion_reference - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
end_last_lower_label_x - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
end_last_upper_label_x - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
endBounds - Variable in class pub.vlsolutions.swing.docking.animation.ComponentAnimator: the component's end bounds
endDragComponent(boolean) - Method in interface pub.vlsolutions.swing.docking.DockableDragSource: notifies the source when the drag operation has ended (by a drop or cancelled)
endDragComponent(boolean) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton
endDragComponent(boolean) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane
endDragComponent(boolean) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab.TabHeader
endDragComponent(boolean) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: notifies the source when the drag operation has ended (by a drop or cancelled)
endPoint - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
endSelection(Point) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
endsWithPattern(String) - Method in class com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterMultipleExtensions
ensureAbsolutePathToJobMetadata(String) - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils: Resolves path of job file
ensureCapacity(int) - Method in class com.pacbio.secondary.vis.common.collection.ByteArrayList: Increases the capacity of this ArrayList instance, if necessary, to ensure that it can hold at least the number of elements specified by the minimum capacity argument.
ensureDirectoryExists(String) - Static method in class com.pacbio.secondary.vis.svc.server.utils.ServiceUtils
epilog - Variable in class com.pacbio.secondary.vis.data.read.EpiProReadInfo
epipro_close_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
epipro_cutoff_filter_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
epipro_cutoff_filter_threshold - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
EPIPRO_CUTOFF_FILTER_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
EPIPRO_FOLDED - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
epipro_help_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
epipro_only_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
EPIPRO_OPTIONS - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
epipro_palette - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper
EPIPRO_PALETTE_BLACK - Static variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
EPIPRO_PALETTE_SCALING_MODE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
EPIPRO_PALETTE_WHITE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
epipro_pane - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
EPIPRO_PROGRAM_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
EPIPRO_READS_BW_PALETTE_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
epipro_reads_data - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase
EPIPRO_READS_MARKER_V1 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
EPIPRO_READS_MARKER_V2 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
epipro_reads_palette - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase
EPIPRO_READS_PALETTE_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
epipro_save_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
EPIPRO_SPLIT - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
epipro_tab - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
EPIPRO_UNFOLDED_MAPPED - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
EPIPRO_UNFOLDED_SUBREAD - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils
epipro_view_mode_cb - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
EpiProColorOptionsPane - Class in com.pacbio.secondary.vis.gui.dialogs: Options panel for EpiPro color options
EpiProColorOptionsPane(VioletApp, TableModelListener, int) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.EpiProColorOptionsPane
EpiProColorOptionsPane.EpiProOptionsTable - Class in com.pacbio.secondary.vis.gui.dialogs
EpiProColorOptionsPane.EpiProOptionsTable(TableModel) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.EpiProColorOptionsPane.EpiProOptionsTable
epiprodistance(Interval) - Method in class com.pacbio.secondary.vis.data.interval.Interval
EpiProPalette - Class in com.pacbio.secondary.vis.common.utils.constants
EpiProPalette(VioletApp) - Constructor for class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
EpiProPalette() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
EpiProPalette.ColorInfo - Class in com.pacbio.secondary.vis.common.utils.constants
EpiProPalette.ColorInfo() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo
EpiProPalette.ColorInfo(double, double) - Constructor for class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo
EpiProPalette.EpiProContigPalette - Class in com.pacbio.secondary.vis.common.utils.constants
EpiProPalette.EpiProContigPalette() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
EpiProPalette.EpiProContigPalette(EpiProPalette.ColorInfo, int, int) - Constructor for class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
EpiProPaletteRenderer - Class in com.pacbio.secondary.vis.gui.table.renderer
EpiProPaletteRenderer() - Constructor for class com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer
EpiProPaletteRenderer.EpiProPaletteDisplay - Class in com.pacbio.secondary.vis.gui.table.renderer
EpiProPaletteRenderer.EpiProPaletteDisplay() - Constructor for class com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer.EpiProPaletteDisplay
EpiProReadInfo - Class in com.pacbio.secondary.vis.data.read: Datum for each segment of a subread: prolog, primary, epilog
EpiProReadInfo(int) - Constructor for class com.pacbio.secondary.vis.data.read.EpiProReadInfo
EpiProReadInfo.EpiProInfo - Class in com.pacbio.secondary.vis.data.read
EpiProReadInfo.EpiProInfo(int, long, long, int, int, int) - Constructor for class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo
EpiProReadsPalettes - Variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
EpiProReadsReader - Class in com.pacbio.secondary.vis.io.epipro: read subreadLength prologSubreadStart prologSubreadEnd prologRefid prologTstrand prologStart prologEnd prologScore prologPctsimilarity prologMapqv primarySubreadStart primarySubreadEnd primaryRefid primaryTstrand primaryStart primaryEnd primaryScore primaryPctsimilarity primaryMapqv epilogSubreadStart epilogSubreadEnd epilogRefid epilogTstrand epilogStart epilogEnd epilogScore epilogPctsimilarity epilogMapqv Are subread start/end coordinates in any way associated with strand? m130131_012042_42161_c100427120310000001523055601121430_s1_p0/664/14142_16905 2763 3 1316 ctg7180000000004 1 2234780 2233515 -5558 91.4371 254 1317 2763 ctg7180000000004 0 2233373 2234779 -6216 91.9137 254 _ _ _ _ _ _ _ _ _ Here looks like both epilog and prolog are located before primary segment.
EpiProReadsReader() - Constructor for class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
equals(Interval) - Method in class com.pacbio.secondary.vis.data.interval.Interval
equals(JobInfo) - Method in class com.pacbio.secondary.vis.svc.server.threads.JobInfo
equals(Object) - Method in class pub.vlsolutions.swing.docking.DockGroup: overriden for storage/comparisons with the "name" property
equals(Object) - Method in class pub.vlsolutions.swing.docking.DockKey: Overriden for Map storage needs
equals(Object) - Method in class pub.vlsolutions.swing.docking.ws.WSDockKey
eraseStrandedReadEdge(Graphics, int, int, int, int, int) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
event - Variable in class pub.vlsolutions.swing.docking.event.DockEvent: The MouseEvent, in target's coordinates
EVENTS_FILTER_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
expand() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel: Expands the currently selected button
expandEnvVarInPath(String) - Static method in class com.pacbio.secondary.vis.svc.server.utils.ServiceUtils
expandPanel - Variable in class pub.vlsolutions.swing.docking.DockingDesktop: container responsible for auto-hidden components expansion
exportCMPH5DataToGFF(DetailsStorage, FileWriter, String, Interval, int) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils
exportCMPH5DataToGFF(DetailsStorage, FileWriter, String, Interval, int) - Method in class com.pacbio.secondary.vis.io.export.ExportRegionAsGFF
exportDataAsGFF() - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils
ExportDataUtils - Class in com.pacbio.secondary.vis.io.export
ExportDataUtils(VioletApp) - Constructor for class com.pacbio.secondary.vis.io.export.ExportDataUtils
exportDetailsAsGFF(VioletApp, String) - Method in class com.pacbio.secondary.vis.io.export.ExportRegionAsGFF
exportDetailsViewDataAsGFF(VioletApp) - Method in class com.pacbio.secondary.vis.io.export.ExportRegionAsGFF
exportGenericMarker(Marker, FileWriter, String, int) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils
exportGenericMarkerTrack(MarkerCollection, FileWriter, String, Interval, int) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils
exportGenericMarkerTrack(MarkerCollection, FileWriter, String, Interval, int) - Method in class com.pacbio.secondary.vis.io.export.ExportRegionAsGFF
exportGraphics() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog
exportModification(Marker, FileWriter, String, int) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils
exportModificationsTrack(MarkerCollection, FileWriter, String, Interval, int) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils
exportRead(Marker, FileWriter, String, int) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils
ExportRegionAsGFF - Class in com.pacbio.secondary.vis.io.export
ExportRegionAsGFF() - Constructor for class com.pacbio.secondary.vis.io.export.ExportRegionAsGFF
exportTableAsGFF(VioletApp, String) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils: exports table view as gff
exportVariant(Marker, FileWriter, String, int) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils
exportVariantsTrack(MarkerCollection, FileWriter, String, Interval, int) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils: coverage=4;length=1;reference=T
exportVariantsTrack(MarkerCollection, FileWriter, String, Interval, int) - Method in class com.pacbio.secondary.vis.io.export.ExportRegionAsGFF: coverage=4;length=1;reference=T
exportViewAsGFF(VioletApp, String, boolean) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils: exports region or details view as gff
ext_mode - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest
extensions - Variable in class com.pacbio.secondary.vis.common.utils.filefilter.FileFilterGeneric
extra_sequence_buffer - Static variable in class com.pacbio.secondary.vis.io.fasta.FastaFileReader

F

factorial(int) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility
FASTA_CONTIG_INDEX_EXTENSION - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
FASTA_INDEX_EXTENSION - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
FASTAFileIndexInfo - Class in com.pacbio.secondary.vis.io.indexer.indexinfo
FASTAFileIndexInfo(int, long, long) - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.FASTAFileIndexInfo
FASTAFileIndexInfo() - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.FASTAFileIndexInfo: de-serialization only
FastaFileReader - Class in com.pacbio.secondary.vis.io.fasta
FastaFileReader(String, int, String, long, long) - Constructor for class com.pacbio.secondary.vis.io.fasta.FastaFileReader
FastaIndexer - Class in com.pacbio.secondary.vis.io.indexer.fasta: FastaIndexer: Helper class to create index files for fast access to large fasta reference files
FastaIndexer() - Constructor for class com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer
fastcosine(double) - Static method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular: ~2x performances of built-in library with ~1-2% error
fastsine(double) - Static method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular: ~2x performances of built-in library with ~1-2% error
FeatureRenderer - Class in com.pacbio.secondary.vis.gui.table.renderer
FeatureRenderer() - Constructor for class com.pacbio.secondary.vis.gui.table.renderer.FeatureRenderer
file - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFileNode
file_info - Variable in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer
file_offset - Variable in class com.pacbio.secondary.vis.io.indexer.indexinfo.ASCIIFileIndexInfo
file_path - Variable in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo
file_type - Variable in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo
file_version - Variable in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase
file_version - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader
FileFilterGeneric - Class in com.pacbio.secondary.vis.common.utils.filefilter: Easy standard file filter.
FileFilterGeneric() - Constructor for class com.pacbio.secondary.vis.common.utils.filefilter.FileFilterGeneric
FileFilterGeneric(String) - Constructor for class com.pacbio.secondary.vis.common.utils.filefilter.FileFilterGeneric
FileFormatException - Exception in com.pacbio.secondary.vis.common.utils.exception
FileFormatException() - Constructor for exception com.pacbio.secondary.vis.common.utils.exception.FileFormatException
FileFormatException(String) - Constructor for exception com.pacbio.secondary.vis.common.utils.exception.FileFormatException
FileIndexInfo - Class in com.pacbio.secondary.vis.io.indexer.indexinfo
FileIndexInfo() - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.FileIndexInfo
FileIndexInfo(long, long, long, long) - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.FileIndexInfo
filename - Variable in class com.pacbio.secondary.vis.data.marker.MarkerCollection
fileName - Variable in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo
fileName - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
fileName - Variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader
FilenameFilterDirectory - Class in com.pacbio.secondary.vis.common.utils.filefilter
FilenameFilterDirectory(boolean) - Constructor for class com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterDirectory
FilenameFilterGeneric - Class in com.pacbio.secondary.vis.common.utils.filefilter
FilenameFilterGeneric(boolean, String) - Constructor for class com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterGeneric
FilenameFilterMultipleExtensions - Class in com.pacbio.secondary.vis.common.utils.filefilter
FilenameFilterMultipleExtensions(boolean, String) - Constructor for class com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterMultipleExtensions
FileUtils - Class in com.pacbio.secondary.vis.common.utils
FileUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.FileUtils
fillMatrix(double[][], double) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility
filter_text_field - Variable in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase
filter_view_btn - Variable in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase
filterMultiSampleVariantType(float) - Static method in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs
filterType(float) - Static method in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
find(Interval) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection: Find all markers intercepting specific interval; Used during drawing
findBin(Interval) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection: returns a bin to use for fast searching intercepting markers
findBin(long) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection: returns a bin to use for fast searching intercepting markers
findCompoundAncestorContainer(Dockable) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: searches up the dockable container hierarchy and returns the first ancestor which is a CompoundDockable (or null if not found).
findCompoundDockableChildren(CompoundDockable) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: Creates a list of all dockable children contained in the given compound dockable.
findDockableContainer(Dockable) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: returns the first DockableContainer which is parent of this dockable component
findNearest(long) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection: Finds the marker lying nearest to the given bp position
findNearestIndex(long) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection: Find nearest marker index with orientation.
findNearestIndexFast(long) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection: Find nearest marker index this is called every time users click on a view...
findNeighbour(Marker, boolean) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection: Find nearest marker, used to search next/previous markers
findReadByPositionAndLane(long, int) - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage
findReadByPositionAndLane(long, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
findSingleDockableContainer(Dockable) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: returns the first DockableContainer which is parent of this dockable component
findSingleDockableContainerAncestor(Component) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: A utility method to find the first single dockable container ancestor of the given component.
findSlow(Interval) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection
findTabbedDockableContainer(Dockable) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: Returns the first TabbedDockableContainer which is parent of this dockable component, or null is there isn't any.
findVariantByPositionAndYCoordinate(MarkerCollection, long, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
finishLayout() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: Notification of completion of layout.
fireAction(ActionEvent) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton: triggers the associated action
fireChangeEvent() - Method in class com.pacbio.secondary.vis.common.collection.ChangeNotifier
fireChangeEvent() - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel
fireEditingCanceled() - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor
fireEditingStopped() - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor
fireSelectionChanged(GenomicViewChangeEvent.GenomicViewEventType) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
fireTreeNodesChanged(Object, Object[], int[], Object[]) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
fireTreeNodesInserted(Object, Object[], int[], Object[]) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
fireTreeNodesRemoved(Object, Object[], int[], Object[]) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
fireTreeStructureChanged(Object, Object[], int[], Object[]) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
first() - Method in class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet
first() - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet
FIT_DENOVO_TABLE_TO_PANEL_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
FIT_TABLE_TO_PANEL_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
fitGenomicTableToPanel - Variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
fixed_range_label - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
fixedwidth - Variable in class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip
floatAction - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab
FloatingDialog - Class in pub.vlsolutions.swing.docking: The floating jdialog for floatable dockables.
FloatingDialog(Dialog) - Constructor for class pub.vlsolutions.swing.docking.FloatingDialog
FloatingDialog(Frame) - Constructor for class pub.vlsolutions.swing.docking.FloatingDialog
FloatingDialog.Resizer - Class in pub.vlsolutions.swing.docking
FloatingDialog.TitlePanel - Class in pub.vlsolutions.swing.docking: Class used as a title for dragging the window around
FloatingDialog.TitlePanel() - Constructor for class pub.vlsolutions.swing.docking.FloatingDialog.TitlePanel
FloatingDockableContainer - Interface in pub.vlsolutions.swing.docking: The interface describing a Floating window used to display one or more dockables
floatSmartIcon - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab
fmod(double, double) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility: Computes a floating point modulo operation of the value x to m such that the result is in the range [0,m)
FONT_ABOUT_DIALOG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_BASEMODTYPE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_CONTIG_LABEL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_FEATURE_LABELS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
font_height - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
font_height - Variable in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog
FONT_IDEOGRAM_HEADER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_PRINT_FOOTER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_PRINT_HEADER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_SMALL_SAMPLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_TABLE_HEADER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_TABLE_PANEL_HEADER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_TABLE_TEXT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_TITLED_BORDER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_TOOLTIPS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FONT_TRACK_HEADER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants
FontConstants - Class in com.pacbio.secondary.vis.common.utils.constants
FontConstants() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.FontConstants
forceGC - Static variable in class com.pacbio.secondary.vis.svc.server.HDFService
format(LoggingEvent) - Method in class com.pacbio.secondary.vis.common.utils.SMRTHTMLLayout: Override HTMLLayout's format() method
FormattedDoubleInputVerifier - Class in com.pacbio.secondary.vis.gui.dialogs
FormattedDoubleInputVerifier(Component, double, double) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.FormattedDoubleInputVerifier
FormattedFieldInputVerifier - Class in com.pacbio.secondary.vis.gui.dialogs
FormattedFieldInputVerifier(Component, int, int) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.FormattedFieldInputVerifier
forward - Variable in class com.pacbio.secondary.vis.data.gene.GeneInfo
fraction - Variable in class com.pacbio.secondary.vis.data.db.MotifData
from - Variable in class com.pacbio.secondary.vis.common.collection.SweepLineIterator.CutLine
from() - Method in class com.pacbio.secondary.vis.common.collection.SweepLineIterator.CutLine
from() - Method in class com.pacbio.secondary.vis.data.base.BaseDataRecord
from - Variable in class com.pacbio.secondary.vis.data.interval.Interval
from() - Method in class com.pacbio.secondary.vis.data.interval.Interval
from() - Method in interface com.pacbio.secondary.vis.data.interval.IntervalScale
full_sequence_name - Variable in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo
FullDump() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
fwdKineticsPalette - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

G

gappedDNAAnnotation - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
gatherBasesData(CMPH5File, ArrayList<WsRead>, AlignmentIndexTable, long, long, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder
gatherMetricsData(CMPH5File, ArrayList<WsRead>, ArrayList<RawRead>, AlignmentIndexTable, long, long, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder
gene_db - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase
gene_id - Variable in class com.pacbio.secondary.vis.data.gene.GeneInfo
gene_label - Static variable in class com.pacbio.secondary.vis.data.gene.GeneInfo
gene_name - Variable in class com.pacbio.secondary.vis.data.gene.GeneInfo
GeneDB - Class in com.pacbio.secondary.vis.data.db: Loads the NCBI gene database seq_gene.md
GeneDB(int) - Constructor for class com.pacbio.secondary.vis.data.db.GeneDB
GeneInfo - Class in com.pacbio.secondary.vis.data.gene
GeneInfo(long, String, boolean) - Constructor for class com.pacbio.secondary.vis.data.gene.GeneInfo
generateDefault(ReferenceInfo) - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB
GENERIC_HTTP_DEFAULT_PORT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
genes - Variable in class com.pacbio.secondary.vis.data.db.GeneDB
genomic_table_panel - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
GENOMIC_TABLE_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
GENOMIC_TABLE_PANEL_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
GENOMIC_TABLE_PANEL_TOOLTIP - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants
GenomicDataAssembler - Class in com.pacbio.secondary.vis.svc.server.hdf
GenomicDataAssembler() - Constructor for class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler
GenomicDataBuilder - Class in com.pacbio.secondary.vis.svc.server.hdf
GenomicDataBuilder() - Constructor for class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder
GenomicDataServer - Class in com.pacbio.secondary.vis.svc.server.hdf
GenomicDataServer() - Constructor for class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataServer
GenomicDataStructures - Class in com.pacbio.secondary.vis.svc.server.hdf
GenomicDataStructures() - Constructor for class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures
GenomicDataStructures.WsReadStructure - Class in com.pacbio.secondary.vis.svc.server.hdf: Inner helper class for sorting structured reads
GenomicDataStructures.WsReadStructure(WsRead) - Constructor for class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure
GenomicTableBase - Class in com.pacbio.secondary.vis.gui.table
GenomicTableBase(TableModelBase) - Constructor for class com.pacbio.secondary.vis.gui.table.GenomicTableBase
GenomicTableDeNovo - Class in com.pacbio.secondary.vis.gui.table
GenomicTableDeNovo(TableModelDeNovo) - Constructor for class com.pacbio.secondary.vis.gui.table.GenomicTableDeNovo
GenomicTableInterval - Class in com.pacbio.secondary.vis.gui.table
GenomicTableInterval(TableModelGenomicInterval) - Constructor for class com.pacbio.secondary.vis.gui.table.GenomicTableInterval
GenomicTablePanel - Class in com.pacbio.secondary.vis.gui.panels: Generic table panel for all experiments
GenomicTablePanel(VioletApp, String, String, String, boolean) - Constructor for class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel
GenomicTablePanel.GenomicTablePanelKeyListener - Class in com.pacbio.secondary.vis.gui.panels
GenomicTablePanel.GenomicTablePanelKeyListener() - Constructor for class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel.GenomicTablePanelKeyListener
GenomicTablePanel.GenomicTablePanelMouseListener - Class in com.pacbio.secondary.vis.gui.panels
GenomicTablePanel.GenomicTablePanelMouseListener() - Constructor for class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel.GenomicTablePanelMouseListener
GenomicTableTrack - Class in com.pacbio.secondary.vis.gui.table
GenomicTableTrack(TableModelTrack) - Constructor for class com.pacbio.secondary.vis.gui.table.GenomicTableTrack
GenomicUtils - Class in com.pacbio.secondary.vis.common.utils
GenomicUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.GenomicUtils
GenomicViewBase - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewBase(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
GenomicViewChangeEvent - Class in com.pacbio.secondary.vis.gui.evt
GenomicViewChangeEvent(Object) - Constructor for class com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent
GenomicViewChangeEvent(Object, GenomicViewChangeEvent.GenomicViewEventType) - Constructor for class com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent
GenomicViewChangeEvent.GenomicViewEventType - Enum in com.pacbio.secondary.vis.gui.evt
GenomicViewCircular - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewCircular(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular
GenomicViewData - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewData(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
GenomicViewDetails - Class in com.pacbio.secondary.vis.gui.draw.views: GenomicViewDetailsData
GenomicViewDetails(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
GenomicViewDetailsData - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewDetailsData(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
GenomicViewDetailsDraw - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewDetailsDraw(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsDraw
GenomicViewDraw - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewDraw(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
GenomicViewEvents - Class in com.pacbio.secondary.vis.gui.draw.views: Handles mouse and keyboards events of genomic view
GenomicViewEvents(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
GenomicViewEvents.GenomicViewKeyListener - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewEvents.GenomicViewKeyListener() - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewKeyListener
GenomicViewEvents.GenomicViewMouseListener - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewEvents.GenomicViewMouseListener() - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewMouseListener
GenomicViewEvents.GenomicViewMouseMotionListener - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewEvents.GenomicViewMouseMotionListener() - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewMouseMotionListener
GenomicViewHorizontal - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewHorizontal(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
GenomicViewInspect - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewInspect(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
GenomicViewInspect.GenomicViewInspectMouseMotionListener - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewInspect.GenomicViewInspectMouseMotionListener() - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect.GenomicViewInspectMouseMotionListener
GenomicViewRegion - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewRegion(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion
GenomicViewRegion() - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion: de-serialization only
GenomicViewSingleContig - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewSingleContig(VioletApp, int) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewSingleContig
GenomicViewSingleContig() - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewSingleContig: de-serialization only
GenomicViewVertical - Class in com.pacbio.secondary.vis.gui.draw.views
GenomicViewVertical(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.draw.views.GenomicViewVertical
genotype_tag - Variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader
get(int) - Method in class com.pacbio.secondary.vis.common.collection.ByteArrayList: Returns the element at the specified position in this list.
get(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
get(int) - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer
get(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger
get(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
get(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel
get(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray
get(int, int) - Method in class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray
get_return() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse: Auto generated getter method
get_return() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse: Auto generated getter method
getAbsMaxContigLength() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getAbsMaxGenomicRange() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getAbsMaxIPD(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getAbsMaxValue() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getAbsolutePath(String, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser
getActionCustomizer() - Method in class pub.vlsolutions.swing.docking.DockKey: Returns the action customizer associated to this dockkey (may return null)
getActionType() - Method in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Returns a field describing the action (ACTION_CLOSE...).
getActiveGenomicView() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges
getActiveView(boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
getActiveViewForKeyEvents() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getAlign() - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout: Returns the alignment of this layout (FlowLayout.LEADING, TRAILING...)
getAlignmentIndexDataChunk(H5ScalarDS, HDF5HyperslabInfo) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Reads a chunk of data from alignment index dataset.
getAlignmentIndexDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the alignment index dataset
getAlignmentIndexTableForContig(String) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Simple method to get cmp.h5 alignment index data for a specific contig.
getAlignmentReadEnd(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns sub-read end on alignment sequence
getAlignmentReadStart(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns sub-read start on alignment sequence
getAllAttributes(DataFormat) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: returns all attributes in dataset or group
getAllChildDatasets(H5Group) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Searches a parent group for all child datasets
getAllChildGroups(H5Group) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Searches a parent group for all child groups
getAlnGroupPathDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the aln group path dataset
getAlwaysShowMemStats() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getAnchor() - Method in class pub.vlsolutions.swing.docking.AnchorConstraints: Returns the anchor value of this contraints object.
getAnchors() - Method in class pub.vlsolutions.swing.docking.RelativeDockablePosition: Returns an integer value representing the anchoring of the dockable relatively to its ancestor container.
getAnn() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getAnnotatedInsertions(HDFServiceStub.GetAnnotatedInsertions) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub: Auto generated method signature
getAnnotatedInsertions(String, String, int, long, long, int) - Method in class com.pacbio.secondary.vis.svc.server.HDFService: Returns annotated reads with insertions from cmp.h5 results file serialized inside gzip archive.
getAnnotatedResults(HDFServiceStub.GetAnnotatedResults) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub: Auto generated method signature
getAnnotatedResults(String, String, int, long, long, int) - Method in class com.pacbio.secondary.vis.svc.server.HDFService: Returns annotated reads and stats from cmp.h5 file serialized inside gzip archive
getAnnotation() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getAnnotations() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getApp_options() - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper
getAppOptions() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getAppTitle() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getAppType() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getArgs() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getAsByte(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.UCharMatrixArray
getAsShort(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.UCharMatrixArray: converts byte to unsigned char values using short data type
getAsyncIPDConsensusFromServer(GenomicViewDetailsData, int, long, long) - Method in class com.pacbio.secondary.vis.data.session.DataStorage
getAttributeFloatValues(DataFormat, String) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Returns array of floating point values from single named attribute
getAttributeLongValues(DataFormat, String) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Returns array of longs from single named attribute Use when HObject element has either int, uint or long attribute with multiple values
getAttributeStringValues(DataFormat, String) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Returns array of strings from single named attribute Use when HObject element has a String attribute with multiple values
getAutoHideBorder() - Method in class pub.vlsolutions.swing.docking.DockKey: Returns the autohide border of this dockable, or null if not set
getAutoHideBorder() - Method in class pub.vlsolutions.swing.docking.ws.WSDockKey: Returns the autohide border of this dockable, or null if not set
getAutoHidePolicy() - Static method in class pub.vlsolutions.swing.docking.DockingPreferences
getAutoIdeogramBandSize() - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB
getAutoIdeogramNumBands() - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB
getAvailableScreenSize() - Static method in class com.pacbio.secondary.vis.common.utils.GUIUtils: returns available screensize accounting for task bars and menu bars
getAvgNumBases() - Method in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics
getAvgNumReads() - Method in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics
getAvgQV() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getAvgRowLenght() - Method in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfoCalculator
getAvgThroughput() - Method in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics
getAvgTime() - Method in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics
getBackgroundPainter() - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanel: Returns the optional background painter for this toolbar panel (may be null)
getBase() - Method in class pub.vlsolutions.swing.docking.event.DockingActionCreateTabEvent: Returns the dockable used as a reference to create a tab (may already belong to a tab)
getBase() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitComponentEvent: Returns the dockable which will be used as a base for the splitting
getBase() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableContainerEvent
getBase() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableEvent: Returns the dockable which will be used as a base for the splitting
getBase64StringFromByteArray(byte[]) - Static method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager
getBaseCall(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.RawRead
getBaseIPD(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.RawRead
getBaseMetric(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.RawRead
getBaseModFileTags(int) - Static method in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
getBaseModLabel(int) - Static method in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader: returns a base mod string from type
getBaseMods() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getBaseModType(String) - Method in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader: returns a base mod type from string
getBaseQV(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.RawRead
getBases() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo: returns total number of bases
getBisDirectory() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation: Auto generated getter method
getBListDirOnly() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList: Auto generated getter method
getBoolean(String, boolean) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getBorderInsets(Component) - Method in class pub.vlsolutions.swing.docking.ShadowBorder
getBorderInsets(Component) - Method in class pub.vlsolutions.swing.toolbars.RoundedBorder
getBorderInsets(Component) - Method in class pub.vlsolutions.swing.toolbars.ToolBarButtonBorder
getBorderInsets(Component) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelBorder
getBorderWidth() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getBorderZone() - Method in class pub.vlsolutions.swing.docking.AutoHideButtonPanel: Returns the border this panel is for.
getBottomDragger() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel: Returns the component used to modify the expand panel size when expanded from the top
getBuffer() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile: Auto generated getter method
getButtonFromActionCommand(String) - Method in class com.pacbio.secondary.vis.gui.control.VioletToolBar
getButtonImageHtml(VioletApp, String, String, int) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage
getByteArrayFromBase64String(String) - Static method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager
getBytesFromFile(String) - Static method in class com.pacbio.secondary.vis.svc.server.utils.ServiceUtils
getBytesPerBase() - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage: returns data bytes used for each base
getBytesPerRead() - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage: returns data bytes used for each base
getCellEditorValue() - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor
getCellEditorValue() - Method in class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor
getCenter() - Method in class com.pacbio.secondary.vis.data.interval.Interval
getCenter() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc
getCenter_pos() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getCenterlocation() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog
getCenterLocation() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
getCenterPositions(String) - Method in class com.pacbio.secondary.vis.data.db.MotifsDB: returns array of center positions for 1 or 2 motifs passed in, eventually separated by '/'
getChild(Object, int) - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
getChild(Object, int) - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
getChildCount(Object) - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
getChildCount(Object) - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
getChildDataset(H5Group, String) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Searches a parent group for a named child dataset
getChildGroup(H5Group, String) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Searches a parent group for a named child group
getChildren() - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileNode: Loads the children, caching the results in the children ivar.
getChildren(Object) - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
getChildren(VisServiceWrapper, String) - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileNode: Loads the children, caching the results in the children array
getChildren(Object) - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
getChromosome() - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand
getChunkSize() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo: Returns the array that contains the dimension sizes of the chunk of the dataset.
getCircularScrollPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getClient_contig_index() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions: Auto generated getter method
getClient_contig_index() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults: Auto generated getter method
getClient_contig_index() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence: Auto generated getter method
getClient_contig_index() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus: Auto generated getter method
getClientData() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler: Get the client data
getClientData() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler: Get the client data
getCloseButton() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar
getClosingState() - Method in class pub.vlsolutions.swing.docking.DockingSelectorDialog: Returns the users close choice as CONFIRM or CANCEL (remember this dialog is modal).
getCmdLineOptionsWithTracks() - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper: adds tracks info programmatically.
getCoarseMode() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getColorEnd() - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
getColorForbaseMod(int, int, float) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
getColorStart() - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
getColumnClass(int) - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
getColumnClass(int) - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
getColumnClass(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase
getColumnClass(int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
getColumnClass(int) - Method in interface com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel: Returns the type for column number column.
getColumnCount() - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
getColumnCount() - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
getColumnCount() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase
getColumnCount() - Method in interface com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel: Returns the number ofs availible column.
getColumnName(int) - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
getColumnName(int) - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
getColumnName(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase
getColumnName(int) - Method in interface com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel: Returns the name for column number column.
getColumnNames() - Method in class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage
getColumnNames() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
getColumnNames() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase
getColumnNames() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelDeNovo: Use denovo summary data
getColumnNames() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval
getColumnNames() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelTrack
getColumns() - Method in class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip
getCommandLineOptions() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getCompleted() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkDoneQueue
getComponent() - Method in class com.pacbio.secondary.vis.gui.panels.base.DockablePaneBase
getComponent() - Method in class com.pacbio.secondary.vis.gui.panels.base.DockableScrollPaneBase
getComponent() - Method in class pub.vlsolutions.swing.docking.CompoundDockable: Returns the component used by this dockable.
getComponent() - Method in interface pub.vlsolutions.swing.docking.Dockable: returns the component wrapped.
getComponent() - Method in class pub.vlsolutions.swing.docking.DockablePanel
getComponentAt(Object) - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer: Returns the component for a given BorderLayout constraints
getComponents() - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout: Returns and ordered array of the contained components
getConfidenceFromRowIndex(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase: work in progress
getConfigurationFilePath() - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper: return path of configuration file
getConfiguredHostName() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getConfiguredHttpPort() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getConfigXMLFilePath() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getConsensusCallsPath(String) - Static method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo
getConsensusSequence(String, long, long) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileData
getConsensusSequence(HDFServiceStub.GetConsensusSequence) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub: Auto generated method signature
getConsensusSequence(String, String, int, long, long) - Method in class com.pacbio.secondary.vis.svc.server.HDFService: get consensus sequence from cmp.h5 file as byte array.
getConsensusSequenceFromFile(String, String, int, long, long) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataServer
getConsensusSequenceFromServer(GenomicViewDetailsData, int, long, long) - Method in class com.pacbio.secondary.vis.data.session.DataStorage
getConstraints(Component) - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer: Returns the BorderLayout constraints of the given component
getConstraints(Component) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout
getContext() - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Returns the docking context used by this desktop (might be shared with other desktop).
getContig() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo
getContig_id() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions: Auto generated getter method
getContig_id() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults: Auto generated getter method
getContig_id() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence: Auto generated getter method
getContig_id() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus: Auto generated getter method
getContig_index() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence: Auto generated getter method
getContig_name() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence: Auto generated getter method
getContigData(Document) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser
getContigEnd() - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
getContigIndex(String) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
getContigIndexFromID(String) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Returns index of contig in cmp.h5 from contig id (ref00001, ref00002...)
getContigIndexRow(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.SortedRefIndexTable: Returns row of index info for specific contig
getContigInfoFromRow(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelDeNovo
getContigLabel() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getContigLabelFromIndex(int, boolean) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getContigLength() - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
getContigLength() - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo
getContigLength() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getContigMaxRange() - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo
getContigMaxRange() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getContigNameFromRowIndex(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
getContigNames(boolean) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Returns list of references in this file.
getContigNames(HDFServiceStub.GetContigNames) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub: Auto generated method signature
getContigNames(String) - Method in class com.pacbio.secondary.vis.svc.server.HDFService: Returns the names of all contigs in cmp.h5
getContigOffsetInIndex(String, String) - Method in class com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer
getContigs_info_array() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getContigsData(Document) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser
getContigsMap() - Method in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo: Get map containing list of all contigs in file and start/end for each contig
getContigStart() - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
getContigSummaryInfo(int) - Method in class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage: Called by DeNovo Table Model
getCtg() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc
getCtg() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getCurrent() - Method in class com.pacbio.secondary.vis.common.collection.SortedMultiIterator
getCurrentDateTimeAsString() - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils
getCurrentMainFrameContig() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getCurrentState() - Method in class pub.vlsolutions.swing.docking.event.DockableStateWillChangeEvent: this method will return null when the event is triggered for initial docking
getData() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getData() - Method in class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray
getDataDirs(String[]) - Static method in class com.pacbio.secondary.vis.update.UpdaterUtils: Parses cmd line args and returns list of directories to update
getDataExportPostFix(GenomicViewEvents) - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils
getDataFiles() - Method in class com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo
getDataInfo() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
getDataInfo() - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer
getDataInfo() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger
getDataInfo() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
getDataInfo() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel
getDataPointForInterval(VariableValuesDataRecord, String, int) - Method in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
getDataPointForInterval(VariableValuesDataRecord, String) - Method in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader
getDataPointForInterval(VariableValuesDataRecord, String) - Method in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader
getDataset(String) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Searches for a dataset by fully qualified path
getDatasetChunkInfo(H5ScalarDS) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Gets chunking info, if chunking was used, of this datasets
getDatasetHyperslabInfo(H5ScalarDS) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: This method returns the default hyperslab selection parameters of the dataset.
getDataStorage() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
getDataStorage() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getDataStorage() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getDataStorage() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getDataStreamFromDataset(H5ScalarDS, long, long, StreamingDataConsumer) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Main method for random access streaming of data.
getDataTitle() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getDataType() - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel
getDataType() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection
getDataTypeAsString(BaseDataModel.eDataType) - Static method in class com.pacbio.secondary.vis.data.base.BaseDataModel: static method
getDataTypeAsString() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection
getDataTypeAsString() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
getDefaultBaseModsMode() - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getDefaultDataFilename(int) - Method in class com.pacbio.secondary.vis.io.export.ExportDataUtils
getDefaultDataFilename(VioletApp) - Method in class com.pacbio.secondary.vis.io.export.ExportRegionAsGFF
getDefaultDirectory() - Method in class com.pacbio.secondary.vis.svc.server.VisService: used by remote filesystem view
getDefaultDirectory() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getDefaultGap() - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy: Returns the default gap between border components
getDefaultHideBorder() - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy: Returns the default hide border (used when not specified in a DockKey)
getDefaultResequencingMode() - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getDefaultVisibleRange() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
getDefaultWorkspaceLayout() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getDeltaAcrossTracks() - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
getDeNovoSummary() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getDeNovoTablePanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getDescription() - Method in class com.pacbio.secondary.vis.common.utils.filefilter.FileFilterGeneric
getDesiredTrackHeight(VariableResolutionDataSet, int, int, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
getDesktop() - Method in class pub.vlsolutions.swing.docking.DockableState: Returns the desktop currently using this dockable, or null if none
getDesktop() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: Returns the desktop associated to this title bar, if one has been registered with #installDocking(DockingDesktop), or null.
getDesktop() - Method in class pub.vlsolutions.swing.docking.event.DockEvent: Returns a reference of the desktop in which the docking event takes place.
getDesktop() - Method in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Returns the desktop used as a receiver (target) of the docking action.
getDesktop(int) - Method in class pub.vlsolutions.swing.docking.ws.Workspace: Returns the index-th desktop contained
getDesktop(String) - Method in class pub.vlsolutions.swing.docking.ws.Workspace: Returns a desktop identified by its name or null if not found
getDesktopCount() - Method in class pub.vlsolutions.swing.docking.ws.Workspace: Return the number of desktops contained in this workspace (default is 1 )
getDesktopList() - Method in class pub.vlsolutions.swing.docking.DockingContext: Returns a list of the desktops sharing this context
getDesktopName() - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Returns the name of this desktop (used by workspace management)
getDesktopName() - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop: Returns the name of this desktop (which must match the name of a real desktop if more than one desktops are used )
getDesktopPage(JFrame) - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel
getDetails_options() - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper
getDetails_view_separator() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getDetailsDataLocus() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
getDetailsDataStorage() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
getDetailsDataStorage() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getDetailsMetricsMode() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getDetailsOptions() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getDetailsOptions() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
getDetailsOptions() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
getDetailsOptions() - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper
getDetailsOptions() - Method in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper
getDetailsPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getDetailsRangeMode() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getDetailsStorage() - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper
getDetailsStorage() - Method in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper
getDetailsView() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getDetailsView() - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper
getDetailsView() - Method in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper
getDim() - Method in class com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper
getDim() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getDims() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo: Returns the array that contains the dimension sizes of the dataset.
getDims() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo: Returns the array that contains the dimension sizes of the dataset.
getDir() - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFile
getDirectory() - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo
getDirectory() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo: Auto generated getter method
getDirectoryList(String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.VisService: Returns list of files or directories in specified directory
getDirectoryList(VisServiceStub.GetDirectoryList) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getDisabledIcon() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton: Returns the disabled icon
getDividorLocation() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitComponentEvent
getDividorLocation() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableEvent
getDna_char_height() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getDna_char_width() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getDna_font() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getDNAReverseComplementSequence(char[]) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getDNASequence(Interval) - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage
getDNASequence(long) - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage
getDockable() - Method in class pub.vlsolutions.swing.docking.AutoHideButton: Returns the dockable this button is for
getDockable() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel
getDockable() - Method in class pub.vlsolutions.swing.docking.CompoundDockingPanel: Returns the compound dockable this container is for
getDockable() - Method in interface pub.vlsolutions.swing.docking.DockableDragSource: Returns the Dockable component this source is for
getDockable() - Method in class pub.vlsolutions.swing.docking.DockableState: Returns the dockable this state is for
getDockable() - Method in class pub.vlsolutions.swing.docking.DockableStoreButton: Return the dockable currently stored (may be null)
getDockable() - Method in class pub.vlsolutions.swing.docking.DockTabbedPane: Returns the Dockable component this source is for
getDockable() - Method in class pub.vlsolutions.swing.docking.DockView: Returns the contained component Returns the dockable this container is displaying
getDockable() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab.TabHeader
getDockable() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: Returns the Dockable component this source is for
getDockable() - Method in interface pub.vlsolutions.swing.docking.DragControler
getDockable() - Method in class pub.vlsolutions.swing.docking.event.DockingActionDockableEvent
getDockable() - Method in interface pub.vlsolutions.swing.docking.SingleDockableContainer: Returns the dockable this container is displaying
getDockableAt(int) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane: Returns the dockable at the index tab
getDockableAt(int) - Method in interface pub.vlsolutions.swing.docking.TabbedDockableContainer: Returns the dockable at the index tab
getDockableByKey(String) - Method in class pub.vlsolutions.swing.docking.DockingContext: Returns the (registered) dockable corresponding to the given key id, or null if not found
getDockableConstraints(Dockable) - Method in class pub.vlsolutions.swing.docking.AnchorManager: Returns the anchor constraints associated to a given dockable
getDockableContainer() - Method in interface pub.vlsolutions.swing.docking.DockableDragSource: returns the DockableContainer responsible for displaying the associated dockable
getDockableContainer() - Method in class pub.vlsolutions.swing.docking.DockableStoreButton
getDockableContainer() - Method in class pub.vlsolutions.swing.docking.DockTabbedPane
getDockableContainer() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab.TabHeader
getDockableContainer() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: Returns the container of the dockable's component
getDockableContainer() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableContainerEvent
getDockableIndex(DockKey) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane: Returns the tab index of the dockable corresponding to the given key, or null if the dockable doesn't belong to this tab.
getDockableLocationFromHierarchy(Component) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: Returns a DockableState value corresponding to this component or null if not found.
getDockableResolver() - Method in class pub.vlsolutions.swing.docking.DockingContext: Returns the dockable resolver used by this context (or null if none defined)
getDockables() - Method in class pub.vlsolutions.swing.docking.DockingContext: Creates and returns an array of all registered dockable with their current state.
getDockables() - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Creates and returns an array of all registered dockable with their current state.
getDockablesByState(DockingDesktop, DockableState.Location) - Method in class pub.vlsolutions.swing.docking.DockingContext: constructs and returns the list of dockables corresponding to a desktop, at a specific state
getDockableState(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingContext: Returns the current state of a dockable (CLOSED, HIDDEN, DOCKED, MAXIMIZED, FLOATING)
getDockableState(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Returns the current state of a dockable (CLOSED, HIDDEN, DOCKED, MAXIMIZED, FLOATING)
getDockGroup() - Method in class pub.vlsolutions.swing.docking.DockKey: returns the dockGroup of this dockable
getDockingAction() - Method in class pub.vlsolutions.swing.docking.event.DockEvent: Returns the DockingActionEvent corresponding to the drag and drop gesture
getDockingContext() - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceButton: Returns the docking context used by this button
getDockingContext() - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem: Returns the docking context used by this menu item
getDockingDesktop() - Method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager
getDockingDesktop() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getDockingFrameworkBuildDate() - Static method in class pub.vlsolutions.swing.docking.DockingDesktop: Returns a String containing the release date of the current version.
getDockingFrameworkVersion() - Static method in class pub.vlsolutions.swing.docking.DockingDesktop: Returns a String containing the version of the docking framework in the format M.m.r where M is the major , m the minor and r the release.
getDockingPanelInsets() - Method in class pub.vlsolutions.swing.docking.DockingDesktop: recalculates and returns the insets taken by autoexpand borders around the docking panel.
getDockKey() - Method in class com.pacbio.secondary.vis.gui.panels.base.DockablePaneBase
getDockKey() - Method in class com.pacbio.secondary.vis.gui.panels.base.DockableScrollPaneBase
getDockKey() - Method in class pub.vlsolutions.swing.docking.CompoundDockable: Returns the key used to describe this dockable
getDockKey() - Method in interface pub.vlsolutions.swing.docking.Dockable: returns the unique key identifying the docked element
getDockKey() - Method in class pub.vlsolutions.swing.docking.DockablePanel
getDockName() - Method in class pub.vlsolutions.swing.docking.DockKey: Deprecated.
use getKey instead
getDouble(String, double) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getDraggedBorder() - Method in class pub.vlsolutions.swing.toolbars.VLToolBar: Returns the border used during drag and drop or the toolbar
getDragSource() - Method in class pub.vlsolutions.swing.docking.event.DockEvent: Returns a reference to the drag source of this event.
getDropReceiver() - Method in interface pub.vlsolutions.swing.docking.DragControler
getDropShape() - Method in interface pub.vlsolutions.swing.docking.DragControler
getDropShape() - Method in class pub.vlsolutions.swing.docking.event.DockDragEvent: Returns the shape to display if drag is accepted.
getDuration() - Method in class pub.vlsolutions.swing.docking.animation.ComponentAnimator: Returns the duration of the animation
getEditingRow() - Method in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable
getElapsedTimeAsString(long) - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils
getEmptyCharArray(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData: Creates array of chars filled in with white spaces
getEmptyIcon() - Method in class pub.vlsolutions.swing.docking.DockableStoreButton: Returns the Icon used with this button when no dockable is selected
getEmptyText() - Method in class pub.vlsolutions.swing.docking.DockableStoreButton: Returns the text used for this button when no dockable is stored
getEmptyTooltip() - Method in class pub.vlsolutions.swing.docking.DockableStoreButton: Returns the text used as tooltip for this button when no dockable is stored
getEnableGraphStructure() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getEnd() - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo
getEnd() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc
getEnd() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getEnd() - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure
getEnd() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence: Auto generated getter method
getEndBounds() - Method in class pub.vlsolutions.swing.docking.animation.ComponentAnimator: Returns the end bounds of the components.
getEndFirstInsertion() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
getEndInsertionReference() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
getEpilogInfo() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo
getEpiProModeFromUIIndex(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getEpiProReadColor(int, long) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
getEpiProReadsDataModel() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getEpiProReadsPalette() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getEpiProUIIndex(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getEventsCoverageFilterThreshold() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getEventType() - Method in class com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent
getExpandMode() - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy: Returns the expand mode in use.
getExpansionDuration() - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy: Returns the expansion duration (in millis)
getExtraRefTrackDistance() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getFactory() - Static method in class pub.vlsolutions.swing.docking.DockableContainerFactory: Returns the current factory.
getFastaSequence(String, int, String, long, long) - Method in class com.pacbio.secondary.vis.svc.server.VisService: get fasta sequence from fasta file as byte array.
getFastaSequence(VisServiceStub.GetFastaSequence) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getFastaSequenceFromDataHandler(DataHandler) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl
getFile() - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileNode
getFile(Object) - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
getFile() - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileNode
getFile(Object) - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
getFile(String) - Method in class com.pacbio.secondary.vis.svc.server.VisService: gets file as byte array
getFile(VisServiceStub.GetFile) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getFile_type() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo
getFileComments() - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getFileDialog(String, String[], String[]) - Static method in class com.pacbio.secondary.vis.common.utils.GUIUtils: create a dialog with specified filters
getFileDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog
getFileExtension(File) - Static method in class com.pacbio.secondary.vis.common.utils.FileUtils
getFileHandle() - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File
getFileHeader() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
getFileHeader() - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer
getFileHeader() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger
getFileHeader() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
getFileHeader() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel
getFileHeader(HDFServiceStub.GetFileHeader) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub: Auto generated method signature
getFileHeader(String) - Method in class com.pacbio.secondary.vis.svc.server.HDFService: Returns header and summary info about cmp.h5
getFileInfo(String) - Static method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo
getFileName() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo
getFilename() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList: Auto generated getter method
getFilename() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile: Auto generated getter method
getFilename() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation: Auto generated getter method
getFilename() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile: Auto generated getter method
getFilename() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile: Auto generated getter method
getFilePath() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
getFilePath() - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer
getFilePath() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger
getFilePath() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
getFilePath() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel
getFilePath() - Method in class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog
getFilePath() - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File
getFileRegionEnd() - Method in class com.pacbio.secondary.vis.io.indexer.indexinfo.FileIndexInfo
getFilesInformation(String, String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.VisService: Returns info about files or directories.
getFilesInformation(VisServiceStub.GetFilesInformation) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getFileType() - Method in class com.pacbio.secondary.vis.io.importer.DataFileInfo
getFileTypeAsString() - Method in class com.pacbio.secondary.vis.io.importer.DataFileInfo
getFitDeNovoTableToPanel() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getFitTableToPanel() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getFixedWidth() - Method in class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip
getFloatButton() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: returns the button used for floating (detach) the view.
getFraction() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getFullSequenceName(String[], String[], int[], int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Reads full sequence (contig) name from cmp.h5 metadata
getFullSequenceName() - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo
getFullText() - Method in class pub.vlsolutions.swing.docking.DockableStoreButton: Returns the text used for this button when a dockable is stored
getFullTooltip() - Method in class pub.vlsolutions.swing.docking.DockableStoreButton: Returns the text used for as tooltip this button when a dockable is stored
getFutureState() - Method in class pub.vlsolutions.swing.docking.event.DockableStateWillChangeEvent: Returns the future (proposed) state of the dockable.
getFwdKineticsPalette() - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getGeneDB() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getGeneDB() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getGeneDB() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getGeneDB() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getGenes() - Method in class com.pacbio.secondary.vis.data.db.GeneDB
getGenesBounds() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getGenesOfCurrentContig() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getGenomePanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getGenomeScrollPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getGenomicTablePanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getGFFFileIndexesAndMetadata(String, int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer: Splits a large gff2 file into desired number of chunks, and creates a list of indexes, offset in the file, and corresponding genome position, e.g.: [file_offset] [genome_position] 0x1234 412 0x9876 3258 ....
getGFFFileRegionIndexesAndMetadata(String, int, int, long, long) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer: Splits a gff2 file region into desired number of chunks, and creates a list of indexes (absolute in the file) and corresponding genome position, e.g.: [file_offset] [genome_position] 0x1234 412 0x9876 3258 ....
getGFFFileRegionInfo(String, int, long, long, int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer
getGFFLength() - Method in class com.pacbio.secondary.vis.data.interval.Interval
getGlobalData(String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser
getGlobalInfo(Document) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser
getGraph() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResults
getGraphStructure() - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage
getGraphStructureType() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getGroup(String) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Searches for a group by fully qualified path
getGZipped() - Method in class com.pacbio.secondary.vis.io.importer.DataFileInfo
getGZippedBytesFromFile(String) - Static method in class com.pacbio.secondary.vis.svc.server.utils.ServiceUtils: Returns the content of a file as a gzipped byte array.
getGZippedError(String) - Static method in class com.pacbio.secondary.vis.svc.server.data.WsResults: Returns gzipped error code
getGZippedFile(String) - Method in class com.pacbio.secondary.vis.svc.server.VisService: gets file as gzipped byte array
getGZippedFile(VisServiceStub.GetGZippedFile) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getGZippedResultsFromFile(String, String, int, long, long, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataServer
getHasBaseMods() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getHasCoverage() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getHasMotifs() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getHasVariants() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getHDFServiceExperienceIndex(String[]) - Method in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex: Tests read performances on one or more files Averages results from three tests for each file Reports results in user-friendly bases/sec metric
getHDFServiceURL() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getHeader() - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo
getHeaderLevel() - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: get header level
getHeaderText() - Method in class com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper
getHeight() - Method in class pub.vlsolutions.swing.docking.RelativeDockablePosition: Returns the relative height of the dockable
getHelpButton() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: MM added
getHideOrDockButton() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: returns the button used for hiding or docking the view.
getHigh_kin_threshold() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getHigh_qv_threshold() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getHoleNumber(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns hole number
getHostCodebaseHttpPort() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getHostCodebaseHttpPort() - Method in class com.pacbio.secondary.vis.gui.app.WebStartApp
getHostName() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getHostName() - Method in class com.pacbio.secondary.vis.gui.app.WebStartApp
getHostname(String[]) - Static method in class com.pacbio.secondary.vis.update.UpdaterUtils: Parses cmd line args and returns host name
getHostURL() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getHtmlText(VioletApp) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage
getHtmlToolTipForTable(GenomicViewEvents, Marker, MarkerCollection, StringBuffer) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: gets tooltip for table view
getHtmlToolTipText(GenomicViewEvents, StringBuffer, Point) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
getHttpPort(String[]) - Static method in class com.pacbio.secondary.vis.update.UpdaterUtils: Parses cmd line args and returns http port
getIcon() - Method in class pub.vlsolutions.swing.docking.DockKey: Returns the icon displayed in title bars
getIcon() - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon: Return the tab icon
getIcon() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton: Returns the default icon
getIconHeight() - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon: Returns the height of this icon
getIconHeight() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton
getIconHeight() - Method in class pub.vlsolutions.swing.toolbars.RolloverIcon
getIconWidth() - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon: Returns the width of this icon
getIconWidth() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton
getIconWidth() - Method in class pub.vlsolutions.swing.toolbars.RolloverIcon
getId() - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo
getIdeogramBounds() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getIdeogramDB() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getIdeogramDB() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getIdeogramDB() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getIdeogramDB() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getIdeogramDBTree() - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB
getIdeogramFile() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getIdeogramTreeOfCurrentContig() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getImage() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest
getImageFile() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest
getImageHtml(RegionsOfInterestStorage.RegionOfInterest, int) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage
getImageIcon(Component, String) - Static method in class com.pacbio.secondary.vis.common.utils.ResourceUtils
getImageIcon(URL) - Static method in class com.pacbio.secondary.vis.common.utils.ResourceUtils
getImageResource(Component, String) - Static method in class com.pacbio.secondary.vis.common.utils.ResourceUtils: Finds an image resource with the given path.
getIndexOfChild(Object, Object) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
getIndexSliceSize() - Method in class com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer
getIndexSliceSize() - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer
getIndexSliceSize() - Method in class com.pacbio.secondary.vis.io.indexer.text.TextFileIndexer
getInfo() - Method in class com.pacbio.secondary.vis.data.marker.Marker
getInfo() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest
getInfo() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResults
getInfoPanelFontSize() - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getInitialExpansionHeight() - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy
getInitialExpansionModel() - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy: returns the expansion model (computation size of first expansion)
getInitialExpansionWidth() - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy
getInitialLocation() - Method in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Returns one of the DockableState states reflecting the state of the dockable before the action
getInsertionContraintsAt(Component, Point) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout: Returns a proposed TooBarContraints for a given insertion point
getInsertionWidth() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
getInspectionIntervalAt(long) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
getInstalledToolbars() - Method in class pub.vlsolutions.swing.toolbars.ToolBarIOReadInfo: returns the list of toolbars that were successfully loaded from the toolbarIO operation
getInstance() - Static method in class pub.vlsolutions.swing.docking.DragControlerFactory
getInstance() - Static method in class pub.vlsolutions.swing.docking.ui.DockingUISettings: returns the singleton instance used to store and install UI settings for the framework
getInt(String, int) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getIntersectedMarkers(StringBuffer, Marker, Marker, GenomicViewEvents) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
getInterval() - Method in class com.pacbio.secondary.vis.data.interval.IntervalTreeNode
getInterval() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo
getIntv() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getInverse(Color) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
getIPDConsensus(HDFServiceStub.GetIPDConsensus) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub: Auto generated method signature
getIPDConsensus(String, String, int, long, long) - Method in class com.pacbio.secondary.vis.svc.server.HDFService: get IPDRatio sequence from cmp.h5 file as two-dimensional short array.
getIPDConsensus_locus() - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage
getIpdconsensus_track_height() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getIPDConsensusDataLocus() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
getIPDConsensusFromDataHandler(DataHandler) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl
getIPDConsensusFromFile(String, String, int, long, long) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataServer: get ipd ratio as int arrays
getIPDConsensusStorage() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
getIPDFwd(long) - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage
getIPDFwd(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.IPDConsensusTable: lower 2 bytes (16 bits)
getIPDFwd(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo
getIPDRatioSequencePath(String) - Static method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo
getIPDRev(long) - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage
getIPDRev(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.IPDConsensusTable: upper 2 bytes (16 bits)
getIPDRev(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo
getIPDSequence(String, long, long) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileData
getIsdirectory() - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo
getIsdirectory() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo: Auto generated getter method
getIsSMRTGroup(String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper: Returns true if host requires group-level access control
getIsverbose(String[]) - Static method in class com.pacbio.secondary.vis.update.UpdaterUtils: Parses cmd line args and returns verbose flag
getJNLPForProjectFile(String[], byte[], byte[], boolean) - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper: Used to save current jnlp
getJNLPFromCmdLine(String[], boolean) - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper: Used to get jnlp from job id as number.
getJNLPFromDataAndTrackFile(String, String, String, String, String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper
getJNLPFromDataFile(String, String, String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper
getJNLPFromDataFile(String, String, String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.JNLPService: Expects a cmp.h5 file path in input, and a path to a reference.info.xml file, not required only for denovo jobs Returns a JNLP file to use to view job
getJNLPFromJobId(long, boolean) - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper: Used to get jnlp from job id as number.
getJNLPFromJobMetadataAndTrackFile(String, String, String, String, String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper
getJNLPFromJobMetadataFile(String, String, String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper
getJNLPFromJobMetadataFile(String, String, String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.JNLPService: Expects a metadata.rdf file path in input, a path to a reference.info.xml file, and optional parameters Returns a JNLP file to use to view job
getJNLPFromJobMetadataFileAndTracks(String, String, String, String, String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.JNLPService: Expects a cmp.h5 file path in input, and a path to a reference.info.xml file, not required only for denovo jobs Returns a JNLP file to use to view job
getJNLPServiceURL() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getJobMetadata() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getJobsRootDirectory() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getJobTitle() - Method in class com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo
getJTableNativeSize(JTable) - Static method in class com.pacbio.secondary.vis.common.utils.GUIUtils
getKey() - Method in class pub.vlsolutions.swing.docking.AutoHideButton: Returns the key of the dockable
getKey() - Method in class pub.vlsolutions.swing.docking.DockKey: Returns the unique id designating the user component.
getKey() - Method in class pub.vlsolutions.swing.docking.ws.WSDockKey: returns the inner key of this object (which must match a DockKey's 'key' instance variable)
getKineticModeFromUIIndex(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getKineticsPalette(int) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getKineticsScaling() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getKineticsScalingLabel(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getLabel() - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon: Return the tab label
getLabelBounds() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getLane() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getLane() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getLanes() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getLanesSeparator() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getLastLocalDataFolderOpen(String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getLastLocalDataFolderSave(String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getLastRemoteDataFiles(String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getLastSelectedDockable() - Method in class pub.vlsolutions.swing.docking.DockingDesktop
getLastusedLayout() - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getLayoutAlignmentX(Container) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout
getLayoutAlignmentX(Container) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout
getLayoutAlignmentX(Container) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout
getLayoutAlignmentX(Container) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout
getLayoutAlignmentY(Container) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout
getLayoutAlignmentY(Container) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout
getLayoutAlignmentY(Container) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout
getLayoutAlignmentY(Container) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout
getLeftDragger() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel: Returns the component used to modify the expand panel size when expanded from the right
getLegendBounds() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getLegendLabelsWidth() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
getLength() - Method in class com.pacbio.secondary.vis.data.interval.Interval
getLength() - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage
getLength() - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo
getLength() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc
getLength() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo
getLength() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo: Auto generated getter method
getLinkBoundingRectangle() - Method in class com.pacbio.secondary.vis.data.graph.GraphPrimitive: returns a pseudo rectangle representing bounding box
getListOfReadsToDraw() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
getLoadUserWorkspaceFilename(Component, VioletApp) - Static method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager
getLocalInfo() - Method in class com.pacbio.secondary.vis.gui.dialogs.AboutDialog
getLocalTooltipText() - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon: Return the local tooltip of this icon (the one associated with inner mouse movements)
getLocation() - Method in class pub.vlsolutions.swing.docking.DockableState: Returns the current location of the dockable (CLOSED, DOCKED, HIDDEN...).
getLocation() - Method in class pub.vlsolutions.swing.docking.DockKey: returns the current visible location of the dockable (see DockableState.Location for enumeration values)
getLocation() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableContainerEvent
getLocationFromInt(int) - Static method in class pub.vlsolutions.swing.docking.DockableState: Utility (compatibility) method used to associate an int to the Location enumeration (opposite to location.ordinal()
getLockGenomeRegionPanels() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getLockRangeExpand() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getLockRegionDetailsPanels() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getLocus() - Method in class com.pacbio.secondary.vis.data.queue.DetailsDataRequest
getLocus() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo
getLocus() - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage
getLogger() - Static method in class com.pacbio.secondary.vis.common.utils.LoggerUtils
getLow_kin_threshold() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getLow_qv_threshold() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getM_contig_length() - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo
getM_contig_length() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo: Auto generated getter method
getM_contigs_info_array() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_contigs_info_array() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_data_file() - Method in class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo
getM_data_file() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo: Auto generated getter method
getM_file() - Method in class com.pacbio.secondary.vis.svc.server.data.WsTrackInfo
getM_file() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo: Auto generated getter method
getM_header() - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo
getM_header() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo: Auto generated getter method
getM_id() - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo
getM_id() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_id() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo: Auto generated getter method
getM_id() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_ideogram_file() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_ideogram_file() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_image_file() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_image_file() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_info() - Method in class com.pacbio.secondary.vis.svc.server.data.WsFastaSequenceInfo
getM_info() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo
getM_ipd_ratio() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo
getM_job_title() - Method in class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo
getM_job_title() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo: Auto generated getter method
getM_max_contig_length() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_max_contig_length() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_name() - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo
getM_name() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_name() - Method in class com.pacbio.secondary.vis.svc.server.data.WsTrackInfo
getM_name() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo: Auto generated getter method
getM_name() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_name() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo: Auto generated getter method
getM_num_contigs() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_num_contigs() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_path() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_path() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_reference_info() - Method in class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo
getM_reference_info() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo: Auto generated getter method
getM_sequence() - Method in class com.pacbio.secondary.vis.svc.server.data.WsFastaSequenceInfo
getM_sequence_file() - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo
getM_sequence_file() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_sequence_file() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo: Auto generated getter method
getM_sequence_file() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_sequence_index_file() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_sequence_index_file() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getM_tracks_info_array() - Method in class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo
getM_tracks_info_array() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo: Auto generated getter method
getM_web_search() - Method in class com.pacbio.secondary.vis.svc.server.data.WsTrackInfo
getM_web_search() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo: Auto generated getter method
getM_web_url() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo
getM_web_url() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: Auto generated getter method
getMainFrame() - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper
getMainWindow() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getMapQV(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns Map QV for specific row
getMapQVPalette() - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getMarker(int) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection
getMarkerCollection() - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage
getMarkerCollection(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getMarkerCollectionFromRowIndex(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
getMarkerCollectionFromRowIndex(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase: Override to return marker collection at this row
getMarkerCollectionFromRowIndex(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval
getMarkerFromRowIndex(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
getMarkerFromRowIndex(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase: Override to return marker at this row
getMarkerFromRowIndex(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval
getMarkerInfo(MarkerCollection, Marker, GenomicViewEvents) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
getMarkers() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection
getMarkers() - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage
getMarkers() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getMarkersBounds() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getMarkersForContig(int) - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel
getMarkerTypeFromRowIndex(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase
getMax() - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getMax_coverage() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue
getMax_details_coverage() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getMax_details_view_coverage() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getMax_details_view_ordinate() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getMax_dynamic_range() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getMax_fixed_range() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getMax_norm_ipd_fwd(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue
getMax_norm_ipd_rev(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue
getMax_value() - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedDoubleInputVerifier
getMax_value() - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedFieldInputVerifier
getMax_variants() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue
getMaxCoverage(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getMaxCoverageFromMode(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getMaxCoverageInInterval(VariableResolutionDataSet) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
getMaxCoverageInInterval(List<Marker>) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
getMaxDetailsViewRange() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions: Returns max genomic range of details view based on user options and max data coverage
getMaxGenomicRange() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getMaxGenomicRange() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
getMaxGenomicRange() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
getMaximizedDockable() - Method in class pub.vlsolutions.swing.docking.DockingDesktop: returns the currently maximized dockable (or null if no dockable is in that state)
getMaximizeOrRestoreButton() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: returns the button used for maximizing or restoring the view.
getMaximumSize() - Method in class pub.vlsolutions.swing.docking.AutoHideButton
getMaxIPDInInterval(Interval) - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage
getMaxIPDToPlot() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
getMaxLane(int) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
getMaxMagnification() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getMaxMagnification() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
getMaxNormIPDFwd(int, int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getMaxNormIPDRev(int, int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getMaxRange() - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog
getMaxReadLength() - Method in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfoCalculator
getMaxVariants(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getMean_coverage() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getMean_ipd() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getMean_score() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getMedianQV() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getMemoryInfo(StringBuffer) - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils
getMetadataInfo() - Method in class com.pacbio.secondary.vis.svc.server.data.parser.MetadataInfoParser
getMetadataInfo(String, int) - Method in class com.pacbio.secondary.vis.svc.server.VisService: Returns reference info from selected metadata.rdf file
getMetadataInfo(VisServiceStub.GetMetadataInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getMetric(int) - Method in class com.pacbio.secondary.vis.data.contig.DeNovoContigInfo
getMetrics() - Method in class com.pacbio.secondary.vis.data.contig.DeNovoContigInfo
getMetricsFactor(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getMetricsInfo(int) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getMetricsLabel(int, boolean) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getMin() - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getMin_value() - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedDoubleInputVerifier
getMin_value() - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedFieldInputVerifier
getMinCoverage() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getMinGenomicRange() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getMinimumSize() - Method in class pub.vlsolutions.swing.docking.AutoHideButton
getMinMagnification() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getMinMagnification() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
getMinMagnification() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
getMinMaxValues() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
getMinMaxValues() - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer
getMinMaxValues() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger
getMinMaxValues() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
getMinMaxValues() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel
getMode() - Method in class com.pacbio.secondary.vis.gui.control.PaletteCtrl
getMode() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions: Auto generated getter method
getMode() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults: Auto generated getter method
getMode() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getModeFromOptions(VioletApp, boolean) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils: Creates mode value for results web services from runtime options
getModels() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet
getModsFilterThreshold() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getMoleculeID(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns molecule id
getMolID() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getMolid() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getMotif() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getMotif_group() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getMotif_partner() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getMotifCenterPosition(String) - Method in class com.pacbio.secondary.vis.data.db.MotifsDB: returns center position for one given motif string
getMotifs() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getMotifsDB() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getMotifsDB() - Method in class com.pacbio.secondary.vis.io.motifs.MotifsReader
getMotifsReport() - Method in class com.pacbio.secondary.vis.data.db.MotifsDB: creates html motif report
getMouseEvent() - Method in class pub.vlsolutions.swing.docking.event.DockEvent: Returns the MouseEvent which is the cause of this DockEvent.
getMouseLocation() - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: Returns the mouse location on screen or null if ran in an untrusted environement/ java 1.4
getMovieFrameRateDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the movie framerate
getMovieFrameRateFromMovieID(int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: public as it is used in cmp.h5 wrapper
getMovieID(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns movie id
getMovieNameFromMovieID(int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: public as it is used in cmp.h5 wrapper
getMovieNameIDsDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the movie name ids
getMovieNamesDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the movie names
getMultiChromosomesPanelConstraints() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
getMultiChromosomesPanelConstraints() - Method in class com.pacbio.secondary.vis.gui.panels.WholeGenomePanel
getN_detected() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getN_genome() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getName() - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand
getName() - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo
getName(boolean) - Method in class com.pacbio.secondary.vis.data.db.GeneDB
getName() - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFile
getName() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection
getName() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getName(boolean) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet: returns filenames
getName() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getName() - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo
getName() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getName() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo: Auto generated getter method
getName() - Method in class pub.vlsolutions.swing.docking.DockGroup: returns the name of this group (which is used as an internal key)
getName() - Method in class pub.vlsolutions.swing.docking.DockKey: Returns the name (or title) displayed in title bars
getNameAsString() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection
getNamedRootObject(String) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Searches for a named H5Group or H5ScalarDS object located on the root of the hdf5 hierarchy
getNewPushpinInfo(VioletApp) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage
getNewState() - Method in class pub.vlsolutions.swing.docking.event.DockableStateChangeEvent: returns the new state of the dockable
getNextLocation() - Method in class pub.vlsolutions.swing.docking.event.DockingActionEvent: Returns one of the DockableState states reflecting the state of the dockable after the action
getNodeAttribute(Document, String, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
getNodeAttributeData(Document, String, String, String, String, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
getNodeAttributeValue(Document, String, String, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
getNodeData(Document, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
getNodePairedData(Document, String, String, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
getNodes() - Method in class com.pacbio.secondary.vis.data.graph.GraphPrimitive: returns all nodes of this graph primitive
getNotInstalledToolbars() - Method in class pub.vlsolutions.swing.toolbars.ToolBarIOReadInfo: returns the list of toolbars that weren't loaded from the stream (but registered)
getNumBasesFromMarkerRead() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead: Helper function for marker read with stats
getNumberFormat(long) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.AxisUtils
getNumChromosomes() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getNumChunks() - Method in class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer
getNumColumns() - Method in class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray
getNumColumns() - Method in class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer
getNumContigs() - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel
getNumContigs() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getNumContigs() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getNumCurrentlyVisibleTracks() - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
getNumDel(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns num deletions for specific row
getNumDimensions() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo: returns the number of dimensions of this hyperslab
getNumIns(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns num insertions for specific row
getNumIPDValues() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue
getNumItems() - Method in class com.pacbio.secondary.vis.data.db.GeneDB
getNumItems() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel
getNumLeft() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getNumLoaded() - Method in class com.pacbio.secondary.vis.data.session.tracks.TracksDataInfoList
getNumMarkerCollections() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getNumMM(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns num mismatches for specific row
getNumReadGroups() - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo
getNumRemote() - Method in class com.pacbio.secondary.vis.data.session.tracks.TracksDataInfoList
getNumRight() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getNumRows() - Method in class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray
getNumRows(H5ScalarDS) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Returns total rows in dataset
getNumRows() - Method in class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer
getNumTracks() - Method in class com.pacbio.secondary.vis.data.session.DataStorage
getNumTracks() - Method in class com.pacbio.secondary.vis.data.session.tracks.TracksDataInfoList
getNumTracksFractional() - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
getObj_score() - Method in class com.pacbio.secondary.vis.data.db.MotifData
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo
getOMElement(QName, org.apache.axiom.om.OMFactory) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo
getOptions() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getOpts() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo: Auto generated getter method
getOrder() - Method in class pub.vlsolutions.swing.docking.event.DockingActionCreateTabEvent: Returns the order of insertion in the tabbed container
getOrientation() - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripper: Returns the orientation of this gripper (SwingConstants.HORIZONTAL/VERTICAL)
getOrientation() - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanel: Returns the orientation of this toolbarpanel
getPageFormat() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getPalette() - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
getPaletteForContig(int) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
getPanelHelpTopic(String) - Static method in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils: This method returns a topic for each panel
getPanelTitle(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw: returns title to use for specific panel
getParent() - Method in class pub.vlsolutions.swing.docking.DockGroup: returns the parent of this group (may be null)
getParentContainer() - Method in class pub.vlsolutions.swing.docking.event.DockingActionAddDockableEvent: Returns the parent container into which this dockable will be added
getParentDividorLocation() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitComponentEvent: returns a dividor location value for the parent split container, or -1 if not needed
getPastelReferenceColor(char) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getPath() - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFile
getPath() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getPathToReferenceIndexFile() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getPathToReferenceMetadataFromID(String) - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils: Resolves path of reference metafile using: - absolute reference id - relative path to reference.info.xml to support portability of reference files - runtime environment variable and config.xml pointing to root of seymour reference repository instance
getPattern() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation: Auto generated getter method
getPileupBounds() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getPolicy() - Static method in class pub.vlsolutions.swing.docking.AutoHidePolicy: Returns the singleton instance of this class
getPosition() - Method in class com.pacbio.secondary.vis.data.locus.Locus
getPosition() - Method in class pub.vlsolutions.swing.docking.DockableState: Returns the relative restore position of the dockable when it is not shown (auto-hide or closed).
getPreferencesHelpTopic(int) - Static method in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils: This method returns a topic for the preferences dialog.
getPreferredSize() - Method in class com.pacbio.secondary.vis.gui.control.JHyperlinksHtmlTooltip
getPreferredSize() - Method in class pub.vlsolutions.swing.docking.AutoHideButton
getPreferredSize() - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Evaluates and returns the preferred size of the desktop, according to its contents and auto-hide borders.
getPressedIcon() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton: Returns the pressed icon
getPreviousDockableState(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Returns the previous state of a hidden or floating dockable (when that dockable was in the DOCKED state.
getPreviousState() - Method in class pub.vlsolutions.swing.docking.event.DockableStateChangeEvent: returns the previous state of the dockable, or null if the component wasn't known to the docking desktop before.
getPrimaryInfo() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo
getPrimitive(int) - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure
getPrimitives() - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure
getPrinterJob() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getPrologInfo() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo
getProperties(String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getProperty(String) - Method in class pub.vlsolutions.swing.docking.DockKey: returns a property associated to this name, or null if the property is undefined
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo: databinding method to get an XML representation of this object
getPullParser(QName) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo: databinding method to get an XML representation of this object
getPushpin(int) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage
getQueryCriteria() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase
getQueryResult() - Method in class com.pacbio.secondary.vis.data.interval.IntervalTreeQuery.FilterVisitor
getQueue() - Method in class com.pacbio.secondary.vis.common.collection.SweepLineIterator
getQV() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getQv() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getQv(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getRange() - Method in class com.pacbio.secondary.vis.data.interval.IntervalTree
getRangeSelection() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getRank() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo: Returns the rank (number of dimensions) of the dataset.
getRawReadEnd(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns index of raw read end in alignindex
getRawReadStart(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns index of raw read start in alignindex
getRDF_Info_FromNodeAttribute(Document, String, String, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
getRDF_Path_FromDataID(Document, String, String, String, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
getRDF_Path_FromResourceIDMarker(Document, String, String, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
getRDF_Title(Document) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
getReaderForGFFFileRegion(String, int, long, long, long, int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer: gets a reader for a specified region of a gff file used for details/sab view allocates block of contiguous memory....
getReaderFromFastaFile(String, int, String, long, long) - Method in class com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer
getReadFontStyle() - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: get font style for read info in table
getReadGroupAlignmentIndexPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: public as it is used in cmp.h5 wrapper
getReadGroupAlignmentIndexPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo: returns path to alignmentindex for read group
getReadGroupDataChunk(H5ScalarDS, HDF5HyperslabInfo) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Reads a chunk of data from a readgroup dataset.
getReadGroupID(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns read group id
getReadGroupIDDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the read group id
getReadGroupIndexFromReadGroupValue(int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: public as it is used in cmp.h5 wrapper
getReadGroupMetricsPath(int, int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Returns path to selected metrics array
getReadGroupNormalizedIPDPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Returns path to normalized IPD metrics
getReadGroupNormalizedIPDPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo: returns path to ipd for read group
getReadGroupPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo
getReadGroupPathIds() - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo
getReadGroupPaths() - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo
getReadGroupPKMIDPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo: returns path to pulse width for read group
getReadGroupPulseWidthPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Returns path to Pulse Width metrics
getReadGroupPulseWidthPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo: returns path to pulse width for read group
getReadGroupQualityValuePath(int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Returns path to QV metrics
getReadGroupQualityValuePath(int) - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo: returns path to quality value for read group
getReadGroupRawIPDPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: Returns path to raw IPD metrics
getReadGroupRawIPDPath(int) - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo: returns path to ipd for read group
getReadInfoFromWsRead(List<Marker>, WsRead) - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage
getReadLenghtColor(int) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getReadLengthPalette() - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getReads() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResults
getReads() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo: returns total number of reads
getReadsDataFromFile(String, String, int, long, long, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder: getAlignedReadsFromFile
getReadsDataPath() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getReadsDataWithInsertionsFromFile(String, String, int, long, long, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder
getRecords() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel
getRectangle() - Method in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo
getRectangle(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
getRefEnd(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns mapped reference end
getRefEnd(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.SortedRefIndexTable
getReference() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getReference_data() - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage
getReference_locus() - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage
getReferenceBounds() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getReferenceDataLocus() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
getReferenceInfo() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getReferenceInfo() - Method in class com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo
getReferenceInfo() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getReferenceInfo() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getReferenceInfo() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getReferenceInfo() - Method in class com.pacbio.secondary.vis.svc.server.data.parser.DeNovoSummaryParser
getReferenceInfo() - Method in class com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser
getReferenceInfo(String) - Method in class com.pacbio.secondary.vis.svc.server.VisService: Returns reference info from selected reference.info.xml file
getReferenceInfo(VisServiceStub.GetReferenceInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getReferenceMetadataFromID(Document, String) - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getReferenceSequenceFromServer(GenomicViewDetailsData, int, long, long) - Method in class com.pacbio.secondary.vis.data.session.DataStorage
getReferenceSequenceStorage() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData
getReferencesRootDirectory() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getRefGroupIDDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the ref group id dataset
getRefGroupPathDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the ref group path dataset
getRefGroupRefInfoIDDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the ref group refinfo id dataset
getRefId() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getRefId(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.SortedRefIndexTable
getRefID(Document) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser
getRefInfoFullNamesDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the refinfo fullname
getRefSeqID(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns mapped reference id
getRefSeqID() - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo
getRefSeqName() - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo
getRefStart(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns mapped reference start
getRefStart(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.SortedRefIndexTable
getRefStrand(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns mapped reference strand
getRegionPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getRegionsOfInterestStorage() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getRegionView() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getRegisteredToolBars() - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer: Returns the list of currently registered toolbars.
getRelativeAncestorContainer() - Method in class pub.vlsolutions.swing.docking.RelativeDockablePosition: Returns the ancestor container used as a reference for the relative potionning
getRemoteDataOnFirstTime() - Method in class com.pacbio.secondary.vis.data.session.DataStorage
getRemoteFileNames() - Method in class com.pacbio.secondary.vis.gui.dialogs.OpenRemoteDataHelper: Returns all paths as string array to match cmd line argument format
getResizeWeight() - Method in class pub.vlsolutions.swing.docking.DockKey
getResolution() - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand: The resolution of the Band specification.
getResult(int, int) - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer
getResult(int, int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel
getResult(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesDataRecord
getResults(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
getResults(int) - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer
getResults(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel
getResultsForDetailsView(int, long, long, boolean) - Method in class com.pacbio.secondary.vis.data.session.DataStorage
getRevKineticsPalette() - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getRightDragger() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel: Returns the component used to modify the expand panel size when expanded from the right
getRolloverIcon() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton: Returns the rollover icon
getRolloverTriggerDelay() - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy: Returns the rollover trigger delay (in millis)
getRoot() - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel
getRootDirectory(String) - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getRootPane(FloatingDockableContainer) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: returns the root pane used by this detached dockable container, regardless of its type (frame or dialog)
getRowCount() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
getRowCount() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelDeNovo
getRowCount() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval
getRowCount() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelTrack
getRowIndex() - Method in class com.pacbio.secondary.vis.svc.server.data.WsReadEx
getRowInterval(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations: Returns the interval associated with this row
getRowInterval(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase: Override to return the interval associated with this row
getRowInterval(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval: Return the interval associated with this row
getRowInterval(int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelTrack: Return the interval associated with this row
getSample() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getSaveUserWorkspaceFilename(Component, String) - Static method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager
getScaledHeight() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getScaledHeight() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion
getScaledHeight() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewSingleContig
getScaledValue() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase.JDoubleSlider
getScaledWidth() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
getScaledWidth() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getScaledWidth() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion
getScaledWidth() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewSingleContig
getScaling() - Method in class com.pacbio.secondary.vis.gui.control.PaletteCtrl
getScor() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getScore() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getSelectedDims() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo: Returns the dimension sizes of the selected subset.
getSelectedDockable() - Method in class pub.vlsolutions.swing.docking.DockingDesktop: Returns the currently selected dockable, or null if none is selected.
getSelectedDockable() - Method in class pub.vlsolutions.swing.docking.DockTabbedPane: Returns the currently selected (front) dockable
getSelectedDockable() - Method in class pub.vlsolutions.swing.docking.event.DockableSelectionEvent: Returns the currently selected Dockable
getSelectedDockable() - Method in interface pub.vlsolutions.swing.docking.TabbedDockableContainer: Returns the currently selected (front) dockable
getSelectedFilePath() - Method in class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog
getSelectedGene() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getSelectedGraphStructureMode() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase: returns current graph mode
getSelectedKineticMode() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase: returns current kinetics mode
getSelectedMarker() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getSelectedRangeColor() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getSelectedSingleContigView() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getSelectedSlotIndex() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getSelectedTrack() - Method in class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog
getSelectionInfo() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getSelectionInfoChromosomes(GenomicViewEvents, StringBuffer) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
getSelectionInfoGenes(StringBuffer, Marker, Marker, GenomicViewData) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
getSelectionInfoMarkers(GenomicViewEvents, StringBuffer) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
getSelectionInfoReads(GenomicViewEvents, StringBuffer) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
getSelectionInfoTracks(GenomicViewEvents, StringBuffer) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
getSelectionPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getSeq() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getSequence() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getSequence_high() - Method in class com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer
getSequence_low() - Method in class com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer
getSequenceFile() - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo
getSequenceFile() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getSequenceIndexFile() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
getSequenceInfo() - Method in class com.pacbio.secondary.vis.io.fasta.FastaFileReader
getServiceExperienceIndex() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub: Auto generated method signature
getServiceExperienceIndex() - Method in class com.pacbio.secondary.vis.svc.server.HDFService
getServiceInfo() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub: Auto generated method signature
getServiceInfo() - Method in class com.pacbio.secondary.vis.svc.server.HDFService: returns info about server and this service
getServiceInfo() - Method in class com.pacbio.secondary.vis.svc.server.JNLPService: returns info about server and this service
getServiceInfo() - Method in class com.pacbio.secondary.vis.svc.server.VisService: returns runtime info about server and this service
getServiceInfo() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getServicesInfo(VioletApp) - Method in class com.pacbio.secondary.vis.gui.dialogs.AboutDialog
getSession() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getSession() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest
getSessionProperties(VioletApp) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: creates html info of all loaded data
getSetNumber(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns set number
getSeymourHome() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils: Returns value of SEYMOUR_HOME env variable
getShowBaseModsInfo() - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getShowGraphStructureOnly() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getShowLabels() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getShowLabels() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getShowMarkerLabels() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getShowMarkerLabels() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getShowMarkers() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getShowMarkers() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getShowTooltips() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getSingleContigsViews() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getSingleRawRead(AlignmentIndexTable, int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileData: Deprecated.
getSingleRawReadUsingCache(H5ScalarDS, H5ScalarDS, AlignmentIndexTable, int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileData
getSize() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkDoneQueue
getSize() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkToDoQueue
getSlotColor(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getSlotIndex() - Method in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo
getSlotMaxCoverage(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getSlotMaxVariants(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getSlots() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getSlots() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
getSlots() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getSlotsDatasets() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getSlotsDatasets() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
getSmartButton(int) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon
getSmrtAnalysisHome() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils: Get equivalent of SEYMOUR_HOME by looking up into directory of .aar file...
getSMRTAnalysisVersion() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getSMRTCloudDataFileInfo(VioletApp) - Static method in class com.pacbio.secondary.vis.smrtcloud.CloudUtils: returns negative value if file is found positive value with size in byte of directory if not found
getSMRTCloudFileSize() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions: returns expected data file size
getSMRTJNLPOptions(String) - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper
getSMRTPortalHomeURL() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getSMRTViewHomeURL() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getSMRTViewLocalHome(String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper: return path of smrtview local data directory
getSortButton() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: MM added
getSortedRefIndexDataset() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase: returns the sorted ref index dataset
getSource() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo
getSource() - Method in class pub.vlsolutions.swing.docking.animation.AnimationEvent: returns the source of animation
getSplitPane(Dockable, int) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: Returns the split pane containing this dockable (if any), or null if this dockable isn't contained in a splitpane.
getSplitPosition() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitComponentEvent
getSplitPosition() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableContainerEvent
getSplitPosition() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableEvent
getStar() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc
getStart() - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo
getStart() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions: Auto generated getter method
getStart() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults: Auto generated getter method
getStart() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence: Auto generated getter method
getStart() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus: Auto generated getter method
getStart() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getStart() - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure
getStart() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence: Auto generated getter method
getStartBounds() - Method in class pub.vlsolutions.swing.docking.animation.ComponentAnimator: Returns the start bounds of the component.
getStartDims() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo: Returns the starting position of a selected subset.
getState() - Method in class pub.vlsolutions.swing.docking.animation.AnimationEvent: returns the state of the animation (ANIMATION_START, ANIMATION_FRAME or ANIMATION_END)
getStatus() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo
getStatus() - Method in class com.pacbio.secondary.vis.data.session.tracks.TracksDataInfoList
getStatus() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getStatusBar() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
getStop() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions: Auto generated getter method
getStop() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults: Auto generated getter method
getStop() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence: Auto generated getter method
getStop() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus: Auto generated getter method
getStride() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo: Returns the selectedStride of the selected dataset.
getString(String, String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getStrn() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc
getStrobe() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getStrobeNumber(int) - Method in class com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable: Returns strobe number
getStrongReferenceColor(char) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getStructID() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo
getStructid() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead
getSub_reads() - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure
getSubreadEnd() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo
getSubreadLength() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo
getSubreadLength() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo
getSubreadStart() - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo
getSummaryKineticsColor(int, int, int) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getSummaryKineticsPalette() - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette
getSummaryStorage() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelDeNovo
getSyncIPDConsensusFromServer(GenomicViewDetailsData, int, long, long) - Method in class com.pacbio.secondary.vis.data.session.DataStorage
getSystemInfo(String) - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getTabCount() - Method in interface pub.vlsolutions.swing.docking.TabbedDockableContainer: Returs the current tab count (which is also the current dockable count)
getTable() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase
getTable() - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel: returns table
getTable() - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel: returns table
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable.TreeTableCellRenderer: TreeCellRenderer method.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.pacbio.secondary.vis.gui.table.renderer.ColorRenderer
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.pacbio.secondary.vis.gui.table.renderer.FeatureRenderer
getTableFontStyle() - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: get font style for tables
getTableMenu() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
getTableModel() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase
getTableWidth() - Method in class com.pacbio.secondary.vis.gui.dialogs.QVThresholdOptionsPane
getTabName() - Method in class pub.vlsolutions.swing.docking.DockKey: Returns the tab name (or tab title) displayed when the component is contained into a tabbed container.
getTabName() - Method in class pub.vlsolutions.swing.docking.SplitContainer: Returns a suitable name for when this container is the main child of a Tab (TabbedDockableContainer)
getTemplate() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getTextFontSize() - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder: get font size for body in table
getTime() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getTimeFromMarkerRead() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead: Helper function for marker read with stats
getTimestamp() - Method in class com.pacbio.secondary.vis.data.queue.DetailsDataRequest
getTimestamp() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest
getTimestamp() - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo
getTimestamp() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo: Auto generated getter method
getTimestampFormat() - Method in class com.pacbio.secondary.vis.common.utils.SMRTHTMLLayout: Getter for timestamp format being used.
getTimeToAssemble() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo
getTitleBar() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel
getTitleBar() - Method in class pub.vlsolutions.swing.docking.DockView: Returns (or creates) the title bar of this dockview
getTitleExt(boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog
getTitleLabel() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar: Returns the label used to display the dockkey name.
getToolBar() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
getToolBarByName(String) - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer: Returns the registered toolbar associated with the given name, or null if not found
getToolbarItems() - Method in class com.pacbio.secondary.vis.gui.control.VioletToolBar
getToolBarPanelAt(Object) - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer: Returns the ToolBarPanel for a given BorderLayout constraints
getTooltip() - Method in class pub.vlsolutions.swing.docking.DockKey: Returns the tooltip associated to the title bar
getToolTipText(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.EpiProColorOptionsPane.EpiProOptionsTable
getToolTipText(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog.BookmarksEditorPane
getToolTipText(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getToolTipText(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
getToolTipText(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.table.GenomicTableBase
getTooltipText() - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon: Return the tooltip of this icon
getTooltipText() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton
getTopDragger() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel: Returns the component used to modify the expand panel size when expanded from the bottom
getTopMostAncestorContainerState(Dockable) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities: searches up the dockable container hierarchy and returns the dockable state of the last (top most) ancestor which is a CompoundDockable (or null if not found).
getTotalBases() - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage: returns total bases loaded
getTotalHeight() - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
getTotalSlicesInContig(int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo: Get number of slices for specific contig
getTrackData(Document, String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.TrackInfoParser
getTrackFromServer(TrackDataInfo, int) - Method in class com.pacbio.secondary.vis.data.session.DataStorage
getTrackHeight() - Method in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo
getTrackHeight(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
getTrackIndex() - Method in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo
getTrackInfo(int) - Method in class com.pacbio.secondary.vis.data.session.tracks.TracksDataInfoList
getTrackInfo() - Method in class com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo
getTrackInfoList() - Method in class com.pacbio.secondary.vis.data.session.tracks.TracksDataInfoList
getTrackName(boolean) - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo
getTrackNameFromFileName(String) - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils
getTracks() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getTracks() - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
getTracksHeight() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
getTracksInfoList() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase
getTracksList() - Method in class com.pacbio.secondary.vis.svc.server.data.parser.TrackInfoParser
getTracksListInfo(String) - Method in class com.pacbio.secondary.vis.svc.server.VisService: Returns tracks list info from selected template.info.xml or tracks.list.xml file(s)
getTracksListInfo(VisServiceStub.GetTracksListInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub: Auto generated method signature
getTree() - Method in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable: Returns the tree that is being shared between the model.
getType() - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure
getTypeObject(String, String, XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.ExtensionMapper
getTypeObject(String, String, XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.ExtensionMapper
getUCharDataChunk(H5ScalarDS, HDF5HyperslabInfo) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Reads a chunk of UChar data from a dataset.
getUIClassID() - Method in class pub.vlsolutions.swing.docking.AutoHideButton
getUIClassID() - Method in class pub.vlsolutions.swing.docking.AutoHideButtonPanel
getUIClassID() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel
getUIClassID() - Method in class pub.vlsolutions.swing.docking.DetachedDockView
getUIClassID() - Method in class pub.vlsolutions.swing.docking.DockView
getUIClassID() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab
getUIClassID() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar
getUIClassID() - Method in class pub.vlsolutions.swing.docking.SplitContainer: Overriden for custom UI delegation
getUIClassID() - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripper
getUIKineticIndex(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils
getUIntDataChunk(H5ScalarDS, HDF5HyperslabInfo) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File: Reads a chunk of UInt data from a dataset.
getUnknownToolbarNames() - Method in class pub.vlsolutions.swing.toolbars.ToolBarIOReadInfo: Return the list of toolbars names (String) found in the stream but not registered (these toolbars cannot be loaded, so the API can only report their name).
getUnmappedReadColor(long) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette
getUnmappedReadsContigPalette(int) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette
getUnmappedReadsCutoffThreshold() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getUrl() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions: Auto generated getter method
getUrl() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults: Auto generated getter method
getUrl() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence: Auto generated getter method
getUrl() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames: Auto generated getter method
getUrl() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader: Auto generated getter method
getUrl() - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus: Auto generated getter method
getUrl() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence: Auto generated getter method
getUrl() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo: Auto generated getter method
getUrl() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo: Auto generated getter method
getUrl() - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo: Auto generated getter method
getUseEpiProReadsMode() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getUseEpiProReadsOnly() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getUseEventsCoverageFilter() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getUseExternalBrowser() - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel
getUseLogScaling() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getUseMapQVFilter() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getUseModsFilter() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getUseQVFilter() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getUser() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getUserData() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest
getUserHome() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils: Returns value of USER_HOME env variable
getUseUnmappedReadsCutoffFilter() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getUseVariantsConfidenceFilter() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getUseVisualFilter() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getValue(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues
getValueAt(Object, int) - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel
getValueAt(Object, int) - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel
getValueAt(int, int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
getValueAt(int, int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelDeNovo: Only the first three columns are fixed, the remaining ones are loaded at runtime from the summary.gff file
getValueAt(int, int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval
getValueAt(int, int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelTrack
getValueAt(Object, int) - Method in interface com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel: Returns the value to be displayed for node node, at column number column.
getVariantLabel(Marker) - Static method in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader: returns a variant string from type
getVariantsConfFilterThreshold() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
getVersion() - Method in class com.pacbio.secondary.vis.svc.server.VersionService
getView() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase: Override to return the view currently associated with this table
getView() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval
getView() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelTrack
getView() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
getViewContig() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getViewContigName() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getViewSubreads() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getVioletApp() - Method in class com.pacbio.secondary.vis.data.session.timer.SessionDataTimer
getVioletApp() - Method in class com.pacbio.secondary.vis.data.session.timer.SessionDataTimerTask
getVioletApp() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelBase: return the app
getVioletApp() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
getVioletApp() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getVioletApp() - Method in class com.pacbio.secondary.vis.smrtcloud.CloudTimer
getVioletContentRootDirectory() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getVioletFrame() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getVioletUserDataRootDirectory() - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
getVisibleButtonCount() - Method in class pub.vlsolutions.swing.docking.AutoHideButtonPanel: Returns the number of buttons currently displayed by this panel.
getVisibleGenomicRange() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw
getVisPort() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getVisServiceURL() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase
getVisualFilter() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
getWebBrowserPanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase
getWebsearchURL() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo
getWidth() - Method in class pub.vlsolutions.swing.docking.RelativeDockablePosition: Returns the relative width of the dockable
getWork() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkDoneQueue
getWork() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkToDoQueue
getWorkspace() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions
getWorkspace() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest
getWorkspace() - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceButton: Returns the workspace used by this button
getWorkspace() - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem: Returns the workspace used by this menu item
getWSResultsFromDataHandler(DataHandler) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl
getX() - Method in class pub.vlsolutions.swing.docking.RelativeDockablePosition: Returns the relative x position of the dockable
getY() - Method in class pub.vlsolutions.swing.docking.RelativeDockablePosition: Returns the relative y position of the dockable
getZone() - Method in class pub.vlsolutions.swing.docking.AutoHideButton: Returns the border zone of this button
getZoom() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
getZoom(long) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
GFF3Reader - Class in com.pacbio.secondary.vis.io.gff
GFF3Reader() - Constructor for class com.pacbio.secondary.vis.io.gff.GFF3Reader
GFF_MODS_SUMMARY_VERSION_133 - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_MODS_SUMMARY_VERSION_140 - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_MODS_SUMMARY_VERSION_200 - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_MODS_SUMMARY_VERSION_210 - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
gff_slice_size - Variable in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo
GFF_SUMMARY_CONTIG_RECORD_TYPE - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_DENOVO_CONTIG_METRICS - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_REGION_RECORD_TYPE - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_COVERAGE - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_CQV - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_DEL - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_DENOVO_METRICS - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_FWD_IPD - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_GAPS - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_ID - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_INS - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_REV_IPD - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_TAG_SVN - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFF_SUMMARY_VERSION_131 - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFFDataModel - Class in com.pacbio.secondary.vis.data.variableresolution.model.gff
GFFDataModel() - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
gfffile_region_size - Variable in class com.pacbio.secondary.vis.io.indexer.indexinfo.FileIndexInfo
gfffile_region_start - Variable in class com.pacbio.secondary.vis.io.indexer.indexinfo.FileIndexInfo
GFFIndexer - Class in com.pacbio.secondary.vis.io.indexer.gff: Helper class to split/index GFF files
GFFIndexer() - Constructor for class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer
GFFIndexInfo - Class in com.pacbio.secondary.vis.io.indexer.indexinfo
GFFIndexInfo(int, long, double, int, long) - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.GFFIndexInfo
GFFIndexInfo() - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.GFFIndexInfo: de-serialization only
GFFIndexInfo(long, long) - Constructor for class com.pacbio.secondary.vis.io.indexer.indexinfo.GFFIndexInfo
GFFMetadataInfo - Class in com.pacbio.secondary.vis.io.indexer.gff.metadata
GFFMetadataInfo() - Constructor for class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo: default constructor required for de-serialization
GFFMetadataInfo(long) - Constructor for class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo
GFFMetadataInfoCalculator - Class in com.pacbio.secondary.vis.io.indexer.gff.metadata
GFFMetadataInfoCalculator() - Constructor for class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfoCalculator
GFFModificationsReader - Class in com.pacbio.secondary.vis.io.gff.modifications
GFFModificationsReader(boolean) - Constructor for class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
GFFSummaryConstants - Class in com.pacbio.secondary.vis.io.gff.summary
GFFSummaryConstants() - Constructor for class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
GFFSummaryReader - Class in com.pacbio.secondary.vis.io.gff.summary
GFFSummaryReader() - Constructor for class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader
GFFV3Marker - Static variable in class com.pacbio.secondary.vis.io.importer.DataFileInfo
GFFVariantsReader - Class in com.pacbio.secondary.vis.io.gff.variants
GFFVariantsReader() - Constructor for class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader
global_rows_cache - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
goBack() - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserEditorPane
goForward() - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserEditorPane
goto_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel
goto_dlg - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions
GoToDialog - Class in com.pacbio.secondary.vis.gui.dialogs
GoToDialog(VioletApp, String[], String) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.GoToDialog
GoToDialog.GoToDialogPanel - Class in com.pacbio.secondary.vis.gui.dialogs: Inner panels to set start/end
GoToDialog.GoToDialogPanel(String) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel
GRADIENT_PANEL_BACKGROUND - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
GRADIENT_PANEL_END - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
GRADIENT_PANEL_START - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants
graph - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResults
GRAPH_LINE_END_LANE_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINE_END_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINE_NUM_DATA_POINTS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINE_START_LANE_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINE_START_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINE_STATUS_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINK_END_LANE_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINK_END_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINK_NUM_DATA_POINTS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINK_START_LANE_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINK_START_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_LINK_STATUS_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_NODE_END_LANE_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_NODE_END_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_NODE_NUM_DATA_POINTS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_NODE_START_LANE_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_NODE_START_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_NODE_STATUS_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STATUS_CHIMERA_ERR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STATUS_DISCORDANT_ERR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STATUS_MULTI_ERR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STATUS_OK - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STATUS_ORDER_ERR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STATUS_OVERLAP_ERR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STATUS_STRAND_ERR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STRUCT_TYPE_MULTILINE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STRUCT_TYPE_MULTILINK - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STRUCT_TYPE_MULTINODE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GRAPH_STRUCT_TYPE_NONE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
graph_structure_type - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions
GRAPH_STRUCTURE_TYPE_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
GraphConstants - Class in com.pacbio.secondary.vis.common.utils.constants
GraphConstants() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.GraphConstants
GraphPrimitive - Class in com.pacbio.secondary.vis.data.graph: Basic abstraction of different graph primitives to use for drawing structure information
GraphPrimitive(int[][]) - Constructor for class com.pacbio.secondary.vis.data.graph.GraphPrimitive: Creates a multi-nodes graph primitive
GraphPrimitive() - Constructor for class com.pacbio.secondary.vis.data.graph.GraphPrimitive: de-serialization only
GraphStructure - Class in com.pacbio.secondary.vis.data.graph
GraphStructure(int, int) - Constructor for class com.pacbio.secondary.vis.data.graph.GraphStructure
GraphStructure() - Constructor for class com.pacbio.secondary.vis.data.graph.GraphStructure
GraphUtil - Class in com.pacbio.secondary.vis.gui.draw.utils: Helper class for specialized graphs drawing
GraphUtil() - Constructor for class com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
gripExpandHImage - Static variable in class pub.vlsolutions.swing.toolbars.ToolBarGripperUI
gripExpandVImage - Static variable in class pub.vlsolutions.swing.toolbars.ToolBarGripperUI
gripImage - Static variable in class pub.vlsolutions.swing.toolbars.ToolBarGripperUI: the "grip" (an alpha blended dot image, 3*3 pixels, hightlighted underneath )
GUIUtils - Class in com.pacbio.secondary.vis.common.utils
GUIUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.GUIUtils
GZIPPED_FILE_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

H

handleUnloadedToolBar(VLToolBar) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPersistence

has_motifs_file - Variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

hasAnyMetric() - Method in class com.pacbio.secondary.vis.io.hdf.data.RawRead

hasBaseMods - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

hasCoverage - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

hasData() - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel

hashCode() - Method in class pub.vlsolutions.swing.docking.DockGroup

overriden for storage/comparisons with the "name" property

hashCode() - Method in class pub.vlsolutions.swing.docking.DockKey

Overriden for Map storage needs

hashCode() - Method in class pub.vlsolutions.swing.docking.ws.WSDockKey

returns this object's hashcode

hasImageBits() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

hasModificationsFile() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

returns true if file list has base mods file use to default base mods specific user options

hasMotifsFile() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

returns true if file list has motifs file use to classify or not base mods

hasNext() - Method in class com.pacbio.secondary.vis.common.collection.MultiIterator

hasNext() - Method in class com.pacbio.secondary.vis.common.collection.SortedMultiIterator

hasNext() - Method in class com.pacbio.secondary.vis.common.collection.SweepLineIterator

hasNext() - Method in class com.pacbio.secondary.vis.common.collection.UndoIterator

hasVariants - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

hasViewHistoryItems() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

haveBaseModsSummary(GenomicViewEvents) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder

haveVariantsSummary(GenomicViewEvents) - Static method in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder

HDF5ChunkInfo - Class in com.pacbio.secondary.vis.io.hdf.hyperslabinfo

This class stores the chunk information of a dataset.

HDF5ChunkInfo(int, long[], long[]) - Constructor for class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo

HDF5ExceptionEx - Exception in com.pacbio.secondary.vis.io.hdf.exception

The class HDF5ExceptionEx returns errors raised by the PacBio hdf wrapper library.

HDF5ExceptionEx() - Constructor for exception com.pacbio.secondary.vis.io.hdf.exception.HDF5ExceptionEx

no arguments constructor

HDF5ExceptionEx(String) - Constructor for exception com.pacbio.secondary.vis.io.hdf.exception.HDF5ExceptionEx

HDF5ExceptionEx(Throwable) - Constructor for exception com.pacbio.secondary.vis.io.hdf.exception.HDF5ExceptionEx

HDF5ExceptionEx(String, Throwable) - Constructor for exception com.pacbio.secondary.vis.io.hdf.exception.HDF5ExceptionEx

HDF5File - Class in com.pacbio.secondary.vis.io.hdf.file.hdf5

Base class for accessing HDF5 files

HDF5File(File, int, int) - Constructor for class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

HDF5HyperslabInfo - Class in com.pacbio.secondary.vis.io.hdf.hyperslabinfo

Encapsulates HDF5 Hyperslab metadata

HDF5HyperslabInfo(long[], long[], long[], long[]) - Constructor for class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo

HDF_ALIGNED_READS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_ALIGNED_READS_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_ALIGNED_READS_MARTIN - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_ALIGNMENT_SUMMARY_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_ALIGNMENT_SUMMARY_GZIP_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_ASSEMBLED_READS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_ASSEMBLED_SUMMARY_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_ASSEMBLED_SUMMARY_GZIP_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_ATTRIBUTE_COL_NAME - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_ATTRIBUTE_LAST_ROW - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_ATTRIBUTE_READ_GROUP_FULL_SEQUENCE_NAME - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_ATTRIBUTE_READ_GROUP_SEQUENCE_LENGTH - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_ATTRIBUTE_READ_GROUP_SEQUENCE_MD5 - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_ATTRIBUTE_READTYPE - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_ATTRIBUTE_VERSION - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_ALIGNMENT_INDEX - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_ALN_GROUP - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_ALN_INDEX - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_ALN_INFO - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_MOVIE_FRAMERATE - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_MOVIE_ID - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_MOVIE_INFO - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_MOVIE_NAME - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_MOVIE_NAME_V1 - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_ALIGNMENT_ARRAY_V1_1 - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_ALIGNMENT_ARRAY_V1_2 - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_CONSENSUS_CALLS - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_CONSENSUS_CONFIDENCE - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_KINETICS_IPDRATIO - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_NORM_IPD - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_PATH - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_PATH_ID - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_PKMID - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_PULSE_WIDTH - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_QUALITY_VALUE - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_READ_GROUP_RAW_IPD - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_REF_GROUP - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_REF_ID - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_REF_INFO - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_REF_INFO_FULL_NAME - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_REF_INFO_ID - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_REF_PATH - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_REF_SEQ_ID - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_REF_SEQ_NAME - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_SORTED_INDEX_TABLE - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_DATASET_SORTED_REF_INDEX - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_EPIPRO_GZIP_READS_V1 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_EPIPRO_GZIP_READS_V2 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_EPIPRO_READS_MARKER_V1 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_EPIPRO_READS_MARKER_V2 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_EPIPRO_READS_V1 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_EPIPRO_READS_V2 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

hdf_file_format - Variable in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

hdf_file_root_group - Variable in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

hdf_file_root_node - Variable in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

HDF_GMAP_JOB_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_GROUP_CONSENSUS - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_GROUP_KINETICS - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_ISOSEQ_FLNC_READS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_ISOSEQ_READS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_LIBRARY_COPYRIGHT_INFO - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.LibraryConstants

HDF_LIBRARY_DESCRIPTION - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.LibraryConstants

HDF_LIBRARY_LAST_MODIFIED - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.LibraryConstants

HDF_LIBRARY_OPTIMAL_IO_BLOCK_TRANSFER_SIZE - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.LibraryConstants

HDF_LIBRARY_VERSION - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.LibraryConstants

HDF_MODIFICATIONS_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_MODIFICATIONS_GFF3_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_MODIFICATIONS_GZIP_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_MOTIFS_CSV - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_MOTIFS_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_MOTIFS_GFF3_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_MOTIFS_GZIP_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_PATH_SEPARATOR - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_READTYPE_CDNA - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_READTYPE_CSS - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_READTYPE_STANDARD - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_READTYPE_STROBE - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

HDF_SERVICE_PROGRAM_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_SERVICE_URL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_SUMMARY_GFF3_GZIP_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_SUMMARY_GFF3_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_SVC_FILE_NOT_FOUND_ERROR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_SVC_GENERIC_ERROR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_VARIANTS_GATK_VCF - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_VARIANTS_GATK_VCF_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_VARIANTS_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_VARIANTS_GFF3_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_VARIANTS_GZIP_GATK_VCF - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_VARIANTS_GZIP_GFF3 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_VARIANTS_GZIP_VCF - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_VARIANTS_VCF - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDF_VARIANTS_VCF_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

HDFService - Class in com.pacbio.secondary.vis.svc.server

HDFService() - Constructor for class com.pacbio.secondary.vis.svc.server.HDFService

default constructor

HDFServiceCallbackHandler - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceCallbackHandler Callback class, Users can extend this class and implement their own receiveResult and receiveError methods.

HDFServiceCallbackHandler(Object) - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

User can pass in any object that needs to be accessed once the NonBlocking Web service call is finished and appropriate method of this CallBack is called.

HDFServiceCallbackHandler() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

Please use this constructor if you don't want to set any clientData

HDFServiceCallbackImpl - Class in com.pacbio.secondary.vis.svc.hdf.client

Class to receive callbacks for asynchronous axis2 web service calls Overrides auto-generated stubs, implements desired specialization

HDFServiceCallbackImpl(VioletApp, Object) - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

HDFServiceExperienceIndex - Class in com.pacbio.secondary.vis.svc.server.hdf

Experience index calculator class.

HDFServiceExperienceIndex() - Constructor for class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex

HDFServiceExperienceIndex.ExperienceIndexMetrics - Class in com.pacbio.secondary.vis.svc.server.hdf

holds metrics used to calc experience index

HDFServiceExperienceIndex.ExperienceIndexMetrics(int) - Constructor for class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics

HDFServiceLocalTest - Class in com.pacbio.secondary.vis.svc.server.test

HDFServiceLocalTest() - Constructor for class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

HDFServiceStub - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub(org.apache.axis2.context.ConfigurationContext, String) - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Constructor that takes in a configContext

HDFServiceStub(org.apache.axis2.context.ConfigurationContext, String, boolean) - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Constructor that takes in a configContext and useseperate listner

HDFServiceStub(org.apache.axis2.context.ConfigurationContext) - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Default Constructor

HDFServiceStub() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Default Constructor

HDFServiceStub.ExtensionMapper - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.ExtensionMapper() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.ExtensionMapper

HDFServiceStub.GetAnnotatedInsertions - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetAnnotatedInsertions() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

HDFServiceStub.GetAnnotatedInsertions.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetAnnotatedInsertions.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions.Factory

HDFServiceStub.GetAnnotatedInsertionsResponse - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetAnnotatedInsertionsResponse() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse

HDFServiceStub.GetAnnotatedInsertionsResponse.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetAnnotatedInsertionsResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse.Factory

HDFServiceStub.GetAnnotatedResults - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetAnnotatedResults() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

HDFServiceStub.GetAnnotatedResults.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetAnnotatedResults.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults.Factory

HDFServiceStub.GetAnnotatedResultsResponse - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetAnnotatedResultsResponse() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse

HDFServiceStub.GetAnnotatedResultsResponse.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetAnnotatedResultsResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse.Factory

HDFServiceStub.GetConsensusSequence - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetConsensusSequence() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

HDFServiceStub.GetConsensusSequence.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetConsensusSequence.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence.Factory

HDFServiceStub.GetConsensusSequenceResponse - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetConsensusSequenceResponse() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse

HDFServiceStub.GetConsensusSequenceResponse.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetConsensusSequenceResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse.Factory

HDFServiceStub.GetContigNames - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetContigNames() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames

HDFServiceStub.GetContigNames.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetContigNames.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames.Factory

HDFServiceStub.GetContigNamesResponse - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetContigNamesResponse() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse

HDFServiceStub.GetContigNamesResponse.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetContigNamesResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse.Factory

HDFServiceStub.GetFileHeader - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetFileHeader() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader

HDFServiceStub.GetFileHeader.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetFileHeader.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader.Factory

HDFServiceStub.GetFileHeaderResponse - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetFileHeaderResponse() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse

HDFServiceStub.GetFileHeaderResponse.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetFileHeaderResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse.Factory

HDFServiceStub.GetIPDConsensus - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetIPDConsensus() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

HDFServiceStub.GetIPDConsensus.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetIPDConsensus.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus.Factory

HDFServiceStub.GetIPDConsensusResponse - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetIPDConsensusResponse() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse

HDFServiceStub.GetIPDConsensusResponse.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetIPDConsensusResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse.Factory

HDFServiceStub.GetServiceExperienceIndexResponse - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetServiceExperienceIndexResponse() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse

HDFServiceStub.GetServiceExperienceIndexResponse.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetServiceExperienceIndexResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse.Factory

HDFServiceStub.GetServiceInfoResponse - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

HDFServiceStub.GetServiceInfoResponse() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse

HDFServiceStub.GetServiceInfoResponse.Factory - Class in com.pacbio.secondary.vis.svc.hdf.client.auto

Factory class that keeps the parse method

HDFServiceStub.GetServiceInfoResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse.Factory

HDFServiceWrapper - Class in com.pacbio.secondary.vis.svc.hdf.client

HDFServiceWrapper(String, VioletApp) - Constructor for class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper

HDFTest - Class in com.pacbio.secondary.vis.io.hdf.test

Test class for hdf library, exercises methods for accessing file data and metadata

HDFTest() - Constructor for class com.pacbio.secondary.vis.io.hdf.test.HDFTest

header - Variable in class com.pacbio.secondary.vis.data.contig.ContigInfo

headSet(T) - Method in class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet

headSet(T) - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet

heartbeat_timer - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

HIDE_BOTTOM - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

A constant describing an auto-hide operation where the component goes on the BOTTOM border

HIDE_LEFT - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

A constant describing an auto-hide operation where the component goes on the LEFT border

HIDE_RIGHT - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

A constant describing an auto-hide operation where the component goes on the RIGHT border

HIDE_TOP - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

A constant describing an auto-hide operation where the component goes on the TOP border

hideAction - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

hideSmartIcon - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

HIGH_KIN_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

high_kin_threshold - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

HIGH_QV_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

high_qv_threshold - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

HINTS_ANTIALIAS_ON - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

host_name - Variable in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

host_name - Variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

htmlPane - Variable in class com.pacbio.secondary.vis.gui.control.JHyperlinksHtmlTooltip

htmlPane - Variable in class com.pacbio.secondary.vis.gui.dialogs.PropertiesDialog

htmlPane - Variable in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog

httpport - Variable in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

httpport - Variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

HUMAN_CHR_LENGTH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

hyperlinkUpdate(HyperlinkEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog.RegionsOfInterestHyperlinkListener

I

IChangeNotifier - Interface in com.pacbio.secondary.vis.gui.evt

id - Variable in class com.pacbio.secondary.vis.data.contig.ContigInfo

ideogram_db - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase

ideogramBounds - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

IdeogramDB - Class in com.pacbio.secondary.vis.data.db

Database class for the NCBI ideogram database.

IdeogramDB(int) - Constructor for class com.pacbio.secondary.vis.data.db.IdeogramDB

IdeogramDB() - Constructor for class com.pacbio.secondary.vis.data.db.IdeogramDB

ideogramLabelBounds - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

IdeogramViewPrintingHelper - Class in com.pacbio.secondary.vis.gui.draw.print

IdeogramViewPrintingHelper(GenomicViewHorizontal) - Constructor for class com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper

IdeogramViewPrintingHelper(VioletFrameIO, GenomicViewSingleContig[]) - Constructor for class com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper

image - Variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

image_file - Variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

importCommonFileTypesFromReader(DataFileInfo.eFileType, Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

reads file types common to interactive and bkg loading

importConsensusSequence(WsFastaSequenceInfo, GenomicViewDetails, boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

importDataFile(File) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

importDataFromInputStream(InputStream, TrackDataInfo) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

ImportDataHelper - Class in com.pacbio.secondary.vis.io.importer

ImportDataHelper(VioletApp) - Constructor for class com.pacbio.secondary.vis.io.importer.ImportDataHelper

constructor

importEpiProReadsFileFromReader(Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importGFF3FileFromReader(Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importGZippedHDFResults(WsResults, TrackDataInfo) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

importGZippedInsertions(GenomicViewInspect, DataHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

called by importhelper...

importGZippedResults(DataHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

called by importhelper...

importHTMLDocument(File) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importIPDConsensus(WsIPDConsensusInfo, GenomicViewDetails, boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

importModificationsGFFFileFromReader(Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importMultiSampleVCFFileFromReader(Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importNCBIGeneDB(Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importReferenceSequence(WsFastaSequenceInfo, GenomicViewDetails, boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

importSessionFromProject() - Method in class com.pacbio.secondary.vis.data.session.timer.SessionDataTimerTask

importSummaryGFFFileFromReader(Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importUCSCGTFFileFromReader(Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importVariantsGFFFileFromReader(Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importVCFFileFromReader(Reader, String) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

importVioletHDFReadsFile(File) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

INACTIVE_TITLE_BACKGROUND - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants

INACTIVE_TITLE_FOREGROUND - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants

indexes - Variable in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo

indexOfDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane

Returns the index of the given dockable

indexOfDockable(Dockable) - Method in interface pub.vlsolutions.swing.docking.TabbedDockableContainer

Returns the index of the given dockable

info - Variable in class com.pacbio.secondary.vis.data.base.BaseDataRecord

info - Variable in class com.pacbio.secondary.vis.data.marker.Marker

An optional pointer to an information object.

info - Variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

info - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResults

INFO_CMM_ELEMENT_CONTIG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

INFO_CMM_ELEMENT_FILE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

INFO_CMM_ELEMENT_FILE_INDEX - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

INFO_CMM_ELEMENT_HOME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

INFO_CMM_ELEMENT_NAME_V13 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

INFO_CMM_ELEMENT_NAME_V14 - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

INFO_CMM_ELEMENT_RSS_FEED - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

INFO_CMM_ELEMENT_WEB_SEARCH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

INFO_CMM_TAG_IMAGE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

INFO_CMM_TAG_WEB - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

InfoBuilder - Class in com.pacbio.secondary.vis.gui.draw.utils

Creates summary information for genes, markers, reads, contigs, etc.

InfoBuilder() - Constructor for class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder

infoPanel - Variable in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel

INFOTABLE_LARGE_FONT_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_LARGE_HEADER_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_LARGE_TEXT_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_MEDIUM_FONT_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_MEDIUM_HEADER_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_MEDIUM_TEXT_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_READ_LARGE_FONT_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_READ_MEDIUM_FONT_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_READ_SMALL_FONT_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_SMALL_FONT_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_SMALL_HEADER_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

INFOTABLE_SMALL_TEXT_STYLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.FontConstants

init() - Method in class com.pacbio.secondary.vis.gui.control.JCheckBoxMenuItemEx

init() - Method in class com.pacbio.secondary.vis.gui.control.JRadioButtonMenuItemEx

init() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase.JDoubleSlider

init(Vector<VariableResolutionDataSet>, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo

init(Vector<VariableResolutionDataSet>, Rectangle, int, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo

init(Dockable, int) - Method in class pub.vlsolutions.swing.docking.AutoHideButton

Initialize the button for a Dockable and a border zone

init() - Method in class pub.vlsolutions.swing.docking.FloatingDialog

initialisation of the title bar

initAutoHidePopUp(JPopupMenu) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab

initAutoHidePopUp(JPopupMenu) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

initBorders() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

Installs borders used to drag the expand panel around

initButton(JButton, Insets, Border) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

initButton(JToggleButton, Insets, Border) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

initCmdButton(AbstractButton, String) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

initColumNames() - Method in class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage

initContigInfo(VioletApp) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

InitDialog(String) - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog

initDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog

initDialog(String, String, boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog

initDNAFont(JComponent) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

InitDockable(String, String, String, String) - Method in class com.pacbio.secondary.vis.gui.panels.base.DockableScrollPaneBase

InitDockable(String) - Method in class com.pacbio.secondary.vis.gui.panels.base.DockableScrollPaneBase

InitDockable(String, String, String) - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase

InitDockable(String, String, String) - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel

InitDockable(String, String, String) - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel

initDockedPopUp(JPopupMenu) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab

initDockedPopUp(JPopupMenu) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

initFloatingPopUp(JPopupMenu) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab

Init the popup displayed as the title bar contextual menu

initFloatingPopUp(JPopupMenu) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

Init the popup displayed as the title bar contextual menu

initFrame() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx

Preferences dialog closes by pressing esc key or the close button on system menu

initHeavyWeightUsage() - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

Facade method used to allow mixing of lightweight and heavyweight components in the desktop.

initHeavyWeightUsage(boolean) - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

Facade method used to allow mixing of lightweight and heavyweight components in the desktop.

INITIAL_EXPAND_COMPONENT_SIZE - Static variable in class pub.vlsolutions.swing.docking.AutoHidePolicy

A constant for initial expantion : based on preferred size of component

INITIAL_EXPAND_CUSTOM_SIZE - Static variable in class pub.vlsolutions.swing.docking.AutoHidePolicy

A constant for initial expantion : based on custom widths and heights

initializeViewBase() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

initLocalData() - Method in class com.pacbio.secondary.vis.gui.dialogs.QVThresholdOptionsPane

initLocals() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails

initLocals() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal

initLocals() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

initLocals() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion

initLocals() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

initMapQVPalette(boolean) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

initMaximizedPopUp(JPopupMenu) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab

Init the popup displayed as the title bar contextual menu

initMaximizedPopUp(JPopupMenu) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

Init the popup displayed as the title bar contextual menu

initPanel() - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

initToolbar(ActionListener) - Method in class com.pacbio.secondary.vis.gui.control.VioletToolBar

initTransientState() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails

initTransientState() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

initTransientState() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

initValues(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

insert(Interval) - Method in class com.pacbio.secondary.vis.data.interval.IntervalTree

Inserts a new interval into the tree so that each children will be contained in its parent interval.

insertion_width - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

InsertNodeException - Exception in com.pacbio.secondary.vis.common.utils.exception

InsertNodeException() - Constructor for exception com.pacbio.secondary.vis.common.utils.exception.InsertNodeException

InsertNodeException(String) - Constructor for exception com.pacbio.secondary.vis.common.utils.exception.InsertNodeException

InspectDataDialog - Class in com.pacbio.secondary.vis.gui.dialogs

InspectDataDialog(VioletApp, long) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog

INSPECTION_VIEW_POST_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

INSPECTION_VIEW_PRE_OFFSET - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

installAccelerators() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the eyboard shortcuts

installAutoHideSettings() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the autohide related properties

installBackground() - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

Installs the default background of the title bar

installBorder(AutoHideButtonPanel) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonPanelUI

installBorder(AutoHideButton) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonUI

installBorders() - Method in class pub.vlsolutions.swing.docking.FloatingDialog

Installs the borders of this dialog and its title header

installBorderSettings() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the borders

installBorderSettingsOrg() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the borders

installButtons() - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

configure the title bar buttons

installButtonUI(AbstractButton) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Install custom UI for this button : a light rollover effet and a custom rounded/shaded border.

installCloseableTabs() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the closable tabs properties

installDecoration() - Method in class pub.vlsolutions.swing.docking.FloatingDialog

Installs or not the window decorations on this dialog.

installDefaults() - Method in class pub.vlsolutions.swing.docking.ui.DockingSplitPaneUI

installDesktopSettings() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the DockinDesktop related properties

installDockableDragSource(DockableDragSource) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

This method is used by DockableContainers in order to register their DockableDragSource(s) to the OldDragControler.

installDockableDragSources(DockableDragSource[]) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Installs multiple drag sources.

installDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

installDocking(DockingDesktop) - Method in interface pub.vlsolutions.swing.docking.DockableContainer

Invoked once after creation, in order to let this component register its DockableDragSources to the DockingDesktop, and have a reference of this Desktop.

installDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane

Invoked once after creation, in order to let this component register its DockableDragSources to the DockingDesktop, and have a reference of this Desktop.

installDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockView

Invoked once after creation, in order to let this component register its DockableDragSources to the DockingDesktop, and have a reference of this Desktop.

installDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab

Invoked once after creation, in order to let this component register its DockableDragSources to the DockingDesktop, and have a reference of this Desktop.

installDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

installDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.FloatingDialog

installDocking(DockingDesktop) - Method in interface pub.vlsolutions.swing.docking.FloatingDockableContainer

This install method is invoked before adding the first dockable

installDockViewSettings() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the DockView related properties

installDockViewTitleBarSettings() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the DockVieTitleBar related properties

installFloatingSettings() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the FloatingDialog related properties

installIcons() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs icons used by the framework

installLabel() - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

Installs default on the titlebar label

installMaximizedDockableBorder(DockView) - Method in class pub.vlsolutions.swing.docking.ui.DockViewUI

Installs a border when the DockView target is unique on the desktop (mamimized, or alone)

installMouseHandler(AbstractButton) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Used internally to add a mouse listener to the button.

installResizers() - Method in class pub.vlsolutions.swing.docking.FloatingDialog

installs the components used for resizing (on left/right/bottom borders)

installSingleDockableBorder(DockView) - Method in class pub.vlsolutions.swing.docking.ui.DockViewUI

Installs a border when the DockView target is a SingleDockableContainer (not nested in a tabbed container )

installSplitContainerSettings() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the splitpanes related properties

installTabbedContainerSettings() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the tabbed pane related properties

installTabbedDockableBorder(DockView) - Method in class pub.vlsolutions.swing.docking.ui.DockViewUI

Installs a border when the DockView target is included in a TabbedDockableContainer.

installTitleBorder(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

installs the border of the title bar

installToolBarSettings() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

installs the toolbar related properties

installUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonPanelUI

installUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonUI

installUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideExpandPanelUI

installUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DetachedDockViewUI

Installs the component's UI

installUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DockingSplitPaneUI

installUI() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

Installs the UI settings.

installUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

installUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DockViewUI

installUI(JComponent) - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripperUI

installs the UI and sets the preferred size of the gripper

instance - Static variable in class pub.vlsolutions.swing.docking.ui.AutoHideButtonUI

INT_HIDE_BOTTOM - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

INT_HIDE_LEFT - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

INT_HIDE_RIGHT - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

INT_HIDE_TOP - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

INT_SPLIT_BOTTOM - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

INT_SPLIT_LEFT - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

INT_SPLIT_RIGHT - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

INT_SPLIT_TOP - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

int_temp - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelBase

int_visible_range - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

IntegerRenderer - Class in com.pacbio.secondary.vis.gui.table.renderer

IntegerRenderer() - Constructor for class com.pacbio.secondary.vis.gui.table.renderer.IntegerRenderer

internalInsert(IntervalTreeNode, Interval) - Method in class com.pacbio.secondary.vis.data.interval.IntervalTree

intersection(Interval) - Method in class com.pacbio.secondary.vis.data.interval.Interval

intersects(Interval) - Method in class com.pacbio.secondary.vis.data.interval.Interval

intersects(int, int) - Method in class com.pacbio.secondary.vis.data.interval.Interval

intersects(Locus) - Method in class com.pacbio.secondary.vis.data.locus.Locus

intersects(int, Interval) - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage

intersects(int, Interval) - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage

intersects(WsIntervalSvc) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc

Interval - Class in com.pacbio.secondary.vis.data.interval

Interval() - Constructor for class com.pacbio.secondary.vis.data.interval.Interval

Interval(long, long) - Constructor for class com.pacbio.secondary.vis.data.interval.Interval

Interval(long, long, int) - Constructor for class com.pacbio.secondary.vis.data.interval.Interval

Interval(Interval) - Constructor for class com.pacbio.secondary.vis.data.interval.Interval

interval - Variable in class com.pacbio.secondary.vis.data.interval.IntervalTreeNode

interval - Variable in class com.pacbio.secondary.vis.data.locus.Locus

interval - Variable in class com.pacbio.secondary.vis.data.marker.Marker

Basepair range.

IntervalRenderer - Class in com.pacbio.secondary.vis.gui.table.renderer

renderer for genomic interval

IntervalRenderer() - Constructor for class com.pacbio.secondary.vis.gui.table.renderer.IntervalRenderer

IntervalScale<T> - Interface in com.pacbio.secondary.vis.data.interval

IntervalTree - Class in com.pacbio.secondary.vis.data.interval

A tree with hierarchical intervals.

IntervalTree() - Constructor for class com.pacbio.secondary.vis.data.interval.IntervalTree

IntervalTreeException - Exception in com.pacbio.secondary.vis.common.utils.exception

IntervalTreeException() - Constructor for exception com.pacbio.secondary.vis.common.utils.exception.IntervalTreeException

IntervalTreeException(String) - Constructor for exception com.pacbio.secondary.vis.common.utils.exception.IntervalTreeException

IntervalTreeNode - Class in com.pacbio.secondary.vis.data.interval

A node of a hierarchy (tree) of intervals

IntervalTreeNode() - Constructor for class com.pacbio.secondary.vis.data.interval.IntervalTreeNode

IntervalTreeNode(Interval) - Constructor for class com.pacbio.secondary.vis.data.interval.IntervalTreeNode

IntervalTreeQuery - Class in com.pacbio.secondary.vis.data.interval

Find nodes in an IntervalTree.

IntervalTreeQuery(IntervalTree) - Constructor for class com.pacbio.secondary.vis.data.interval.IntervalTreeQuery

IntervalTreeQuery.FilterVisitor - Class in com.pacbio.secondary.vis.data.interval

IntervalTreeVisitor - Interface in com.pacbio.secondary.vis.data.interval

intv - Variable in class com.pacbio.secondary.vis.svc.server.data.WsRead

invalidate() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

invalidate() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger

invalidateAndRepaintAllViews() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

invalidateLayout(Container) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout

invalidateLayout(Container) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout

invalidateLayout(Container) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout

invalidateLayout(Container) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout

invalidatePaintBuffer() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular

Call this function if the view changes.

invalidatePaintBuffer() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

Call this function if the view changes.

ipd_baseline - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails

ipd_consensus_data - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

ipd_consensus_request_queue - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

ipd_nan_marker - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails

ipdconsensus_track_height - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

IPDConsensusStorage - Class in com.pacbio.secondary.vis.data.session

IPDConsensusStorage() - Constructor for class com.pacbio.secondary.vis.data.session.IPDConsensusStorage

IPDConsensusTable - Class in com.pacbio.secondary.vis.io.hdf.data

IPDConsensusTable(long, long, Object) - Constructor for class com.pacbio.secondary.vis.io.hdf.data.IPDConsensusTable

IProgressNotifier - Interface in com.pacbio.secondary.vis.gui.evt

is64BitSystem() - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils

is64BitVM() - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils

is_v13 - Variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader

is_valid - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

is_visible - Variable in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo

is_vPacBio - Variable in class com.pacbio.secondary.vis.io.vcf.VCFReader

isAccepted() - Method in class pub.vlsolutions.swing.docking.event.DockableStateWillChangeEvent

isActivateEvent() - Method in class com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent

isActive() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

isActive() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

Returns true if this panel is the ancestor of the focused component

isActive() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

Returns true if the dockable is the currently active one.

isAncestorOf(DockGroup) - Method in class pub.vlsolutions.swing.docking.DockGroup

returns true if this group is the ancestor of group g.

isAttachButtonDisplayed - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

isAutoGenerated - Variable in class com.pacbio.secondary.vis.data.db.IdeogramDB

isAutoGenerated() - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB

isAutoHideEnabled() - Method in class pub.vlsolutions.swing.docking.DockKey

Returns try if autohiding is enabled

isAutoIdeogramUsesFixedNumBands() - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB

isBaseMods(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isBases(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isBorderOpaque() - Method in class pub.vlsolutions.swing.docking.ShadowBorder

isBorderOpaque() - Method in class pub.vlsolutions.swing.toolbars.RoundedBorder

isBorderOpaque() - Method in class pub.vlsolutions.swing.toolbars.ToolBarButtonBorder

isBorderOpaque() - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelBorder

isCancelled() - Method in class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog

isCancelled() - Method in interface com.pacbio.secondary.vis.gui.evt.IProgressNotifier

isCDNADataAvailable() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

returns true if there is trace of gmap todo: should read from cmp.h5

isCDNADataAvailable() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

do we have cdna in the dataset?

isCellEditable(EventObject) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor

isCellEditable(Object, int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel

By default, make the column with the Tree in it the only editable one.

isCellEditable(Object, int) - Method in interface com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel

Indicates whether the the value for node node, at column number column is editable.

isChildOfCompoundDockable(Dockable) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities

checks if this dockable is a child of a compound dockable

isChunked() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo

isCircular() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions

isCircular() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

isCloseButtonDisplayed - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

isClosed() - Method in class pub.vlsolutions.swing.docking.DockableState

Convenience method returning wether the dockable is in the CLOSED state

isCloseEnabled() - Method in class pub.vlsolutions.swing.docking.DockKey

Returns true if this dockable can be closed

isCollapsed() - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripper

Return true is this toolbar is currently collapsed

isCollapsed() - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Returns true if this toolbar is currently collapsed

isCollapsible() - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripper

Return true is this toolbar can be collapsed (default is true)

isCollapsible() - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

isCompatibleGroup(DockGroup) - Method in class pub.vlsolutions.swing.docking.DockGroup

returns true is this group is compatible with the given parameter.

isDataLoaded() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

isDeNovo() - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

isDesktop() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions

isDetails() - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

isDetails() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

isDirectory - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFile

isDirectory() - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFile

isdirectory - Variable in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo

isDNABaseShown() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

isDNABaseShown() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

isDockButtonDisplayed - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

isDocked() - Method in class pub.vlsolutions.swing.docking.DockableState

Convenience method returning wether the dockable is in the DOCKED state

isDragAccepted() - Method in class pub.vlsolutions.swing.docking.event.DockDragEvent

returns true if drag is accepted.

isDragDelegated() - Method in class pub.vlsolutions.swing.docking.event.DockDragEvent

If drag is not accepted, this method will be invoked to evaluate a delegating event processing.

isDragging - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

isDraggingEvent() - Method in class com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent

isDrawIPDConsensus() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

should we draw consensus ipd based on user options, etc.

isDrawIPDConsensus() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

should we draw consensus ipd based on user options, etc.

isDropAccepted() - Method in class pub.vlsolutions.swing.docking.event.DockDropEvent

Indicates if the drop operation is accepted.

isEmpty() - Method in class com.pacbio.secondary.vis.gui.control.JHyperlinksHtmlTooltip

isEmpty() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkToDoQueue

isEnabled() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Returns the enabled state

isEnableTestWebBrowser() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions

isEpiProFolded(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isEpiProReads() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

isEpiProReadsDataAvailable() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

returns true if we have an unmapped reads file around

isEpiProSplit(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isEpiProUnFoldedMapped(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isEpiProUnFoldedSubread(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isFasta_file_exists() - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage

isFloatButtonDisplayed - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

isFloatEnabled() - Method in class pub.vlsolutions.swing.docking.DockKey

Returns true if this dockable can be detached from its desktop

isFloating() - Method in class pub.vlsolutions.swing.docking.DockableState

Convenience method returning wether the dockable is in the FLOATING state

isFloatingShape() - Method in interface pub.vlsolutions.swing.docking.DragControler

isGeneType() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection

returns true if this is modifications type

isGenome() - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

isHDFReads() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

isHeavyWeightComponent(Component) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities

isHidden() - Method in class pub.vlsolutions.swing.docking.DockableState

Convenience method returning wether the dockable is in the HIDDEN state

isHideButtonDisplayed - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

isHorizontal() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

isIdeogramDBLoaded() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

isIdeogramDBLoaded() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal

Do not draw ideogram in horizontal views

isInspection() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

isInteger(String) - Static method in class com.pacbio.secondary.vis.common.utils.StringUtils

isIPDConsensusDataAvailable() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

returns true if we have a modifications.gff file around todo: should read from cmp.h5

isIPDConsensusDataAvailable() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

do we have consensus ipd in the dataset?

isLeaf(Object) - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel

isLeaf(Object) - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel

isLeaf(Object) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel

isLightWeightUsageEnabled() - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

isMacOSSystem() - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils

isMacOSX() - Static method in class com.pacbio.secondary.vis.common.utils.WebBrowserUtils

isMarkerType() - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel

returns true if this is marker type

isMarkerType() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection

returns true if this is modifications type

isMatchesRegEx(String, String) - Method in class com.pacbio.secondary.vis.common.utils.StringUtils

test string for regex match

isMaximizeButtonDisplayed - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

isMaximized() - Method in class pub.vlsolutions.swing.docking.DockableState

Convenience method returning wether the dockable is in the MAXIMIZED state

isMaximizeEnabled() - Method in class pub.vlsolutions.swing.docking.DockKey

Returns true if this dockable can be maximized

isModifications() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

isModificationsType() - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel

returns true if this is base mods data type

isModificationsType() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection

returns true if this is modifications type

isModified() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

returns true if modified and unsaved

isMultiLine() - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure

isMultiLink() - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure

isMultiNode() - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure

isMultisampleDataAvailable() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

returns true if we have a multisample .vcf file around

isNoMetrics(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isNoStructures(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isNotification() - Method in class pub.vlsolutions.swing.docking.DockKey

Returns true is a notification has been set.

isOffline() - Static method in class com.pacbio.secondary.vis.gui.app.WebStartApp

isOpaqueContents() - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Returns whether this desktop's contents are opaque or not.

isOptimizedDrawingEnabled() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

isPressed() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Returns the pressed state

isPressed() - Method in class pub.vlsolutions.swing.toolbars.ToolBarButtonBorder

isPW(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isQV(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isRawIPD(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isRawKinetics(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

isReaderMTOMAware

isReaderMTOMAware(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

isReaderMTOMAware

isReadsFile(String) - Static method in class com.pacbio.secondary.vis.data.session.DataStorageBase

isReadsType() - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel

returns true if this is reads type or unmapped read type

isReadsType() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection

returns true if this is reads type

isReferenceSequenceFileInfo() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

isRegion() - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

isRescaleEvent() - Method in class com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent

isRestoreButtonDisplayed - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

isResultsLinesGraph(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isResultsNodesGraph(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isResultsStructures(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isResultsStructuresOnly(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isRollover() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Returns the rollover state

isRolloverBorderPainter() - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Returns the state of the rolloverBorderPainted property

isRolloverContentAreaFilled() - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Returns the value of the rolloverContentAreaFilled property

isScreenResolutionMaximizable() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

isScreenResolutionValid() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

isSelected() - Method in class pub.vlsolutions.swing.docking.AutoHideButton

True when the button is currently selected.

isSelectedMarkerEvent() - Method in class com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent

isSelection() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

isSeparateStrands(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isServerInWhiteList(String) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

isSettingsInstalled - Variable in class pub.vlsolutions.swing.docking.ui.DockingUISettings

Field for installing settings only once

isSingleDockableTitleBarPopUpCustomizer() - Method in class pub.vlsolutions.swing.docking.DockableActionCustomizer

Returns wether this customizer is used in the context of a SingleDockableContainer

isSingleHeavyWeightComponent() - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

isSMRTCloud() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions

isSmrtCloud() - Method in class com.pacbio.secondary.vis.svc.server.data.parser.MetadataInfoParser

true if request is for cloud based deployment

isSMRTGroups() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions

isSMRTJNLP() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions

isSortable() - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

Returns 1 if whole genome panel and multi contigs.

isSorted() - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

isStandAlone() - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

Determine if both client and server are running on same machine.

isStrobeReadType() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

ReadType attribute

isSummary() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

isSummaryOnly() - Method in class com.pacbio.secondary.vis.data.session.options.CommandLineOptions

isSummaryType() - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel

returns true if this is summary type

isSummaryType() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection

returns true if this is summary type

isTabSelectorPopUpCustomizer() - Method in class pub.vlsolutions.swing.docking.DockableActionCustomizer

Returns wether this customizer is used in the context of a TabbedDockableContainer

isUpdateDataRequest(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

isUseCustomUI() - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Return the value of the useCustomUI property

isV13() - Method in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader

isV131 - Variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader

isV133 - Variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader

isValid(Object[]) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ArrayConstants

isValid(byte[]) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ArrayConstants

isValid() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

isValidView() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

isVariantPosInsertionAt(int) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

isVariants() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

isVariantsType() - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel

returns true if this is variants or vcf data type

isVariantsType() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection

returns true if this is variants or vcf data type

isVCFMultiSample() - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

isVerbose - Variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

isVersion1_3() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

Version specific tags

isVersion2_0() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

Version specific tags

isVersionAtLeast1_2() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

Version specific tags

isViewInsertions(int) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

returns true when mode is raw data with insertions

isVisible() - Method in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo

isVisible() - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Returns the visible state

isVisJnlpPresent(VioletApp, String) - Static method in class com.pacbio.secondary.vis.smrtcloud.CloudUtils

isWindowsPlatform() - Static method in class com.pacbio.secondary.vis.common.utils.WebBrowserUtils

Try to determine whether this application is running under Windows or some other platform by examining the "os.name" property.

isWinOSSystem() - Static method in class com.pacbio.secondary.vis.common.utils.ProgramUtils

iterator() - Method in class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet

iterator() - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet

iterator() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel

iterator() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger

IVariableResolutionDataModelServer - Interface in com.pacbio.secondary.vis.data.variableresolution.model

serves filtered generic records data.

J

JCheckBoxMenuItemEx - Class in com.pacbio.secondary.vis.gui.control

JCheckBoxMenuItemEx(String) - Constructor for class com.pacbio.secondary.vis.gui.control.JCheckBoxMenuItemEx

JCheckBoxMenuItemEx() - Constructor for class com.pacbio.secondary.vis.gui.control.JCheckBoxMenuItemEx

JComboBoxCtrl - Class in com.pacbio.secondary.vis.gui.control

JComboBoxCtrl(Object[]) - Constructor for class com.pacbio.secondary.vis.gui.control.JComboBoxCtrl

JHyperlinksHtmlTooltip - Class in com.pacbio.secondary.vis.gui.control

JHyperlinksHtmlTooltip() - Constructor for class com.pacbio.secondary.vis.gui.control.JHyperlinksHtmlTooltip

JLabelCtrl - Class in com.pacbio.secondary.vis.gui.control

JLabelCtrl(String) - Constructor for class com.pacbio.secondary.vis.gui.control.JLabelCtrl

JMultiLineHtmlToolTip - Class in com.pacbio.secondary.vis.gui.control

JMultiLineHtmlToolTip() - Constructor for class com.pacbio.secondary.vis.gui.control.JMultiLineHtmlToolTip

JMultiLineToolTip - Class in com.pacbio.secondary.vis.gui.control

JMultiLineToolTip() - Constructor for class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip

JNLP_32BIT_SEARCH_TAG - Static variable in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

JNLP_64BIT_REPLACE_TAG - Static variable in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

JNLP_ARGUMENT_SEARCH_TAG - Static variable in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

JNLP_EXTENSION - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLP_HOST_NAME_TAG - Static variable in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

JNLP_HOST_NAME_TAG - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLP_HTTPPORT_NAME_TAG - Static variable in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

JNLP_HTTPPORT_NAME_TAG - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLP_JOB_METADATA_TAG - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLP_SERVICE_PROGRAM_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

JNLP_SERVICE_URL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

JNLP_TEMPLATE - Static variable in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

JNLP_TEMPLATE - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLP_V11_METADATA_END_TAG - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLP_V11_METADATA_START_TAG - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLP_v12_VERSION - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLP_v12_VERSION_TAG - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLP_VERSION_TAG - Static variable in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

JNLP_VERSION_TAG - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

JNLPFileBuilder - Class in com.pacbio.secondary.vis.svc.server.jnlp

JNLPFileBuilder() - Constructor for class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileBuilder

JNLPFileWrapper - Class in com.pacbio.secondary.vis.svc.server.jnlp

JNLPFileWrapper() - Constructor for class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

used by server side

JNLPFileWrapper(String, String) - Constructor for class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

used by client to save session using current host/port info...

JNLPService - Class in com.pacbio.secondary.vis.svc.server

This service returns properly formatted jnlp files to use for launching SMRT View

JNLPService() - Constructor for class com.pacbio.secondary.vis.svc.server.JNLPService

job_id - Variable in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser

job_title - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase

JobInfo - Class in com.pacbio.secondary.vis.svc.server.threads

JobInfo() - Constructor for class com.pacbio.secondary.vis.svc.server.threads.JobInfo

JobInfo(JobInfo) - Constructor for class com.pacbio.secondary.vis.svc.server.threads.JobInfo

JobMetadataInfo - Class in com.pacbio.secondary.vis.data.xmlinfo

JobMetadataInfo() - Constructor for class com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo

JRadioButtonMenuItemEx - Class in com.pacbio.secondary.vis.gui.control

JRadioButtonMenuItemEx(String) - Constructor for class com.pacbio.secondary.vis.gui.control.JRadioButtonMenuItemEx

JRadioButtonMenuItemEx() - Constructor for class com.pacbio.secondary.vis.gui.control.JRadioButtonMenuItemEx

JRadioButtonMenuItemEx(String, Icon) - Constructor for class com.pacbio.secondary.vis.gui.control.JRadioButtonMenuItemEx

JTabbedPaneSmartIcon - Class in pub.vlsolutions.swing.tabbedpane

An Icon allowing the use of closeable tabs by simulating the entire tabpane tab-painting.

JTabbedPaneSmartIcon(Icon, String, SmartIconJButton[]) - Constructor for class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

Constructs a new smart icon with a given set of additional buttons

JTabbedPaneSmartIconManager - Class in pub.vlsolutions.swing.tabbedpane

This class is the interface between a JTabbedPane and a smart icon.

JTabbedPaneSmartIconManager(JTabbedPane) - Constructor for class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIconManager

Constructs a new tabbedPane manager for a given JTabbedPane

JToolbarToggleButton - Class in com.pacbio.secondary.vis.gui.control

JToolbarToggleButton() - Constructor for class com.pacbio.secondary.vis.gui.control.JToolbarToggleButton

JToolbarToggleButton(Icon, Boolean) - Constructor for class com.pacbio.secondary.vis.gui.control.JToolbarToggleButton

JTreeTable - Class in com.pacbio.secondary.vis.gui.control.treetable

JTreeTable component, uses a JTree as renderer for the cells in the first column of the JTable Adapted from: http://java.sun.com/products/jfc/tsc/articles/treetable1/index.html

JTreeTable(TreeTableModel) - Constructor for class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable

JTreeTable.TreeTableCellRenderer - Class in com.pacbio.secondary.vis.gui.control.treetable

A TreeCellRenderer that displays a JTree.

JTreeTable.TreeTableCellRenderer(TreeModel) - Constructor for class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable.TreeTableCellRenderer

K

key - Variable in class com.pacbio.secondary.vis.gui.panels.base.DockablePaneBase

key_pressed - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewKeyListener

keyPressed(KeyEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewKeyListener

keyPressed(KeyEvent) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel.GenomicTablePanelKeyListener

Invoked when a key has been pressed.

keyReleased(KeyEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewKeyListener

keyTyped(KeyEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewKeyListener

KIN_FWD_COLOR - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

KIN_FWD_COLOR_HEATMAP - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

KIN_REV_COLOR - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

KIN_REV_COLOR_HEATMAP - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

KINETIC_PALETTE_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

kinetics_ann_label - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_close_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_help_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_max_label - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_max_slider - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_max_text - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_min_label - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_min_slider - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_min_text - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_palette - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_save_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

KINETICS_SCALING - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

kinetics_scaling - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

kinetics_scaling_cb - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_scaling_label - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

kinetics_tab - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

KineticsComparator - Class in com.pacbio.secondary.vis.svc.server.data

KineticsComparator() - Constructor for class com.pacbio.secondary.vis.svc.server.data.KineticsComparator

L

lane - Variable in class com.pacbio.secondary.vis.svc.server.data.WsRead

LANE_EXTRA_DISTANCE - Static variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

LANE_EXTRA_DISTANCE - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

LANE_OFFSET_PIXELS - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

lanes - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

lanes_separator - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

last() - Method in class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet

last() - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet

last_busy - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase

last_data - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase

last_message - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase

last_progress - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase

last_selected_dockable_view - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

LAST_USED_LAYOUT - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

LAST_USED_LOCAL_DIR_OPEN - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

LAST_USED_LOCAL_DIR_SAVE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

LAST_USED_REMOTE_PATH - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

lastDropGeneralPath - Variable in class pub.vlsolutions.swing.docking.DockView

remember the last drop position to cache the shape used for showing the drop position

lastDropShape - Variable in class pub.vlsolutions.swing.docking.DockView

remember the last drop position to cache the shape used for showing the drop position

lastMarker - Variable in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel

lastModified() - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFile

lastSource - Variable in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel

launchHelpTopicInWebBrowser(String) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

launchPanelHelpInWebBrowser(String) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

launchWebSiteInWebBrowser(String) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

layout_info - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

LAYOUT_RES_FOLDER - Static variable in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager

layoutComponent(Component) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils

layoutContainer(Container) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout

overridden to adjust position (x(top) = width(left), y(left) = height(top)

layoutContainer(Container) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout

overridden to adjust position (x(top) = width(left), y(left) = height(top)

layoutContainer(Container) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout

layoutContainer(Container) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout

overridden to adjust position (x(top) = width(left), y(left) = height(top)

layoutDetailsTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

layoutDialog(boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog

layoutDialogComponents() - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog

layoutEpiProReadsTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

layoutKineticsTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

layoutLabel(int, FontMetrics, int, String, Icon, Rectangle, Rectangle, Rectangle, boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.AlignedTabbedPaneUI

layoutPanelComponents() - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

layoutProgramTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

layoutQVTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

layoutStructuresTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

Graph structures options

layoutTitleBar() - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

layoutVariantsTab() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

LEFT - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition

convenience field referencing the LEFT border of the DockingDesktop

LEFT_CENTER - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition

convenience field referencing the CENTER part of the LEFT border of the DockingDesktop

LEFT_PANEL - Static variable in class pub.vlsolutions.swing.toolbars.ToolBarPanelBorder

leftBorderPane - Variable in class pub.vlsolutions.swing.docking.DockingDesktop

panel used to display autohide buttons

leftLegendBounds - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

leftMarkerBounds - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

leftVisible - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

length - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFile

length() - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFile

length - Variable in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo

LibraryConstants - Class in com.pacbio.secondary.vis.io.hdf.constants

Contains various constants used in the library

LibraryConstants() - Constructor for class com.pacbio.secondary.vis.io.hdf.constants.LibraryConstants

link - Variable in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

link_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

link_genome_region_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

link_region_details_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

LinkedSortedMultiSet<T extends java.lang.Comparable<T>> - Class in com.pacbio.secondary.vis.common.collection

LinkedSortedMultiSet() - Constructor for class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet

LINUX_FILE_SEPARATOR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

listenerList - Variable in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor

listenerList - Variable in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel

loadDefaultWorkspace() - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

loadDefaultWorkspace(String) - Method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager

loadFrom(DockingContext) - Method in class pub.vlsolutions.swing.docking.ws.Workspace

Loads and configures this workspace from a given docking context.

loadFromFile(File, VioletApp) - Method in class com.pacbio.secondary.vis.io.motifs.MotifsReader

loadFromReader(Reader, String, VioletApp) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

loadFromReader(Reader, String, VioletApp) - Method in class com.pacbio.secondary.vis.io.gff.GFF3Reader

loadFromReader(Reader, String, VioletApp) - Method in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

loadFromReader(Reader, String, VioletApp) - Method in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader

loadFromReader(Reader, String, VioletApp) - Method in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader

loadFromReader(Reader, String, VioletApp) - Method in class com.pacbio.secondary.vis.io.motifs.MotifsReader

loadFromReader(Reader, String, VioletApp) - Method in class com.pacbio.secondary.vis.io.ucsc.gtf.reader.UCSCGTFReader

loadFromReader(Reader, String, VioletApp) - Method in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

loadFromReader(Reader, String, VioletApp) - Method in class com.pacbio.secondary.vis.io.vcf.VCFReader

loadReferenceInfo(ProgressDialog, CommandLineOptions) - Method in class com.pacbio.secondary.vis.data.session.DataStorage

loadROIsFromProject() - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

load bookmarks if present in same directory as project.jnlp

loadToolBarLayout() - Method in class pub.vlsolutions.swing.toolbars.ToolBarPersistence

Load the toolbar configuration.

loadWorkspaceFromBase64String(String) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

loadWorkspaceFromByteArray(byte[]) - Method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager

loadWorkspaceFromResource(String) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

loadWorkspaceFromResource(String) - Method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager

loadWorkspaceFromServer() - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

loadWorkspaceFromServer(String) - Method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager

local_return - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse

field for _return This was an Array!

local_return - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse

field for _return This was an Array!

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse

field for _return This was an Array!

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse

field for _return

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse

field for _return This was an Array!

local_return - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse

field for _return

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse

local_returnTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse

localBisDirectory - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

field for BisDirectory

localBisDirectoryTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

localBListDirOnly - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

field for BListDirOnly

localBListDirOnlyTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

localBuffer - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

field for Buffer

localBufferTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

localClient_contig_index - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

field for Client_contig_index

localClient_contig_index - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

field for Client_contig_index

localClient_contig_index - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

field for Client_contig_index

localClient_contig_index - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

field for Client_contig_index

localClient_contig_indexTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

localClient_contig_indexTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

localClient_contig_indexTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

localClient_contig_indexTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

localContig_id - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

field for Contig_id

localContig_id - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

field for Contig_id

localContig_id - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

field for Contig_id

localContig_id - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

field for Contig_id

localContig_idTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

localContig_idTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

localContig_idTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

localContig_idTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

localContig_index - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

field for Contig_index

localContig_indexTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

localContig_name - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

field for Contig_name

localContig_nameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

localCreateIdeogramAndGenesDB() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

Deprecated.

localDirectory - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

field for Directory

localDirectoryTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

localEnd - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

field for End

localEndTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

localFilename - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

field for Filename

localFilename - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile

field for Filename

localFilename - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

field for Filename

localFilename - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile

field for Filename

localFilename - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

field for Filename

localFilenameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

localFilenameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile

localFilenameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

localFilenameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile

localFilenameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

LocalFileNode - Class in com.pacbio.secondary.vis.data.filesystem

LocalFileNode(File) - Constructor for class com.pacbio.secondary.vis.data.filesystem.LocalFileNode

LocalFileSystemModel - Class in com.pacbio.secondary.vis.data.filesystem

FileSystemModel is a TreeTableModel representing a hierarchical file system.

LocalFileSystemModel(String) - Constructor for class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel

localIsdirectory - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

field for Isdirectory

localIsdirectoryTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

localLength - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

field for Length

localLengthTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

localLoadReferenceInfo(String) - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

localM_contig_length - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

field for M_contig_length

localM_contig_lengthTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

localM_contigs_info_array - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_contigs_info_array This was an Array!

localM_contigs_info_arrayTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_data_file - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

field for M_data_file

localM_data_fileTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

localM_file - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

field for M_file

localM_fileTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

localM_header - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

field for M_header

localM_headerTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

localM_id - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

field for M_id

localM_id - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_id

localM_ideogram_file - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_ideogram_file

localM_ideogram_fileTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_idTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

localM_idTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_image_file - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_image_file

localM_image_fileTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_job_title - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

field for M_job_title

localM_job_titleTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

localM_max_contig_length - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_max_contig_length

localM_max_contig_lengthTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_name - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

field for M_name

localM_name - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_name

localM_name - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

field for M_name

localM_nameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

localM_nameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_nameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

localM_num_contigs - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_num_contigs

localM_num_contigsTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_path - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_path

localM_pathTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_reference_info - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

field for M_reference_info

localM_reference_infoTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

localM_sequence_file - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

field for M_sequence_file

localM_sequence_file - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_sequence_file

localM_sequence_fileTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

localM_sequence_fileTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_sequence_index_file - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_sequence_index_file

localM_sequence_index_fileTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localM_tracks_info_array - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

field for M_tracks_info_array This was an Array!

localM_tracks_info_arrayTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

localM_web_search - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

field for M_web_search

localM_web_searchTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

localM_web_url - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

field for M_web_url

localM_web_urlTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

localMode - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

field for Mode

localMode - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

field for Mode

localModeTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

localModeTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

localName - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

field for Name

localNameTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

localOpts - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

field for Opts

localOptsTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

localPattern - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

field for Pattern

localPatternTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

localStart - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

field for Start

localStart - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

field for Start

localStart - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

field for Start

localStart - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

field for Start

localStart - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

field for Start

localStartTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

localStartTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

localStartTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

localStartTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

localStartTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

localStop - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

field for Stop

localStop - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

field for Stop

localStop - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

field for Stop

localStop - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

field for Stop

localStopTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

localStopTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

localStopTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

localStopTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

LocalTestApp - Class in com.pacbio.secondary.vis.gui.app

LocalTestApp(String[]) - Constructor for class com.pacbio.secondary.vis.gui.app.LocalTestApp

localTimestamp - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

field for Timestamp

localTimestampTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

localUrl - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

field for Url

localUrl - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

field for Url

localUrl - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

field for Url

localUrl - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames

field for Url

localUrl - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader

field for Url

localUrl - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

field for Url

localUrl - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

field for Url

localUrl - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

field for Url

localUrl - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo

field for Url

localUrl - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo

field for Url

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo

localUrlTracker - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo

LOCK_RANGE_EXPANSION - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

lockGenomeRegionPanels - Variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

lockRangeExpand - Variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

lockRegionDetailsPanels - Variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

locus - Variable in class com.pacbio.secondary.vis.data.base.BaseDataRecord

Locus - Class in com.pacbio.secondary.vis.data.locus

A genomic locus: contig/chromosome and start and stop basepairs.

Locus() - Constructor for class com.pacbio.secondary.vis.data.locus.Locus

Locus(Locus) - Constructor for class com.pacbio.secondary.vis.data.locus.Locus

Locus(int, long, long) - Constructor for class com.pacbio.secondary.vis.data.locus.Locus

Locus(int, long, long, int) - Constructor for class com.pacbio.secondary.vis.data.locus.Locus

locus - Variable in class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo

LoggerUtils - Class in com.pacbio.secondary.vis.common.utils

LoggerUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.LoggerUtils

LongRenderer - Class in com.pacbio.secondary.vis.gui.table.renderer

formats long values

LongRenderer() - Constructor for class com.pacbio.secondary.vis.gui.table.renderer.LongRenderer

lookIntoFile(String, VioletApp) - Method in class com.pacbio.secondary.vis.io.importer.DataFileInfo

LOW_BASE_MODS_THRESHOLD - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

LOW_KIN_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

low_kin_threshold - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

LOW_QV_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

low_qv_threshold - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

M

main(String[]) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

main(String[]) - Static method in class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils

main(String[]) - Static method in class com.pacbio.secondary.vis.data.db.IdeogramDB

main(String[]) - Static method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

main(String[]) - Static method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

test only

main(String[]) - Static method in class com.pacbio.secondary.vis.data.session.SessionDataHelper

local test method

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.app.DesktopApp

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.app.LocalTestApp

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.app.WebStartApp

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.control.VioletStatusBar

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.control.VioletToolBarTest

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.dialogs.AboutDialog

test dialog locally

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx

test dialog locally

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.dialogs.PrintOptionsDialog

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.dialogs.PropertiesDialog

test only

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular

main(String[]) - Static method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel

main(String[]) - Static method in class com.pacbio.secondary.vis.io.fasta.FastaFileReader

main(String[]) - Static method in exception com.pacbio.secondary.vis.io.hdf.exception.HDF5ExceptionEx

test only

main(String[]) - Static method in class com.pacbio.secondary.vis.io.hdf.file.bash5.BaseH5FileBase

main(String[]) - Static method in class com.pacbio.secondary.vis.io.hdf.test.HDFTest

runs all tests

main(String[]) - Static method in class com.pacbio.secondary.vis.io.importer.VioletFileAnalyzer

main(String[]) - Static method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper

main(String[]) - Static method in class com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper

main(String[]) - Static method in class com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper

main(String[]) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper

Test only...

main(String[]) - Static method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileBuilder

main(String[]) - Static method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

main(String[]) - Static method in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

main(String[]) - Static method in class com.pacbio.secondary.vis.svc.server.test.VisServiceLocalTest

main(String[]) - Static method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper

main(String[]) - Static method in class com.pacbio.secondary.vis.update.SMRTViewUpdater

main22(String[]) - Static method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular

main_app - Static variable in class com.pacbio.secondary.vis.common.utils.ProgramGlobals

main_app - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper

main_app - Variable in class com.pacbio.secondary.vis.data.session.timer.SessionDataTimer

main_app - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelBase

main_app - Variable in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager

main_app - Variable in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog

main_app - Variable in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog

main_app - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

main_app - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular

main_app - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

main_app - Variable in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase

main_app - Variable in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel

main_app - Variable in class com.pacbio.secondary.vis.io.export.ExportDataUtils

main_app - Variable in class com.pacbio.secondary.vis.smrtcloud.CloudTimer

main_frame - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase

majorOrder - Variable in class pub.vlsolutions.swing.toolbars.ToolBarConstraints

The major order is the row index for horizontal toolbars, and the column index for vertical toolbars.

makeGridBagLayout(Container, int, int) - Static method in class com.pacbio.secondary.vis.common.utils.GUIUtils

Updates a GridbagLayout with the desired number of rows and columns.

makeNavigationButton(ActionListener, String, String) - Method in class com.pacbio.secondary.vis.gui.control.VioletToolBar

makeToggleButton(Class<?>, ActionListener, String, String) - Static method in class com.pacbio.secondary.vis.gui.control.JToolbarToggleButton

map - Variable in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser

MAPPED_COORD_CORRECTION - Static variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

mapqv_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

MapQVPalette - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

Marker - Class in com.pacbio.secondary.vis.data.marker

Marker(Interval, float[]) - Constructor for class com.pacbio.secondary.vis.data.marker.Marker

Marker(Interval, GeneInfo) - Constructor for class com.pacbio.secondary.vis.data.marker.Marker

Marker(WsRead) - Constructor for class com.pacbio.secondary.vis.data.marker.Marker

marker_max_read_length - Static variable in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

marker_state - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

MarkerCollection - Class in com.pacbio.secondary.vis.data.marker

A collection of genomic markers.

MarkerCollection() - Constructor for class com.pacbio.secondary.vis.data.marker.MarkerCollection

MarkerCollection(BaseDataModel.eDataType) - Constructor for class com.pacbio.secondary.vis.data.marker.MarkerCollection

MarkerCollection(LinkedList<String>) - Constructor for class com.pacbio.secondary.vis.data.marker.MarkerCollection

Gives the MarkerCollection a name.

MarkerComparator - Class in com.pacbio.secondary.vis.data.marker

MarkerComparator() - Constructor for class com.pacbio.secondary.vis.data.marker.MarkerComparator

markers - Variable in class com.pacbio.secondary.vis.data.marker.MarkerCollection

markers - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

markerToSampleIndex(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData

MathConstants - Class in com.pacbio.secondary.vis.common.utils.constants

MathConstants() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.MathConstants

MathUtility - Class in com.pacbio.secondary.vis.common.collection

MathUtility() - Constructor for class com.pacbio.secondary.vis.common.collection.MathUtility

max - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

MAX_CACHED_KINETOGRAM_LENGTH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

MAX_CACHED_REFERENCE_LENGTH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

MAX_CDNA_MAP_QV_VALID_RANGE - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

MAX_CONSENSUS_LENGHT_TEST - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

max_coverage - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue

MAX_COVERAGE - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

MAX_DETAILS_COVERAGE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

max_details_coverage - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

max_details_view_coverage - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

MAX_DETAILS_VIEW_DYNAMIC_RANGE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

MAX_DETAILS_VIEW_FIXED_RANGE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

max_details_view_ordinate - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

MAX_DNA_FONT_HEIGHT - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

max_dynamic_range - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

max_field - Variable in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

max_fixed_range - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

MAX_INSPECTION_VIEW_REGION_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

MAX_IPD_CONSENSUS_TRACK_HEIGHT - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

max_lane - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

MAX_LIST_INTERSECT_ITEMS_PER_TRACK - Static variable in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder

max_norm_ipd_fwd - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue

max_norm_ipd_rev - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue

MAX_NUM_CACHED_OBJECTS - Static variable in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

MAX_NUM_CACHED_OBJECTS_KINETOGRAM - Static variable in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

MAX_NUM_VIEW_HISTORY_ENTRIES - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

MAX_ORDINATE_PILEUP - Static variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

MAX_ORDINATE_PILEUP - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

MAX_PACBIO_MAP_QV_VALID_RANGE - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

MAX_RAINBOW_COLOR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette

max_read_length - Variable in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo

MAX_REQUEST_KINETOGRAM_LENGTH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

MAX_REQUEST_REFERENCE_LENGTH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

MAX_TEXT_FILE_ROW_LENGTH - Static variable in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

MAX_TRACK_HEIGHT - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails

MAX_TRACK_HEIGHT - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion

max_variants - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue

MAX_VIEW_RANGE_EXTRA - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

maxDouble(Iterator<Double>) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

maximize(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Extends the size of this dockable to fill the docking panel.

maximizeAction - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

maximizeAction() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab

MaximizedDockView - Class in pub.vlsolutions.swing.docking

A dockView suitable for maximized dockables

MaximizedDockView(Dockable) - Constructor for class pub.vlsolutions.swing.docking.MaximizedDockView

MaximizedDockViewAsTab - Class in pub.vlsolutions.swing.docking

A maximized view to use with the TabFactory.

MaximizedDockViewAsTab(Dockable) - Constructor for class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab

MaximizedDockViewAsTab.MaximizedTabHeader - Class in pub.vlsolutions.swing.docking

MaximizedDockViewAsTab.MaximizedTabHeader() - Constructor for class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab.MaximizedTabHeader

maximizeFrame(Frame) - Static method in class com.pacbio.secondary.vis.common.utils.GUIUtils

maximizeSmartIcon - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

maximumLayoutSize(Container) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout

maximumLayoutSize(Container) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout

maximumLayoutSize(Container) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout

maximumLayoutSize(Container) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout

maxWidth - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

mc - Variable in class com.pacbio.secondary.vis.data.base.BaseDataModel

mean_coverage - Variable in class com.pacbio.secondary.vis.data.db.MotifData

mean_ipd - Variable in class com.pacbio.secondary.vis.data.db.MotifData

mean_score - Variable in class com.pacbio.secondary.vis.data.db.MotifData

menuAddTracks - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuAddTracksFromServer - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuAutoFitTableView - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuBookmarks - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuDecreaseDNASize - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuDecreaseKinetogramSize - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuDecreaseTrackSize - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuDefaultScale - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuExit - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuExportMarkers - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuFitViewsToPanels - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuGoToDevnet - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuGoToLocation - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuGoToPacBio - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuGroupFile - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuGroupHelp - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuGroupTools - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuGroupView - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuGroupWindow - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuHelpAbout - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuHelpContent - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuIncreaseDNASize - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuIncreaseKinetogramSize - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuIncreaseTrackSize - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuInstallShortcut - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuLargeFont - Static variable in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel

menuLayoutAnnotate - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuLayoutDefault - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuLayoutDetails - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuLayoutOverview - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuLinkGenomeRegionPanels - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuLinkRegionDetailsPanels - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuLockRegionGenomicRangeM - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuLockRegionGenomicRangeS - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuMediumFont - Static variable in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel

menuNew - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuOpenJobDataFromServer - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuPanLeft - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuPanRight - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuPreviousScale - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuPrint - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuPrintSettings - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuProgramOptions - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuRemoveTrack - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuResetView - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuSaveAsGraphics - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuSaveSession - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuSelectNext - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuSelectPrevious - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuSessionInfo - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuShowAllInTableView - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuShowContigLabels - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuShowDetailsInTableView - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuShowMarkerLabels - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuShowRegionInTableView - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuShowTracks - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuSmallFont - Static variable in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel

menuViewInsertions - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuZoomBases - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuZoomIn - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

menuZoomOut - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

merge(int, int, int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.MergeSort

merger - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

MergeSort - Class in com.pacbio.secondary.vis.gui.control.treetable

An implementation of MergeSort, needs to be subclassed to compare the terms.

MergeSort() - Constructor for class com.pacbio.secondary.vis.gui.control.treetable.MergeSort

mergeSort(int, int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.MergeSort

message - Static variable in class com.pacbio.secondary.vis.io.hdf.file.bash5.BaseH5FileBase

MessageUtils - Class in com.pacbio.secondary.vis.common.utils

MessageUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.MessageUtils

METADATA_CACHE_EXTENSION - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

MetadataInfoParser - Class in com.pacbio.secondary.vis.svc.server.data.parser

MetadataInfoParser(String, int) - Constructor for class com.pacbio.secondary.vis.svc.server.data.parser.MetadataInfoParser

metrics - Variable in class com.pacbio.secondary.vis.data.contig.DeNovoContigInfo

MID_BASE_MODS_THRESHOLD - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

min - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

min_coverage_no_structures - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

min_coverage_with_structures - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

MIN_DELTA_FORCE_UPDATE_AFTER_ZOOM - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

MIN_DNA_FONT_HEIGHT - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

MIN_EXTRA_DELTA_ADD_RANGE_REQUEST - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

min_field - Variable in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

min_gff_chunk_lenght - Static variable in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

MIN_HALF_DATA_ON_DEMAND_REQUEST - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

MIN_IPD_CONSENSUS_TRACK_HEIGHT - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

min_ipdratio_plot - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails

MIN_LINES_FOR_DATA_HEAVY - Static variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

MIN_MAP_QV_VALID_RANGE - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

min_max_values - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

min_max_values - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

MIN_RAINBOW_COLOR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette

MIN_RANGE_REFERENCE_OR_IPD_REQUEST - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

MIN_TRACK_HEIGHT - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails

MIN_TRACK_HEIGHT - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion

MIN_VIEW_RANGE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

minDouble(Iterator<Double>) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

minimumLayoutSize(Container) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout

minimumLayoutSize(Container) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout

minimumLayoutSize(Container) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout

minimumLayoutSize(Container) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout

minorOrder - Variable in class pub.vlsolutions.swing.toolbars.ToolBarConstraints

The minor order is the column index for horizontal toolbars, and the row index for vertical toolbars.

minViewGenomicRange - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

minWidth - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

mode - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

model_annotations - Variable in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

model_interval - Variable in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

model_track - Variable in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

MODIFICATION_CONFIDENCE_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

MODIFICATION_COVERAGE_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

MODIFICATION_FRAC_MODIFIED - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

MODIFICATION_IPDRATIO_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

MODIFICATION_TYPE_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

mods_filter_threshold - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

MODS_FILTER_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

MODS_VALUE_CONTEXT_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

MODS_VALUE_COVERAGE_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

MODS_VALUE_FRAC_MOD_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

MODS_VALUE_ID_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

MODS_VALUE_IDENT_QV_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

MODS_VALUE_IPD_RATIO_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

MODS_VALUE_MOTIF_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

molid - Variable in class com.pacbio.secondary.vis.data.read.ReadInfo

molid - Variable in class com.pacbio.secondary.vis.svc.server.data.WsRead

motif - Variable in class com.pacbio.secondary.vis.data.db.MotifData

motif_group - Variable in class com.pacbio.secondary.vis.data.db.MotifData

motif_partner - Variable in class com.pacbio.secondary.vis.data.db.MotifData

MotifData - Class in com.pacbio.secondary.vis.data.db

stores stats about a motif

MotifData() - Constructor for class com.pacbio.secondary.vis.data.db.MotifData

motifID(float) - Static method in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

motifs - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

MOTIFS_CENTERPOS_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

motifs_db - Variable in class com.pacbio.secondary.vis.data.db.MotifsDB

motifs_db - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase

motifs_db - Variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MOTIFS_FRACTION_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MOTIFS_GROUP_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

motifs_map - Variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

MOTIFS_MEANCOVERAGE_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MOTIFS_MEANIPDRATIO_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MOTIFS_MEANSCORE_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MOTIFS_NDETECTED_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MOTIFS_NGENOME_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MOTIFS_OBJSCORE_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MOTIFS_PANEL_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

MOTIFS_PANEL_TOOLTIP - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

MOTIFS_PARTNER_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MOTIFS_STRING_TAG - Static variable in class com.pacbio.secondary.vis.io.motifs.MotifsReader

MotifsDB - Class in com.pacbio.secondary.vis.data.db

stores motif summary data

MotifsDB() - Constructor for class com.pacbio.secondary.vis.data.db.MotifsDB

MotifsReader - Class in com.pacbio.secondary.vis.io.motifs

reads motifs_summary.csv into motifs database

MotifsReader() - Constructor for class com.pacbio.secondary.vis.io.motifs.MotifsReader

mouseClicked(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewMouseListener

mouseClicked(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel.DeNovoTablePanelMouseListener

mouseClicked(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel.GenomicTablePanelMouseListener

double click event handler

mouseClicked(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel.SelectionInfoPanelMouseListener

mouseClicked(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIconManager

MouseListener implementation, not used.

mouseDragged(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewMouseMotionListener

mouseDragged(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIconManager

MouseMotionListener implementation, not used.

mouseEntered(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIconManager

MouseListener implementation, not used.

mouseExited(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIconManager

MouseListener implementation, use to track mouse behaviour inside the tab selector bounds and forward them to the appropriate smart icon.

mouseMoved(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewMouseMotionListener

mouseMoved(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect.GenomicViewInspectMouseMotionListener

mouseMoved(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIconManager

MouseListener implementation, use to track mouse behaviour inside the tab selector bounds and forward them to the appropriate smart icon.

mousePressed(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewMouseListener

mousePressed(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel.DeNovoTablePanelMouseListener

mousePressed(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel.GenomicTablePanelMouseListener

mousePressed(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel.SelectionInfoPanelMouseListener

mousePressed(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIconManager

MouseListener implementation, use to track mouse behaviour inside the tab selector bounds and forward them to the appropriate smart icon.

mouseReleased(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewMouseListener

mouseReleased(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel.DeNovoTablePanelMouseListener

mouseReleased(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel.GenomicTablePanelMouseListener

mouseReleased(MouseEvent) - Method in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel.SelectionInfoPanelMouseListener

mouseReleased(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIconManager

MouseListener implementation, use to track mouse behaviour inside the tab selector bounds and forward them to the appropriate smart icon.

move(Dockable, Dockable, DockingConstants.Split) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Moves a dockable to another position (relative to a destination dockable)

movie_frame_rates - Variable in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

movie_names_info - Variable in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

MULTI_CHROMOSOMES_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

MULTI_CHROMOSOMES_VIEW_PANEL_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

MULTI_CHROMOSOMES_VIEW_PANEL_TOOLTIP - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

MultiIterator<T> - Class in com.pacbio.secondary.vis.common.collection

Iterates over multiple iterators

MultiIterator(Iterator<T>[]) - Constructor for class com.pacbio.secondary.vis.common.collection.MultiIterator

multisample_enabled - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase

MULTISAMPLE_VARIANTS_SAMPLE_IDX_MASK - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

MULTISAMPLE_VARIANTS_TYPE_MASK - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

MY_QNAME - Static variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse

N

n_detected - Variable in class com.pacbio.secondary.vis.data.db.MotifData

n_genome - Variable in class com.pacbio.secondary.vis.data.db.MotifData

NA - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

name - Variable in class com.pacbio.secondary.vis.data.contig.ContigInfo

name - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFile

name - Variable in class com.pacbio.secondary.vis.svc.server.data.WsRead

NAMED_SERVERS_WHITELIST - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

NCBI_REFSEQ_GENES_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

newline - Variable in class com.pacbio.secondary.vis.gui.control.VioletToolBarTest

next() - Method in class com.pacbio.secondary.vis.common.collection.MultiIterator

next() - Method in class com.pacbio.secondary.vis.common.collection.SortedMultiIterator

next() - Method in class com.pacbio.secondary.vis.common.collection.SweepLineIterator

Do NOT change the return value!!

next() - Method in class com.pacbio.secondary.vis.common.collection.UndoIterator

nextAll() - Method in class com.pacbio.secondary.vis.common.collection.SortedMultiIterator

nf - Variable in class com.pacbio.secondary.vis.common.utils.PerformanceUtils

nf - Variable in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel

nf - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel

no_data_msg - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

NO_MORE_WORK - Static variable in class com.pacbio.secondary.vis.svc.server.threads.VisThreadPool

noDataFound() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

nodes - Variable in class com.pacbio.secondary.vis.data.graph.GraphPrimitive

noDNAAnnotation - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

normalCursor() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

Sets the current mouse cursor to a normal cursor.

num_bases - Variable in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics

num_chunks - Variable in class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer

num_columns - Variable in class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray

num_columns - Variable in class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer

num_reads - Variable in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics

num_repeats - Variable in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics

NUM_RESULTS - Variable in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

NUM_RESULTS - Variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader

NUM_RESULTS - Static variable in class com.pacbio.secondary.vis.io.ucsc.gtf.reader.UCSCGTFReader

NUM_RESULTS - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

NUM_RESULTS - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFReader

num_rows - Variable in class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray

num_rows - Variable in class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer

num_total_rows - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations

num_tracks - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper

numNodes() - Method in class com.pacbio.secondary.vis.data.graph.GraphPrimitive

numPrimitives() - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure

O

obj_score - Variable in class com.pacbio.secondary.vis.data.db.MotifData

OLD_EXTENSION - Static variable in class com.pacbio.secondary.vis.update.SMRTViewUpdater

onClose() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx

close dialog

onEscClose() - Method in class com.pacbio.secondary.vis.gui.dialogs.PrintOptionsDialog

onEscClose() - Method in class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog

onEscClose() - Method in class com.pacbio.secondary.vis.gui.dialogs.SMRTViewDialog

do any required cleanup in derived classes when dialog closes by pressing esc

onFrameClosing() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

onFrameCreated() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

onFrameStateChanged(int, int) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

onMouseExited(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

Process the mouse exited event.

onMouseMoved(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

Process the mouse moved event.

onMousePressed(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

Process the mouse pressed event.

onMouseReleased(MouseEvent) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

Process the mouse released event.

OPEN_REMOTEDATA_NO_ERROR - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase

openPage(URL) - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserEditorPane

OpenRemoteDataHelper - Class in com.pacbio.secondary.vis.gui.dialogs

OpenRemoteDataHelper(VioletApp, String) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.OpenRemoteDataHelper

openROIsFile() - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog

openURL(VioletAppBase, URL) - Static method in class com.pacbio.secondary.vis.common.utils.WebBrowserUtils

out_queue - Variable in class com.pacbio.secondary.vis.svc.server.threads.VisWorkSenderThread

output - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

P

PACBIO_DEVNET_URL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

PACBIO_HOME_URL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

pack(FloatingDockableContainer) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities

packs a detached dockable, regardless of its type (frame or dialog)

pageFormat - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

paint(Graphics) - Method in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable.TreeTableCellRenderer

Sublcassed to translate the graphics such that the last visible row will be drawn at 0,0.

paint(Graphics) - Method in class com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer.EpiProPaletteDisplay

paint(Graphics) - Method in class pub.vlsolutions.swing.docking.SplitContainer

overriden for a bug workaround reason

paint(Graphics, JComponent) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonUI

Overriden to paint properly the button on vertical sides.

paint(Graphics, JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

Custom title bar painting : uses a gradient from the background color to the control highlight color.

paint(Graphics, JComponent) - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripperUI

Paints gripper dots

paint(Graphics, JComponent) - Method in class pub.vlsolutions.swing.toolbars.VLButtonUI

PAINT_PANEL_BACKGROUND - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants

PAINT_USING_DECORATED_FRAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

paintActiveBorder(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

Draws a frame around this ideogram if its active.

paintBackground(JComponent, Graphics) - Method in interface pub.vlsolutions.swing.toolbars.BackgroundPainter

paintBorder(Component, Graphics, int, int, int, int) - Method in class pub.vlsolutions.swing.docking.ShadowBorder

paintBorder(Component, Graphics, int, int, int, int) - Method in class pub.vlsolutions.swing.toolbars.RoundedBorder

paintBorder(Component, Graphics, int, int, int, int) - Method in class pub.vlsolutions.swing.toolbars.ToolBarButtonBorder

paintBorder(Component, Graphics, int, int, int, int) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelBorder

paintBuffer - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

paintBufferValid - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

paintComponent(Graphics) - Method in class com.pacbio.secondary.vis.gui.control.PaletteCtrl

draw dual palette for kinetics

paintComponent(Graphics) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

paintComponent(Graphics) - Method in class com.pacbio.secondary.vis.gui.panels.WholeGenomePanel

paintComponent(Graphics) - Method in class pub.vlsolutions.swing.docking.DragControlerGlassPane

paintComponent(Graphics) - Method in class pub.vlsolutions.swing.docking.FloatingDialog.Resizer

paintComponent(Graphics) - Method in class pub.vlsolutions.swing.docking.FloatingDialog.TitlePanel

paintComponent(Graphics) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanel

Overriden for optional background painting

paintIcon(Component, Graphics, int, int) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

paints the icon (and the associated label and sub-icons)

paintIcon(Component, Graphics, int, int) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

paints the appropriate icon according to its internal state (pressed, rollover...)

paintIcon(Component, Graphics, int, int) - Method in class pub.vlsolutions.swing.toolbars.RolloverIcon

paintLegendBackground(Graphics, int, int, int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

paintTabBorder(Graphics, int, int, int, int, int, int, boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.AlignedTabbedPaneUI

this function draws the border around each tab note that this function does now draw the background of the tab.

paintText(Graphics, int, Font, FontMetrics, int, String, Rectangle, boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.AlignedTabbedPaneUI

palette - Variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette

palette - Variable in class com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer.EpiProPaletteDisplay

palette_display - Variable in class com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer

PaletteCtrl - Class in com.pacbio.secondary.vis.gui.control

Palette control to use in dialogs

PaletteCtrl(GenomicViewDetails) - Constructor for class com.pacbio.secondary.vis.gui.control.PaletteCtrl

panel_status_text - Variable in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase

PanelConstants - Class in com.pacbio.secondary.vis.common.utils.constants

Names of dockable panels.

PanelConstants() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

PARAM_SEPARATOR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

parent - Variable in class com.pacbio.secondary.vis.data.interval.IntervalTreeNode

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parse(XMLStreamReader) - Static method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo.Factory

static method to create the object Precondition: If this object is an element, the current or next start element starts this object and any intervening reader events are ignorable If this object is not an element, it is a complex type and the reader is at the event just after the outer start element Postcondition: If this object is an element, the reader is positioned at its end element If this object is a complex type, the reader is positioned at the end element of its outer element

parseDeNovoSummaryFile(String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.DeNovoSummaryParser

parseGeneInfo(Vector<String>, Vector<String>, String) - Method in class com.pacbio.secondary.vis.data.db.GeneDB

parseInfoFile(String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.TrackInfoParser

parseReferenceFile(String) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser

parseTemplateInfo(ProgressDialog) - Method in class com.pacbio.secondary.vis.data.session.DataStorage

parseTracksInfo(String) - Method in class com.pacbio.secondary.vis.data.session.DataStorage

parseXmlFile(String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser

pattern - Variable in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel

pattern - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel

perf_name - Variable in class com.pacbio.secondary.vis.common.utils.PerformanceUtils

PerformanceUtils - Class in com.pacbio.secondary.vis.common.utils

performance timing utilities

PerformanceUtils(String) - Constructor for class com.pacbio.secondary.vis.common.utils.PerformanceUtils

PileUpContigResultsWithoutStructure(List<Marker>) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

PileUpResultsWithoutStructure(WsResults, List<WsRead>) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

PileUpResultsWithoutStructureForBaseMods(WsResults, List<WsRead>) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

PileUpResultsWithStructures(GenomicDataStructures.WsReadStructure[], WsResults, int, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

Pileup of results with graphics structures Supports CCS and strobe reads

popmenu - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

popup - Variable in class pub.vlsolutions.swing.docking.DockTabbedPane

The pop-up menu used to provide fast "close" shortcuts (close all, close others)

popupmenu - Variable in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog

popupmenu - Variable in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel

popupmenu - Variable in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

popupmenu - Variable in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel

popupTab - Variable in class pub.vlsolutions.swing.docking.DockTabbedPane

the tab currently associated with the pop-up

popView() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

postRequestToUpdateApplicationFrame() - Method in class com.pacbio.secondary.vis.data.session.DataStorage

postRequestToUpdateDetailsView() - Method in class com.pacbio.secondary.vis.data.session.DataStorage

postRequestToUpdateGenomicTableDetails() - Method in class com.pacbio.secondary.vis.data.session.DataStorage

preferences_dlg - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

PreferencesDialogBase - Class in com.pacbio.secondary.vis.gui.dialogs

PreferencesDialogBase(String) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

PreferencesDialogBase.JDoubleSlider - Class in com.pacbio.secondary.vis.gui.dialogs

private slider class

PreferencesDialogBase.JDoubleSlider(int, int, double, float) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase.JDoubleSlider

PreferencesDialogEx - Class in com.pacbio.secondary.vis.gui.dialogs

User preferences dialog

PreferencesDialogEx(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx

preferredLayoutSize(Container) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout

preferredLayoutSize(Container) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout

preferredLayoutSize(Container) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout

preferredLayoutSize(Container) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout

prepareDrawVariant(Graphics, Marker) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

prepareResults(WsResults, int, ArrayList<WsRead>, boolean, boolean, long, int, long, long, long) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder

pressedIcon - Variable in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

the icno for the pressed effect

PREVIOUS_ZOOM - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

previousFloatingDockableStates - Variable in class pub.vlsolutions.swing.docking.DockingDesktop

return state for floating dockables

previousSelectedDockable - Variable in class pub.vlsolutions.swing.docking.DockTabbedPane

The tab that was selected before the current one

primary - Variable in class com.pacbio.secondary.vis.data.read.EpiProReadInfo

primitives - Variable in class com.pacbio.secondary.vis.data.graph.GraphStructure

print(Graphics, PageFormat, int) - Method in class com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper

print(Graphics, PageFormat, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

PRINT_CONSENSUS_DETAILS - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

PRINT_HEADER_DETAILS - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

PRINT_KINETICS_DETAILS - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

PRINTABLE_CLIENT_PROGRAM_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

printDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog

print

printElapsedTimeToConsole(String) - Method in class com.pacbio.secondary.vis.common.utils.PerformanceUtils

printerJob - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

printHeaderFooter(Graphics2D, double, double, double, double) - Method in class com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper

printIndexes() - Method in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo

PrintOptionsDialog - Class in com.pacbio.secondary.vis.gui.dialogs

PrintOptionsDialog(JFrame, boolean, Boolean[]) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.PrintOptionsDialog

PrintOptionsDialog.myActionListener - Class in com.pacbio.secondary.vis.gui.dialogs

PrintOptionsDialog.myActionListener() - Constructor for class com.pacbio.secondary.vis.gui.dialogs.PrintOptionsDialog.myActionListener

printProgress(int, int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

printStatistics() - Method in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo

printStatistics(File, long, long, FileIndexInfo, long) - Method in class com.pacbio.secondary.vis.io.indexer.text.TextFileIndexer

printStatistics(String, long, int, long) - Method in class com.pacbio.secondary.vis.io.indexer.text.TextFileIndexer

printUsage() - Static method in class com.pacbio.secondary.vis.update.SMRTViewUpdater

Print usage string

processDockableDrag(DockDragEvent) - Method in class pub.vlsolutions.swing.docking.BorderSplitter

processDockableDrag(DockDragEvent) - Method in class pub.vlsolutions.swing.docking.CompoundDockingPanel

act the same as a splitContainer : allow drop on the borders

processDockableDrag(DockDragEvent) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton

when a dockable is dragged above this button, the button stores it as its new target dockable.

processDockableDrag(DockDragEvent) - Method in interface pub.vlsolutions.swing.docking.DockDropReceiver

The component is notified of a drag operation.

processDockableDrag(DockDragEvent) - Method in class pub.vlsolutions.swing.docking.DockingPanel

act the same as a splitContainer : allow drop on the borders

processDockableDrag(DockDragEvent) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane

processDockableDrag(DockDragEvent) - Method in class pub.vlsolutions.swing.docking.DockView

The component is notified of a drag operation.

processDockableDrag(DockDragEvent) - Method in class pub.vlsolutions.swing.docking.MaximizedDockView

maximized dockable don't support drag and drop

processDockableDrag(DockDragEvent) - Method in class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab

processDockableDrag(DockDragEvent) - Method in class pub.vlsolutions.swing.docking.SplitContainer

The component is notified of a drag operation.

processDockableDrop(DockDropEvent) - Method in class pub.vlsolutions.swing.docking.BorderSplitter

processDockableDrop(DockDropEvent) - Method in class pub.vlsolutions.swing.docking.CompoundDockingPanel

processDockableDrop(DockDropEvent) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton

Rejects the drop as this action isn't possible on this component

processDockableDrop(DockDropEvent) - Method in interface pub.vlsolutions.swing.docking.DockDropReceiver

The component is requested to perform a docking drop action.

processDockableDrop(DockDropEvent) - Method in class pub.vlsolutions.swing.docking.DockingPanel

processDockableDrop(DockDropEvent) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane

The component is requested to perform a docking drop action.

processDockableDrop(DockDropEvent) - Method in class pub.vlsolutions.swing.docking.DockView

The component is requested to perform a docking drop action.

processDockableDrop(DockDropEvent) - Method in class pub.vlsolutions.swing.docking.MaximizedDockView

maximized dockable don't support drag and drop

processDockableDrop(DockDropEvent) - Method in class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab

processDockableDrop(DockDropEvent) - Method in class pub.vlsolutions.swing.docking.SplitContainer

The component is requested to perform a docking drop action.

processPacBioVersion(String[], VariableValuesDataRecord) - Method in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

parses records in pacbio format

processReadRecord(VioletApp, String[], int) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

processSplitReadRecord(TreeMap<Integer, Integer>, ArrayList<Marker>, String[], int) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

processStreamingDataChunk(Object) - Method in class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer

this method receives a chunk of data as soon as it is read from the file

processStreamingDataChunk(Object) - Method in class com.pacbio.secondary.vis.io.hdf.streaming.UCharStreamingDataConsumer

This method receives a chunk of data as soon as it is read from the file.

processStreamingDataChunk(Object) - Method in class com.pacbio.secondary.vis.io.hdf.streaming.UIntStreamingDataConsumer

This method receives a chunk of data as soon as it is read from the file.

processVCFBaseRecord(String[], int) - Method in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

processes the base part of a vcf record, single sample

processVCFHeaderInfo(String) - Method in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

process fileheader, get version

processVCFMultiSampleRecord(VariableValuesDataRecord, String[]) - Method in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

processVCFSampleInfo(String) - Method in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

process sample info, eventually returns list of sample names

processVFCVersionInfo(String) - Method in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

get vcf version

prod(int, int) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

program_close_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

program_help_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

program_save_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

program_tab - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

ProgramConstants - Class in com.pacbio.secondary.vis.common.utils.constants

ProgramConstants() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

ProgramGlobals - Class in com.pacbio.secondary.vis.common.utils

ProgramGlobals() - Constructor for class com.pacbio.secondary.vis.common.utils.ProgramGlobals

ProgramUtils - Class in com.pacbio.secondary.vis.common.utils

ProgramUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.ProgramUtils

progress_interval_factor - Static variable in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

ProgressDialog - Class in com.pacbio.secondary.vis.gui.dialogs

progress dialog

ProgressDialog(boolean, boolean) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog

prolog - Variable in class com.pacbio.secondary.vis.data.read.EpiProReadInfo

PropertiesDialog - Class in com.pacbio.secondary.vis.gui.dialogs

Shows summary of loaded data, references and server connections

PropertiesDialog(Frame, String) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.PropertiesDialog

PropertiesHelper - Class in com.pacbio.secondary.vis.common.utils

App preferences and default properties

PropertiesHelper() - Constructor for class com.pacbio.secondary.vis.common.utils.PropertiesHelper

PROPERTY_AUTOHIDE - Static variable in class pub.vlsolutions.swing.docking.DockViewTitleBar

Property name designating the autohide button selection

PROPERTY_AUTOHIDEABLE - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the autohideEnabled property

PROPERTY_BORDERZONE - Static variable in class pub.vlsolutions.swing.docking.AutoHideButtonPanel

The property name associated with the "border" property

PROPERTY_CLOSEABLE - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the closeEnabled property

PROPERTY_CLOSED - Static variable in class pub.vlsolutions.swing.docking.DockViewTitleBar

Property name designating the close button selection

PROPERTY_DEFAULT_GAP - Static variable in class pub.vlsolutions.swing.docking.AutoHidePolicy

a constant designing the bound property DEFAULT_GAP

PROPERTY_DEFAULT_HIDE_BORDER - Static variable in class pub.vlsolutions.swing.docking.AutoHidePolicy

a constant designing the bound property DEFAULT_HIDE_BORDER

PROPERTY_DOCKABLE_STATE - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the dockable dockableState

PROPERTY_DOCKKEY - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the dockKey property

PROPERTY_DRAGGED - Static variable in class pub.vlsolutions.swing.docking.DockViewTitleBar

Property name designating a drag gesture beginning

PROPERTY_EXPAND_MODE - Static variable in class pub.vlsolutions.swing.docking.AutoHidePolicy

a constant designing the bound property EXPAND_MODE (enum type)

PROPERTY_EXPANDED - Static variable in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

Constant for the Expanded property (a bound property)

PROPERTY_EXPANSION_DURATION - Static variable in class pub.vlsolutions.swing.docking.AutoHidePolicy

a constant designing the bound property EXPANSION_DURATION

PROPERTY_FLOAT - Static variable in class pub.vlsolutions.swing.docking.DockViewTitleBar

Property name designating the float button selection

PROPERTY_FLOATABLE - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the floatableEnabled property

PROPERTY_ICON - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the icon property

PROPERTY_MAXIMIZABLE - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the maximizedEnabled property

PROPERTY_MAXIMIZED - Static variable in class pub.vlsolutions.swing.docking.DockViewTitleBar

Property name designating the maximized button selection

PROPERTY_NAME - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the name property

PROPERTY_NOTIFICATION - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the notification property

PROPERTY_ORIENTATION - Static variable in class pub.vlsolutions.swing.toolbars.ToolBarGripper

Id for the orientation property

PROPERTY_ROLLOVER_TRIGGER_DELAY - Static variable in class pub.vlsolutions.swing.docking.AutoHidePolicy

a constant designing the bound property ROLLOVER_TRIGGER_DELAY

PROPERTY_TAB_NAME - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the tabname property (title used by tabbed containers)

PROPERTY_TOOLTIP - Static variable in class pub.vlsolutions.swing.docking.DockKey

Key identifying a change in the tooltip property

PROPERTY_ZONE - Static variable in class pub.vlsolutions.swing.docking.AutoHideButton

property name associated to the "zone" (border) property

propertyChange(PropertyChangeEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

propertyChange(PropertyChangeEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog

propertyChange(PropertyChangeEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx

propertyChange(PropertyChangeEvent) - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel

propertyChange(PropertyChangeEvent) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonPanelUI

propertyChange(PropertyChangeEvent) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonUI

propertyChange(PropertyChangeEvent) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

Listen to property changes in the DockKey or the title bar

propertyChange(PropertyChangeEvent) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Do not call directly as it a side effect of listening to the action changes.

pub.vlsolutions.swing.docking - package pub.vlsolutions.swing.docking

Dockable windows framework

pub.vlsolutions.swing.docking.animation - package pub.vlsolutions.swing.docking.animation

Dockable windows framework

pub.vlsolutions.swing.docking.event - package pub.vlsolutions.swing.docking.event

Dockable windows framework

pub.vlsolutions.swing.docking.ui - package pub.vlsolutions.swing.docking.ui

Dockable windows framework

pub.vlsolutions.swing.docking.ws - package pub.vlsolutions.swing.docking.ws

Dockable windows framework

pub.vlsolutions.swing.tabbedpane - package pub.vlsolutions.swing.tabbedpane

Dockable windows framework

pub.vlsolutions.swing.toolbars - package pub.vlsolutions.swing.toolbars

Dockable windows framework

pushView() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

putDockableContraints(Dockable, AnchorConstraints) - Method in class pub.vlsolutions.swing.docking.AnchorManager

Associates an anchor constraints to a given dockable

putFile(String, byte[]) - Method in class com.pacbio.secondary.vis.svc.server.VisService

generic method to write bits to file on server

putFile(VisServiceStub.PutFile) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature

putProperty(String, Object) - Method in class pub.vlsolutions.swing.docking.DockKey

Allows any property to be stored in a map associated with this dockkey.

Q

quantile(Vector<T>, Comparator<T>, float) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

quantile(double[], double) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

Query(Interval, byte, byte) - Method in class com.pacbio.secondary.vis.data.interval.IntervalTreeQuery

Finds all node intersecting the given Interval interval and with a level between minLevel and maxLevel.

queue - Variable in class com.pacbio.secondary.vis.svc.server.threads.VisWorkDoneQueue

queue - Variable in class com.pacbio.secondary.vis.svc.server.threads.VisWorkToDoQueue

qv - Variable in class com.pacbio.secondary.vis.svc.server.data.WsRead

qv_close_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

qv_column_index - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations

QV_DRIVEN_INCREMENT_FACTOR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants

qv_help_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

qv_save_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

qv_tab - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

qv_thresholds_panel - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

QVThresholdOptionsPane - Class in com.pacbio.secondary.vis.gui.dialogs

Options panel for QV annotations

QVThresholdOptionsPane(TableModelListener, GenomicViewDetails) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.QVThresholdOptionsPane

R

RANGE_START - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

rangeSelection - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

rank - Variable in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo

raw_read - Variable in class com.pacbio.secondary.vis.io.hdf.data.RawRead

RawRead - Class in com.pacbio.secondary.vis.io.hdf.data

raw, encoded read as stored inside cmph5

RawRead() - Constructor for class com.pacbio.secondary.vis.io.hdf.data.RawRead

RDF_INFO_HAS_DATA - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

RDF_INFO_NODE_ABOUT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

RDF_INFO_NODE_DESCRIPTION - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

RDF_INFO_NODE_RESOURCE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

RDF_INFO_NODE_TITLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

RDF_INFO_SMRTOWL_LOCAL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

RDF_INFO_USES_REFERENCE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

RDF_JOB_METADATA_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

read(ReferenceInfo, Reader, String, IProgressNotifier) - Method in class com.pacbio.secondary.vis.data.db.GeneDB

Loads a gene database from a stream.

READ_CONSENSUS - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

read_group_info - Variable in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

read_group_path - Variable in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo

read_group_path_id - Variable in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo

READ_HEADER - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

read_ipd - Variable in class com.pacbio.secondary.vis.io.hdf.data.RawRead

READ_KINETICS - Static variable in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

read_metrics - Variable in class com.pacbio.secondary.vis.io.hdf.data.RawRead

read_num_annotations - Variable in class com.pacbio.secondary.vis.io.indexer.indexinfo.GFFIndexInfo

read_qv - Variable in class com.pacbio.secondary.vis.io.hdf.data.RawRead

read_qv - Variable in class com.pacbio.secondary.vis.io.indexer.indexinfo.GFFIndexInfo

read_type - Variable in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

readApplicationProperties() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

Read generic app properties

readCmpH5ReferenceInfo() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

reads reference info from file and stores in local arraylist

readContigFeature(DeNovoSummaryStorage, String[], TreeMap<Integer, Integer>) - Method in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader

parses a denovo contig record

readDataset(BaseH5FileBase, String) - Static method in class com.pacbio.secondary.vis.io.hdf.file.bash5.BaseH5FileBase

readDatasetHyperslab(H5ScalarDS, HDF5HyperslabInfo) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

Reads the data from file to a memory buffer and returns the memory buffer.

readDetailsOptionsFromPropertiesFile() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

readDetailsOptionsFromSession() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO

read details options from user session file

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.io.gff.GFF3Reader

Loads a marker collection from a stream.

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

Loads base mods or motifs info

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader

Loads summary information

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader

Loads variants info

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.io.motifs.MotifsReader

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.io.ucsc.gtf.reader.UCSCGTFReader

Loads a marker collection from a stream.

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

readElements(VioletApp, Reader) - Method in class com.pacbio.secondary.vis.io.vcf.VCFReader

readFastaSequenceFromReader(Reader, int) - Method in class com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer

read and parse at once....

readFileAsString(File) - Static method in class com.pacbio.secondary.vis.update.UpdaterUtils

readFileInfoFromCacheFile(String, int, int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

readIdeogramData(Reader, IProgressNotifier) - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB

readIdeogramProperties(IdeogramDB) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

readImageFromByteArray(byte[]) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils

ReadInfo - Class in com.pacbio.secondary.vis.data.read

Local storage class for read info

ReadInfo() - Constructor for class com.pacbio.secondary.vis.data.read.ReadInfo

serialization only

ReadInfo(WsRead) - Constructor for class com.pacbio.secondary.vis.data.read.ReadInfo

readJNLPTemplateFromResource(String, boolean) - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper

Retrieves the jnlp template from the jar file

readJNLPTemplateFromResource(String) - Method in class com.pacbio.secondary.vis.update.SMRTViewUpdater

Retrieves the jnlp template from the jar file

ReadLengthPalette - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

READLN_MAX_LENGHT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

READLN_PALETTE_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

readMotifsFile(VioletApp, String) - Method in class com.pacbio.secondary.vis.data.db.MotifsDB

readMotifSummaryFile() - Method in class com.pacbio.secondary.vis.data.session.DataStorage

reads from motif_summary.csv file

readProperties() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO

read options now

readRegionFeature(String[], Vector<String>, Vector<String>, Vector<String>, TreeMap<Integer, Integer>) - Method in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader

Parses a standard region record

readROIsDataFromByteArray(byte[]) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

readROIsFromFile(Component, VioletApp, File) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

reads - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResults

reads - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

READS_FOR_BASE_MODS - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

READS_SEPARATE_STRANDS - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

READS_UPDATE_DATA_REQUEST - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

READS_WITH_INSERTIONS - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

READS_WITHOUT_STRUCTURES - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

readSessionData(File) - Static method in class com.pacbio.secondary.vis.data.session.SessionDataHelper

readSessionDataFromByteArray(byte[]) - Static method in class com.pacbio.secondary.vis.data.session.SessionDataHelper

readSpecialFiles() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

readUnsignedDatasetHyperslab(H5ScalarDS, HDF5HyperslabInfo) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

A convenient but not memory-efficient method to read a hyperslab of unsigned integers.

readWorkspaceFromResource(String) - Method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager

readXML(InputStream) - Method in class pub.vlsolutions.swing.docking.DockingContext

Reads an XML encoded stream as the new desktop configuration.

readXML(InputStream) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Reads an XML encoded stream as the new desktop configuration.

readXML(InputStream) - Method in class pub.vlsolutions.swing.docking.ws.Workspace

readXML(InputStream) - Method in class pub.vlsolutions.swing.toolbars.ToolBarIO

Reads an XML encoded stream as the toolbar configuration.

readXMLObject(File) - Static method in class com.pacbio.secondary.vis.common.utils.XMLObjectSerializerUtils

Loads an object from an XML file (using XStreamer).

readXMLObject(byte[]) - Static method in class com.pacbio.secondary.vis.common.utils.XMLObjectSerializerUtils

Loads an object from a byte array

rebuildAllViewsMarkerCollectionsAndUpdateViews() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO

receiveErrorgetAnnotatedInsertions(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getAnnotatedInsertions operation

receiveErrorgetAnnotatedInsertions(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

error response from getAnnotatedInsertions operation

receiveErrorgetAnnotatedResults(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getAnnotatedResults operation

receiveErrorgetAnnotatedResults(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

error response from getAnnotatedResults operation

receiveErrorgetConsensusSequence(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getConsensusSequence operation

receiveErrorgetConsensusSequence(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

error response from getConsensusSequence operation

receiveErrorgetContigNames(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getContigNames operation

receiveErrorgetDefaultDirectory(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getDefaultDirectory operation

receiveErrorgetDirectoryList(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getDirectoryList operation

receiveErrorgetFastaSequence(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getFastaSequence operation

receiveErrorgetFastaSequence(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceCallbackImpl

Error handler method for getFastaSequence

receiveErrorgetFile(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getFile operation

receiveErrorgetFile(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceCallbackImpl

Error handler for getFile method

receiveErrorgetFileHeader(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getFileHeader operation

receiveErrorgetFilesInformation(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getFilesInformation operation

receiveErrorgetGZippedFile(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getGZippedFile operation

receiveErrorgetGZippedFile(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceCallbackImpl

Error handler for getGZippedFile method

receiveErrorgetIPDConsensus(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getIPDConsensus operation

receiveErrorgetIPDConsensus(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

error response from getIPDConsensus operation

receiveErrorgetMetadataInfo(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getMetadataInfo operation

receiveErrorgetReferenceInfo(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getReferenceInfo operation

receiveErrorgetServiceExperienceIndex(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getServiceExperienceIndex operation

receiveErrorgetServiceInfo(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getServiceInfo operation

receiveErrorgetServiceInfo(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getServiceInfo operation

receiveErrorgetTracksListInfo(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from getTracksListInfo operation

receiveErrorputFile(Exception) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 Error handler override this method for handling error response from putFile operation

receiveResultgetAnnotatedInsertions(HDFServiceStub.GetAnnotatedInsertionsResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 call back method for getAnnotatedInsertions method override this method for handling normal response from getAnnotatedInsertions operation

receiveResultgetAnnotatedInsertions(HDFServiceStub.GetAnnotatedInsertionsResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

normal response from getAnnotatedInsertions operation

receiveResultgetAnnotatedResults(HDFServiceStub.GetAnnotatedResultsResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 call back method for getAnnotatedResults method override this method for handling normal response from getAnnotatedResults operation

receiveResultgetAnnotatedResults(HDFServiceStub.GetAnnotatedResultsResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

normal response from getAnnotatedResults operation

receiveResultgetConsensusSequence(HDFServiceStub.GetConsensusSequenceResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 call back method for getConsensusSequence method override this method for handling normal response from getConsensusSequence operation

receiveResultgetConsensusSequence(HDFServiceStub.GetConsensusSequenceResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

normal response from getConsensusSequence operation

receiveResultgetContigNames(HDFServiceStub.GetContigNamesResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 call back method for getContigNames method override this method for handling normal response from getContigNames operation

receiveResultgetDefaultDirectory(VisServiceStub.GetDefaultDirectoryResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getDefaultDirectory method override this method for handling normal response from getDefaultDirectory operation

receiveResultgetDirectoryList(VisServiceStub.GetDirectoryListResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getDirectoryList method override this method for handling normal response from getDirectoryList operation

receiveResultgetFastaSequence(VisServiceStub.GetFastaSequenceResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getFastaSequence method override this method for handling normal response from getFastaSequence operation

receiveResultgetFastaSequence(VisServiceStub.GetFastaSequenceResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceCallbackImpl

call back method for getFastaSequence

receiveResultgetFile(VisServiceStub.GetFileResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getFile method override this method for handling normal response from getFile operation

receiveResultgetFile(VisServiceStub.GetFileResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceCallbackImpl

call back for getFile method

receiveResultgetFileHeader(HDFServiceStub.GetFileHeaderResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 call back method for getFileHeader method override this method for handling normal response from getFileHeader operation

receiveResultgetFilesInformation(VisServiceStub.GetFilesInformationResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getFilesInformation method override this method for handling normal response from getFilesInformation operation

receiveResultgetGZippedFile(VisServiceStub.GetGZippedFileResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getGZippedFile method override this method for handling normal response from getGZippedFile operation

receiveResultgetGZippedFile(VisServiceStub.GetGZippedFileResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceCallbackImpl

call back for getGZippedFile method

receiveResultgetIPDConsensus(HDFServiceStub.GetIPDConsensusResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 call back method for getIPDConsensus method override this method for handling normal response from getIPDConsensus operation

receiveResultgetIPDConsensus(HDFServiceStub.GetIPDConsensusResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

normal response from getIPDConsensus operation

receiveResultgetMetadataInfo(VisServiceStub.GetMetadataInfoResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getMetadataInfo method override this method for handling normal response from getMetadataInfo operation

receiveResultgetReferenceInfo(VisServiceStub.GetReferenceInfoResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getReferenceInfo method override this method for handling normal response from getReferenceInfo operation

receiveResultgetServiceExperienceIndex(HDFServiceStub.GetServiceExperienceIndexResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 call back method for getServiceExperienceIndex method override this method for handling normal response from getServiceExperienceIndex operation

receiveResultgetServiceInfo(HDFServiceStub.GetServiceInfoResponse) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler

auto generated Axis2 call back method for getServiceInfo method override this method for handling normal response from getServiceInfo operation

receiveResultgetServiceInfo(VisServiceStub.GetServiceInfoResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getServiceInfo method override this method for handling normal response from getServiceInfo operation

receiveResultgetTracksListInfo(VisServiceStub.GetTracksListInfoResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for getTracksListInfo method override this method for handling normal response from getTracksListInfo operation

receiveResultputFile(VisServiceStub.PutFileResponse) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler

auto generated Axis2 call back method for putFile method override this method for handling normal response from putFile operation

REF_INDEX_TAG_REFERENCE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INDEX_TAG_REFERENCE_ID - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INDEX_TAG_REFERENCE_METADATA - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INFO_CONTIG_ELEMENT_CONTIG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INFO_CONTIG_ELEMENT_CONTIGS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INFO_CONTIG_ELEMENT_HEADER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INFO_CONTIG_ELEMENT_LENGTH - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INFO_ELEMENT_MAX_CONTIG_LEN - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INFO_ELEMENT_NUM_CONTIGS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INFO_TAG_DESCRIPTION - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INFO_TAG_IDEOGRAM - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

REF_INFO_TAG_REFERENCE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

ref_seq_id - Variable in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo

ref_seq_name - Variable in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo

reference_data - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

reference_info - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase

reference_info - Variable in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

reference_request_queue - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

ReferenceInfo - Class in com.pacbio.secondary.vis.data.xmlinfo

ReferenceInfo(VisServiceStub.WsReferenceInfo) - Constructor for class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

ReferenceInfo(WsReferenceInfo) - Constructor for class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

ReferenceInfoParser - Class in com.pacbio.secondary.vis.svc.server.data.parser

ReferenceInfoParser(String) - Constructor for class com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser

REFERENCES_INDEX_XML_FILE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

ReferenceSequenceStorage - Class in com.pacbio.secondary.vis.data.session

ReferenceSequenceStorage() - Constructor for class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage

reflectUpdatedDetailsRange() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion

refreshPanel() - Method in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel

region_interval - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper

REGION_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

region_scroller - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

region_tracks_height - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper

region_view - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

REGION_VIEW_PANEL_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

REGION_VIEW_PANEL_TOOLTIP - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

regions - Variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

RegionsOfInterestDialog - Class in com.pacbio.secondary.vis.gui.dialogs

RegionsOfInterestDialog(VioletApp, RegionsOfInterestStorage) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog

RegionsOfInterestDialog.BookmarksEditorPane - Class in com.pacbio.secondary.vis.gui.dialogs

internal class with custom tooltips

RegionsOfInterestDialog.BookmarksEditorPane() - Constructor for class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog.BookmarksEditorPane

RegionsOfInterestDialog.RegionsOfInterestHyperlinkListener - Class in com.pacbio.secondary.vis.gui.dialogs

RegionsOfInterestDialog.RegionsOfInterestHyperlinkListener() - Constructor for class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog.RegionsOfInterestHyperlinkListener

RegionsOfInterestStorage - Class in com.pacbio.secondary.vis.data.session

RegionsOfInterestStorage() - Constructor for class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

RegionsOfInterestStorage.RegionOfInterest - Class in com.pacbio.secondary.vis.data.session

RegionsOfInterestStorage.RegionOfInterest(String, String, byte[], byte[], byte[]) - Constructor for class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

RegionsOfInterestStorage.RegionOfInterest() - Constructor for class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

registerDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingContext

Every dockable must be registered in order to be managed by a DockingDesktop.

registerDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Every dockable must be registered in order to be shown in the DockingDesktop.

registeredDockables - Variable in class pub.vlsolutions.swing.docking.DockingContext

All dockables must be registered (even if not shown) in order to be processed by the XML Parser or to be displayed in the DockingSelectorDialog

registerToolBar(VLToolBar) - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer

Registers a new ToolBar.

rejectDrag() - Method in class pub.vlsolutions.swing.docking.event.DockDragEvent

Used to reject the drag (e.g.

rejectDrop() - Method in class pub.vlsolutions.swing.docking.event.DockDropEvent

It is still time to reject a drop, although the standard way is by denying the previous drag operation.

RelativeDockablePosition - Class in pub.vlsolutions.swing.docking

This class is an immutable object used to remember the relative positionning of docked components.

RelativeDockablePosition() - Constructor for class pub.vlsolutions.swing.docking.RelativeDockablePosition

Constructs an empty relative position (all fields are initialized with 0.0 values)

RelativeDockablePosition(double, double, double, double) - Constructor for class pub.vlsolutions.swing.docking.RelativeDockablePosition

Constructs a relative position with given location and size.

RelativeDockablePosition(Container, double, double, double, double) - Constructor for class pub.vlsolutions.swing.docking.RelativeDockablePosition

Constructs a relative position with a given location and size, relative to a container

RemoteFile - Class in com.pacbio.secondary.vis.data.filesystem

Represents information about a remote file

RemoteFile(String, String, boolean, long, long) - Constructor for class com.pacbio.secondary.vis.data.filesystem.RemoteFile

RemoteFileNode - Class in com.pacbio.secondary.vis.data.filesystem

RemoteFileNode(RemoteFile) - Constructor for class com.pacbio.secondary.vis.data.filesystem.RemoteFileNode

RemoteFileNode(VisServiceWrapper) - Constructor for class com.pacbio.secondary.vis.data.filesystem.RemoteFileNode

Special constructor for root filenode

RemoteFileSystemModel - Class in com.pacbio.secondary.vis.data.filesystem

RemoteFileSystemModel is a TreeTableModel representing a remote file system.

RemoteFileSystemModel(VioletApp, String, String) - Constructor for class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel

remove(int) - Method in class com.pacbio.secondary.vis.common.collection.ByteArrayList

Removes the element at the specified position in this list.

remove(int, int) - Method in class com.pacbio.secondary.vis.common.collection.ByteArrayList

Removes from this list all of the elements whose index is between fromIndex, inclusive and toIndex, exclusive.

remove() - Method in class com.pacbio.secondary.vis.common.collection.MultiIterator

remove() - Method in class com.pacbio.secondary.vis.common.collection.SortedMultiIterator

remove() - Method in class com.pacbio.secondary.vis.common.collection.SweepLineIterator

remove(Object) - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet

remove() - Method in class com.pacbio.secondary.vis.common.collection.UndoIterator

remove(AutoHideButton) - Method in class pub.vlsolutions.swing.docking.AutoHideButtonPanel

Removes an AutoHideButton

remove(Dockable) - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

Removes a dockable (if it was the currently expanded one)

remove(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Removes a visible dockable from the containment hierarchy (including autohide border buttons).

remove(Component) - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer

Overriden to keep track of component constraints

remove(int) - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer

Overriden to keep track of component constraints

remove(Component) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanel

removeAll() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkToDoQueue

removeAll() - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer

Overriden to keep track of component constraints

removeCellEditorListener(CellEditorListener) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor

removeChangeListener(ChangeListener) - Method in class com.pacbio.secondary.vis.common.collection.ChangeNotifier

removeChangeListener(ChangeListener) - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel

removeChangeListener(ChangeListener) - Method in interface com.pacbio.secondary.vis.gui.evt.IChangeNotifier

Removes the given listener from the list.

removeContainer(SingleDockableContainer) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Removes a dockable container.

removeDataAboveThreshold() - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

eventually remove reads and structures with lane above max coverage threshold

removeDataAboveThreshold(WsResults, List<WsRead>, int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder

eventually remove reads and structures with lane above max coverage threshold

removeDesktop(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockingContext

Removes a desktop from this context

removeDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane

Removes a dockable from the tabs

removeDockable(int) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane

Remove the dockable at specified index tab

removeDockable(Dockable) - Method in interface pub.vlsolutions.swing.docking.TabbedDockableContainer

Removes a dockable from the tabs

removeDockable(int) - Method in interface pub.vlsolutions.swing.docking.TabbedDockableContainer

Remove the dockable at specified index tab

removeDockableConstraints(Dockable) - Method in class pub.vlsolutions.swing.docking.AnchorManager

Removes an anchor constraints to a given dockable

removeDockableSelectionListener(DockableSelectionListener) - Method in class pub.vlsolutions.swing.docking.DockingContext

Removes a DockableSelectionListener from this desktop.

removeDockableSelectionListener(DockableSelectionListener) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Removes a DockableSelectionListener from this desktop.

removeDockableStateChangeListener(DockableStateChangeListener) - Method in class pub.vlsolutions.swing.docking.DockingContext

Removes a DockableStateChangeListener from this desktop.

removeDockableStateChangeListener(DockableStateChangeListener) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Removes a DockableStateChangeListener from this desktop.

removeDockableStateWillChangeListener(DockableStateWillChangeListener) - Method in class pub.vlsolutions.swing.docking.DockingContext

Removes a DockableStateWillChangeListener from this desktop.

removeDockableStateWillChangeListener(DockableStateWillChangeListener) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Removes a DockableStateWillChangeListener from this desktop.

removeDockingActionListener(DockingActionListener) - Method in class pub.vlsolutions.swing.docking.DockingContext

removeDockingActionListener(DockingActionListener) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Removes a DockingActionListener from this desktop.

removeElementByLocus(Locus) - Method in class com.pacbio.secondary.vis.data.queue.DetailsDataRequestsQueue

removeElementByTimestamp(long) - Method in class com.pacbio.secondary.vis.data.queue.DetailsDataRequestsQueue

removeFromTabbedGroup(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Unregisters a dockable from its current tab group (when it's removed from it).

removeLayoutComponent(Component) - Method in class pub.vlsolutions.swing.docking.AutoHideBorderLayout

removeLayoutComponent(Component) - Method in class pub.vlsolutions.swing.docking.DockingBorderLayout

removeLayoutComponent(Component) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout

removeLayoutComponent(Component) - Method in class pub.vlsolutions.swing.toolbars.VLToolBarLayout

removeNotify() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

Overriden as a means to unregister internal listeners, do not call directly

removeProperty(String) - Method in class pub.vlsolutions.swing.docking.DockKey

returns and removes a property associated to this name, or null if the property is undefined

removePropertyChangeListener(PropertyChangeListener) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

Remove a property change notification

removePropertyChangeListener(String, PropertyChangeListener) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

Remove a property change notification

removePropertyChangeListener(PropertyChangeListener) - Method in class pub.vlsolutions.swing.docking.DockKey

Remove a property change notification

removePushpin(int) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

removeStructuresAboveThreshold(int) - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure

RemoveTrackDialog - Class in com.pacbio.secondary.vis.gui.dialogs

RemoveTrackDialog(VioletApp, Frame) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog

removeTreeModelListener(TreeModelListener) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel

replace(Dockable, Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Replaces a dockable by another one.

replaceChild(Container, Component, Component) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities

Child replacement

replaceModel(IVariableResolutionDataModelServer) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

replaceStringInFile(String, String, String) - Static method in class com.pacbio.secondary.vis.common.utils.FileUtils

reportError(Exception) - Method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl

reportError(Exception, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.VisServiceCallbackImpl

Shows error in status bar, eventually sets file error status

reset_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

resetBorders() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

Creates the default borders for the expand panel

resetContigInfo() - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

resetRelativePosition(Container, Dockable) - Method in class pub.vlsolutions.swing.docking.RelativeDockablePosition

Updates the current relative ancestor container and anchor positionning

resetTabIcons() - Method in class pub.vlsolutions.swing.docking.DockViewAsTab

resetTime() - Method in class com.pacbio.secondary.vis.common.utils.PerformanceUtils

resetToPreferredSize() - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Request this desktop to reset it's contained views to their preferred size, if possible.

resetToPreferredSize() - Method in class pub.vlsolutions.swing.docking.DockingPanel

resetToPreferredSizes() - Method in class pub.vlsolutions.swing.docking.SplitContainer

Resest recursively the left and right components to their preferred size if possible.

resetVisibleGenomicRange(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails

resetVisibleGenomicRange(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Zoom fully out.

resetVisibleGenomicRange(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal

Zoom fully out.

resetVisibleGenomicRangeOfViews() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

resizeImage(BufferedImage, int, int) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils

resolveDockable(String) - Method in interface pub.vlsolutions.swing.docking.DockableResolver

Returns the dockable which should be associated to this DockKey identifier, or null if not found.

ResourceUtils - Class in com.pacbio.secondary.vis.common.utils

ResourceUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.ResourceUtils

restore(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Restore the dockable to the docking position it was before beeing maximized.

restoreAllGenomicViews(VioletFrame) - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper

Restores views data into app

restoreAppOptions(VioletApp) - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper

Restores app options into app

restoreDetailsOptions(GenomicViewDetails) - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper

Restores details options into app

restrict(double, double, double) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

Restricts the given value value to the interval [lower,upper].

restrict(float, float, float) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

restrict(int, int, int) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

Restricts the given value value to the interval [lower,upper].

result - Variable in class com.pacbio.secondary.vis.common.collection.SweepLineIterator.CutLine

result() - Method in class com.pacbio.secondary.vis.common.collection.SweepLineIterator.CutLine

results - Variable in class com.pacbio.secondary.vis.data.marker.Marker

results - Variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesDataRecord

RESULTS_METRICS_BITMASK - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants

RESULTS_OPTION_LINES_GRAPH - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

RESULTS_OPTION_NODES_GRAPH - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

RESULTS_OPTION_STRUCTURES - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

RESULTS_OPTION_STRUCTURES_ONLY - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

retrieveDataOnDemand() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

this method can be called concurrently

reverse(Color[]) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

Reverses the order of the given array.

reverse(byte[]) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

Reverses the order of the given array.

reverse(short[]) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

Reverses the order of the given array.

reverse(float[]) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

Reverses the order of the given array.

reverseComplement(char) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

reverseComplementSequence(String) - Static method in class com.pacbio.secondary.vis.common.utils.GenomicUtils

Strings are immutable, use stringbuffer

reverseRawRead(RawRead) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

handles reverse strand data

revKineticsPalette - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

RIGHT - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition

convenience field referencing the RIGHT border of the DockingDesktop

RIGHT_CENTER - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition

convenience field referencing the CENTER part of the RIGHT border of the DockingDesktop

RIGHT_PANEL - Static variable in class pub.vlsolutions.swing.toolbars.ToolBarPanelBorder

rightBorderPane - Variable in class pub.vlsolutions.swing.docking.DockingDesktop

panel used to display autohide buttons

rightLegendBounds - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

rightMarkerBounds - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

rightVisible - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

ROIS_HTML_HREF_TAG_EDIT - Static variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

ROIS_HTML_HREF_TAG_NAVIGATE - Static variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

ROIS_HTML_HREF_TAG_REMOVE - Static variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

rois_storage - Variable in class com.pacbio.secondary.vis.gui.app.VioletAppBase

rolloverIcon - Variable in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

the icon for the rollover effect

RolloverIcon - Class in pub.vlsolutions.swing.toolbars

A custom Icon to have a nice rollover effect for toolbar icons.

RolloverIcon(Icon) - Constructor for class pub.vlsolutions.swing.toolbars.RolloverIcon

root - Variable in class com.pacbio.secondary.vis.data.interval.IntervalTree

root - Variable in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel

RoundedBorder - Class in pub.vlsolutions.swing.toolbars

A simple rounded border.

RoundedBorder() - Constructor for class pub.vlsolutions.swing.toolbars.RoundedBorder

row_index - Variable in class com.pacbio.secondary.vis.svc.server.data.WsReadEx

rowHasBeenSelected(int, int) - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase

Notification of newly selected row.

rowHasBeenSelected(int, int) - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel

Show selected contig when user clicks on row...

RStartComparator - Class in com.pacbio.secondary.vis.svc.server.data

Specialized strand comparator for ccs pileup

RStartComparator() - Constructor for class com.pacbio.secondary.vis.svc.server.data.RStartComparator

run() - Method in class com.pacbio.secondary.vis.data.session.timer.SessionDataTimerTask

main method for this timer task, called at each predefined interval

run() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges.setOptimumZoomFactorsThreaded

run() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkerThread

run() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkSenderThread

run() - Method in class pub.vlsolutions.swing.toolbars.ToolBarPersistence

Save the toolbar configuration.

RuntimeConfigUtils - Class in com.pacbio.secondary.vis.common.utils

RuntimeConfigUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils

S

S_LINUX_FILE_SEPARATOR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

S_WINDOWS_FILE_SEPARATOR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

safeAddModelToSlots(VariableResolutionDataModel) - Method in class com.pacbio.secondary.vis.io.importer.ImportDataHelper

safeUpdateApplicationFrame() - Method in class com.pacbio.secondary.vis.data.session.DataStorage

safeUpdateDetailsView() - Method in class com.pacbio.secondary.vis.data.session.DataStorage

safeUpdateGenomicTablePanel(boolean) - Method in class com.pacbio.secondary.vis.data.session.DataStorage

sampleIndex(float) - Static method in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SampleInfo - Class in com.pacbio.secondary.vis.data.xmlinfo

SampleInfo() - Constructor for class com.pacbio.secondary.vis.data.xmlinfo.SampleInfo

sampleToMarkerIndex(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData

sampleToMarkerIndex(int, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData

save_text - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

saveApplicationProperties() - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

Save generic app properties

saveDefaultLayout() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

saveGraphicsFile(File, String, Boolean[]) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO

saveIdeogramProperties(IdeogramDB) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

saveJFrameAsImage(JFrame, String) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils

export screenshot of jframe as image file

saveLastPosition(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails

saveMaxValuesForRecord(VariableValuesDataRecord, int) - Method in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader

saveProperties() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO

save options

saveROIsFile() - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog

saveToClipboard() - Method in class com.pacbio.secondary.vis.gui.app.WebStartApp

saveToolBarLayout() - Method in class pub.vlsolutions.swing.toolbars.ToolBarPersistence

Save the toolbar configuration.

saveWorkspaceToByteArray() - Method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager

saveWorkspaceToServer() - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

saveWorkspaceToServer(String) - Method in class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager

SCALE_FACTOR_READS_WITH_BASES - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

SCALE_FACTOR_READS_WITH_PW - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

SCALE_FACTOR_READS_WITH_QV - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

SCALE_FACTOR_READS_WITH_RAW_IPD - Static variable in class com.pacbio.secondary.vis.common.utils.GenomicUtils

scalePalette(Color[], int, int, int) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

scalePalette(Color[], int) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

scaleX - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

scaleX(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

scaleY - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

scaleY(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

scanDrop(DockEvent, boolean) - Method in class pub.vlsolutions.swing.docking.DetachedDockView

scanDrop(DockEvent, boolean) - Method in class pub.vlsolutions.swing.docking.DockView

scanDrop(DockEvent, boolean) - Method in class pub.vlsolutions.swing.docking.TabbedDockView

scanGFFV2Slice(List<GFFIndexInfo>, GFFMetadataInfoCalculator, String, int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

this method scans a slice of data to find an F3 read and stores the info into the indexes array

scor - Variable in class com.pacbio.secondary.vis.svc.server.data.WsRead

ScreenCaptureUtils - Class in com.pacbio.secondary.vis.common.utils

ScreenCaptureUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils

scroll(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

scrollToCenter() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog

scrollVisibleGenomicRangeToTopOrBottom(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

sel - Variable in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo

select(AutoHideButton) - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

Selects a button (may collapse a prevoiusly selected button)

selectDefaultButton(int) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

selected_gene - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

selectedMarker - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

selectedSlotIndex - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

selectedTrackIndex - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

SelectFileDialog - Class in com.pacbio.secondary.vis.gui.dialogs

SelectFileDialog(VioletApp, Frame, String, String, String, boolean, boolean) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog

SELECTION_INFO_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

SELECTION_INFO_PANEL_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants

selection_panel - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

SELECTION_PANEL_FONT_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

selectionChanged(DockableSelectionEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

selectionChanged(DockableSelectionEvent) - Method in interface pub.vlsolutions.swing.docking.event.DockableSelectionListener

This method is invoked when a new dockable is selected.

selectionChangedListeners - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

SelectionInfoPanel - Class in com.pacbio.secondary.vis.gui.panels

SelectionInfoPanel(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel

SelectionInfoPanel.SelectionInfoPanelMouseListener - Class in com.pacbio.secondary.vis.gui.panels

SelectionInfoPanel.SelectionInfoPanelMouseListener() - Constructor for class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel.SelectionInfoPanelMouseListener

selectNextPreviousContig(int, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

selectNextPreviousGeneContig(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Selects gene in next or previous contig

selectNextPreviousMarker(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

selectPoint(Point) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Selects a feature in the view

selectPoint(Point) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal

TODO: implement???

selectRemoteData() - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

sendClientDataBlock(OutputStream) - Method in class com.pacbio.secondary.vis.svc.server.threads.JobInfo

seq - Variable in class com.pacbio.secondary.vis.svc.server.data.WsRead

sequence_file - Variable in class com.pacbio.secondary.vis.data.contig.ContigInfo

sequence_position - Variable in class com.pacbio.secondary.vis.io.indexer.indexinfo.ASCIIFileIndexInfo

serializationCloneTest(Object) - Static method in class com.pacbio.secondary.vis.common.utils.XMLObjectSerializerUtils

Clones a serializable object with a byte stream.

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

serialize(QName, org.apache.axiom.om.OMFactory, org.apache.axis2.databinding.utils.writer.MTOMAwareXMLStreamWriter, boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

serialVersionUID - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

serialVersionUID - Static variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

serverCreateIdeogramAndGenesDB(ProgressDialog, VisServiceWrapper) - Method in class com.pacbio.secondary.vis.data.session.DataStorage

serverLoadReferenceInfo(ProgressDialog, String) - Method in class com.pacbio.secondary.vis.data.session.DataStorage

ServiceUtils - Class in com.pacbio.secondary.vis.svc.server.utils

ServiceUtils() - Constructor for class com.pacbio.secondary.vis.svc.server.utils.ServiceUtils

session - Variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

session_id - Variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

SessionDataHelper - Class in com.pacbio.secondary.vis.data.session

Helper class for writing/reading user session data to xml Session data is embedded inside an app's project file using base64 encoding Member variables of this class should not be removed for compatibility with previous versions New member variables can be added, their value is not affected when reading from previous versions' serialized data

SessionDataHelper() - Constructor for class com.pacbio.secondary.vis.data.session.SessionDataHelper

deserialization only

SessionDataHelper(VioletApp) - Constructor for class com.pacbio.secondary.vis.data.session.SessionDataHelper

Save session data from app into this class

SessionDataTimer - Class in com.pacbio.secondary.vis.data.session.timer

helper class containing an instance of timer used to restore session data when all tracks are loaded the timer is created as a daemon thread

SessionDataTimer(VioletApp) - Constructor for class com.pacbio.secondary.vis.data.session.timer.SessionDataTimer

SessionDataTimerTask - Class in com.pacbio.secondary.vis.data.session.timer

SessionDataTimerTask(SessionDataTimer) - Constructor for class com.pacbio.secondary.vis.data.session.timer.SessionDataTimerTask

set(int, byte) - Method in class com.pacbio.secondary.vis.common.collection.ByteArrayList

Replaces the element at the specified position in this list with the specified element.

set_return(DataHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse

Auto generated setter method

set_return(DataHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse

Auto generated setter method

set_return(DataHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse

Auto generated setter method

set_return(String[]) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse

Auto generated setter method

set_return(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse

Auto generated setter method

set_return(DataHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse

Auto generated setter method

set_return(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse

Auto generated setter method

set_return(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse

Auto generated setter method

set_return(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse

Auto generated setter method

set_return(String[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse

Auto generated setter method

set_return(DataHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse

Auto generated setter method

set_return(DataHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse

Auto generated setter method

set_return(VisServiceStub.WsFileInfo[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse

Auto generated setter method

set_return(DataHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse

Auto generated setter method

set_return(VisServiceStub.WsJobMetadataInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse

Auto generated setter method

set_return(VisServiceStub.WsReferenceInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse

Auto generated setter method

set_return(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse

Auto generated setter method

set_return(VisServiceStub.WsTrackInfo[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse

Auto generated setter method

set_return(boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse

Auto generated setter method

setAbsMaxContigLength(int) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

setActionCustomizer(DockableActionCustomizer) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the action customizer of this dockable

setActive(boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Shows an activation frame around the ideogram.

setActive(boolean) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

Updates the active property.

setAlign(int) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout

setAllLanes(int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure

Set lane for all sub-reads

setAlwaysShowMemStats(boolean) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setAnn(byte[]) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

setAnnotations(byte[]) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

setAnnotations() - Method in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations

resets num rows, creates local cache

setApplicationLookAndFeel(int) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setApplicationLookAndFeelOld(int) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setAppOptions(PropertiesHelper) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setArm(String) - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand

setAutoHide(Dockable, boolean) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Toggles the position of a view between hidden (true) and docked (false).

setAutoHideBorder(DockingConstants.Hide) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the autohide border property

setAutoHideBorder(DockingConstants.Hide) - Method in class pub.vlsolutions.swing.docking.ws.WSDockKey

Updates the autohide border property

setAutoHideEnabled(boolean) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the autohideEnabled propety.

setAutoIdeogramBandSize(int) - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB

setAutoIdeogramNumBands(int) - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB

setAutoIdeogramUsesFixedNumBands(boolean) - Method in class com.pacbio.secondary.vis.data.db.IdeogramDB

setAutoResizableDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Deprecated.
use setResizeWeight() in every dockKey for a better resizing behaviour

setBand(String) - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand

setBases(long) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setBisDirectory(boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

Auto generated setter method

setBListDirOnly(boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

Auto generated setter method

setBoolean(String, boolean) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setBounds(int, int, int, int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable.TreeTableCellRenderer

This is overridden to set the height to match that of the JTable.

setBuffer(DataHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

Auto generated setter method

setCancelButtonText(String) - Method in class pub.vlsolutions.swing.docking.DockingSelectorDialog

Change the cancel button text (hook for i18n)

setCancelButtonTooltipText(String) - Method in class pub.vlsolutions.swing.docking.DockingSelectorDialog

Change the cancel button tootip text (hook for i18n)

setCenter_pos(int) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setCenterlocation(long) - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog

setChromosome(String, int) - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand

setClient_contig_index(int) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

Auto generated setter method

setClient_contig_index(int) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

Auto generated setter method

setClient_contig_index(int) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

Auto generated setter method

setClient_contig_index(int) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

Auto generated setter method

setCloseEnabled(boolean) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the closeEnabled propety.

setCoarseMode(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setCollapsed(boolean) - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripper

setCollapsed(boolean) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Hides the toolbar (just showing the gripper)

setCollapsible(boolean) - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripper

setCollapsible(boolean) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

setColorEnd(float) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette

setColorStart(float) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette

setColumns(int) - Method in class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip

setCompleted(boolean) - Method in class com.pacbio.secondary.vis.svc.server.threads.VisWorkDoneQueue

setComponent(Component) - Method in class pub.vlsolutions.swing.docking.DockablePanel

Removes all contained components (normally no more than one), and put this comp on the center area of the BorderLayout.

setConfirmButtonText(String) - Method in class pub.vlsolutions.swing.docking.DockingSelectorDialog

Change the confirm button text (hook for i18n)

setConfirmButtonTooltipText(String) - Method in class pub.vlsolutions.swing.docking.DockingSelectorDialog

Change the confirm button tooltip text (hook for i18n)

setConsensusData(WsFastaSequenceInfo) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

setContext(DockingContext) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Updates the docking context used by this desktop.

setContig_id(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

Auto generated setter method

setContig_id(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

Auto generated setter method

setContig_id(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

Auto generated setter method

setContig_id(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

Auto generated setter method

setContig_index(int) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

Auto generated setter method

setContig_length(int) - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo

setContig_name(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

Auto generated setter method

setContigEnd(int) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette

setContigMetricsLabels(String) - Method in class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage

Called by summary parser

setContigs_info_array(ContigInfo[]) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

setContigStart(int) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette

setCtg(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc

setCtg(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setCurrentContig(int) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setCurrentMainFrameContig(int) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

setCustomSplitDesktopStyle(BufferedImage, BufferedImage) - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

Another docking style with custom tiles between dockables.

setDataFiles(String) - Method in class com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo

setDataInfoText(String, boolean) - Method in class com.pacbio.secondary.vis.gui.control.VioletStatusBar

setDataType(BaseDataModel.eDataType) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection

setDefaultGap(int) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

Updates the gap (in pixels) between auto-hide buttons

setDefaultHideBorder(DockingConstants.Hide) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

Updates the default hide border.

setDefaultViewPort(Component, double, double) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate

setDensity(String) - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand

setDescription(String) - Method in class com.pacbio.secondary.vis.common.utils.filefilter.FileFilterGeneric

setDesktop(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockableState

Updates the desktop field (desktop using this dockable)

setDesktopName(String) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Updates the name of this desktop (used by workspace management)

setDesktopName(String) - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop

Updates the name of this workspace desktop

setDetails_options(DetailsOptions) - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper

setDetails_view_separator(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setDetailsMetricsMode(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setDetailsOptions(DetailsOptions) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setDetailsOptions(DetailsOptions) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

setDetailsRangeMode(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setDetailsViewData(WsResults, TrackDataInfo) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

setDetailsViewMagnification(double, double, boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

setDialogInfoInFrame(GoToDialog) - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog

setDialogLookAndFeel() - Static method in class com.pacbio.secondary.vis.common.utils.GUIUtils

Sets look and feel for test dialogs

setDirectory(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo

setDirectory(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

Auto generated setter method

setDisabledIcon(Icon) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Update the disabled icon property

setDividerLocation(double) - Method in class pub.vlsolutions.swing.docking.SplitContainer

Overriden for a bug workaround

setDividerLocation(int) - Method in class pub.vlsolutions.swing.docking.SplitContainer

setDna_char_height(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setDna_font(Font) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton

setDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockView

Adds the dockable's component to this DockView.

setDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab

setDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

Changes the dockable this title bar is for

setDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.event.DockingActionDockableEvent

setDockableAsTab(Dockable) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab

setDockableHeight(Dockable, double) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Changes the height of a dockable (the dockable must already be visible).

setDockableResolver(DockableResolver) - Method in class pub.vlsolutions.swing.docking.DockingContext

Updates the dockable resolver used by this context (can be set to null)

setDockableState(Dockable, DockableState) - Method in class pub.vlsolutions.swing.docking.DockingContext

Updates the current state of a dockable

setDockableWidth(Dockable, double) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Changes the width of a dockable (the dockable must already be visible).

setDockGroup(DockGroup) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the dockGroup of this dockable.

setDockingAction(DockingActionEvent) - Method in class pub.vlsolutions.swing.docking.event.DockEvent

Set the docking action corresponding to this drag and drop gesture.

setDockingContext(DockingContext) - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceButton

Updates the docking context used by this button

setDockingContext(DockingContext) - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem

Updates the docking context used by this menu item

setDockingDesktop(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockingSelectorDialog

Requiered to initialize this dialog.

setDockKey(DockKey) - Method in class pub.vlsolutions.swing.docking.DockablePanel

setDockName(String) - Method in class pub.vlsolutions.swing.docking.DockKey

Deprecated.
use setKey instead

setDottedDesktopStyle() - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

Another docking style with ligh dots between dockables.

setDouble(String, double) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setDraggedBorder(Border) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Changes the border used during drag and drop of the toolbar.

setDrawDelimitors(boolean) - Static method in class pub.vlsolutions.swing.docking.ui.DockingSplitPaneUI

Deprecated.
use UIManager.put("SplitContainer.drawDotsDelimitors", Boolean) instead

setDuration(float) - Method in class pub.vlsolutions.swing.docking.animation.ComponentAnimator

Sets the duration of the animation.

setEditorPane(WebBrowserPanel.WebBrowserEditorPane) - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserToolBar

setEmptyIcon(Icon) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton

Updates the icon used for this button when no dockable is stored

setEmptyText(String) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton

updates the text used for this button when no dockable is stored

setEmptyTooltip(String) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton

Updates the text used as tooltip for this button when no dockable is stored

setEnabled(boolean) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Update the enabled state

setEnableGraphStructure(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setEnd(float) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo

setEnd(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc

setEnd(long) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setEnd(int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure

setEnd(long) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

Auto generated setter method

setEndBounds(Rectangle) - Method in class pub.vlsolutions.swing.docking.animation.ComponentAnimator

Sets the end bounds of the component.

setEndInsertions(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

setEpilogInfo(int, long, long, int, int, int) - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo

setEpiProReadsDataIfAvailable(EpiProReadsReader, GenomicViewDetails, int, boolean) - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage

setEpiProReadsDataModel(EpiProReadsReader) - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

setEpiProReadsPalette(EpiProPalette) - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

setEventsCoverageFilterThreshold(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setExpandMode(AutoHidePolicy.ExpandMode) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

Updates the expand mode.

setExpansionDuration(int) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

Updates the expansion duration (time in millis)

setFactory(DockableContainerFactory) - Static method in class pub.vlsolutions.swing.docking.DockableContainerFactory

Changes the factory to be used by DockingDesktop.

setFile_type(DataFileInfo.eFileType) - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

setFileInfo(String, String, boolean, long, long) - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo

setFileName(String) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel

setFilename(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList

Auto generated setter method

setFilename(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile

Auto generated setter method

setFilename(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

Auto generated setter method

setFilename(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile

Auto generated setter method

setFilename(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile

Auto generated setter method

setFitDeNovoTableToPanel(boolean) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setFitRegionViewToWindowHeight(boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

setFitTableToPanel(boolean) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setFixedWidth(int) - Method in class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip

setFlatDesktopStyle() - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

Convenience method to use the VLDocking 2.0 layout and border style.

setFloatEnabled(boolean) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the floatEnabled propety.

setFloating(Dockable, boolean) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Detach or attach the dockable from/to the desktop.

setFloating(Dockable, boolean, Point) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Detach or attach the dockable from/to the desktop.

setFloating(WSDockKey, Rectangle, RelativeDockablePosition) - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop

Adds a new floating dockable

setFont(Font) - Method in class com.pacbio.secondary.vis.gui.control.VioletStatusBar

Set the font for controls in this statusbar.

setFraction(double) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setFullText(String) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton

Returns the text used for this button when a dockable is stored

setFullTooltip(String) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton

Updates the text used as tooltip for this button when no dockable is stored.

setGenomicTrack(GenomicViewEvents, int) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelTrack

setGenomicView(GenomicViewEvents) - Method in class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval

setGoToDialog(GoToDialog) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

setGraph(GraphStructure) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResults

setGraphStructure(GraphStructure) - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage

setGraphStructureType(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setHasBaseMods(boolean) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

setHasBaseMods(TreeMap<String, Integer>) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

copy motifs to string array, index is motif id

setHasCoverage(boolean) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

setHasMotifs(TreeMap<String, Integer>) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

copy motifs to string array, index is motif id

setHasMotifs(ArrayList<String>) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

setHasVariants(boolean) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

setHeader(String) - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo

setHigh_kin_threshold(double) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setHigh_qv_threshold(double) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setIcon(Icon) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the icon property.

setIcon(Icon) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

Update the main icon (left) to be displayed on the tab

setIcon(Icon) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Update the default icon property

setIconForTabbedPane(JTabbedPane) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

Specify which container will use this icon.

setId(String) - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo

setIdeogramFile(String) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

setImageFile(File) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

setIndeterminate(JPanel) - Method in class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog

setIndexSliceSize(long) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

setInfo(Object) - Method in class com.pacbio.secondary.vis.data.marker.Marker

setInfo(WsResultsInfo) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResults

setInfoPanelFontSize(int) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setInitialDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.FloatingDialog

setInitialDockable(Dockable) - Method in interface pub.vlsolutions.swing.docking.FloatingDockableContainer

adds the initial dockable to this top-level container

setInitialExpansionHeight(int) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

sets the first expansion height (only used with INITIAL_EXPAND_CUSTOM_SIZE model)

setInitialExpansionModel(int) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

setInitialExpansionWidth(int) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

sets the first expansion width (only used with INITIAL_EXPAND_CUSTOM_SIZE model)

setInitialTabbedDockableContainer(TabbedDockableContainer) - Method in class pub.vlsolutions.swing.docking.FloatingDialog

setInitialTabbedDockableContainer(TabbedDockableContainer) - Method in interface pub.vlsolutions.swing.docking.FloatingDockableContainer

adds the initial tabbdeddockablecontainer to this top-level container.

setInnerPanelWidth(int) - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel

setInstance(DragControlerFactory) - Static method in class pub.vlsolutions.swing.docking.DragControlerFactory

setInstance(DockingUISettings) - Static method in class pub.vlsolutions.swing.docking.ui.DockingUISettings

Allows replacement of the settings instance (used to override global look and feel settings of the framework.

setInt(String, int) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setIntv(WsIntervalSvc) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

setIPDConsensus_data(int[]) - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage

setIpdconsensus_track_height(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setIPDConsensusData(WsIPDConsensusInfo) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

setIsCDNADataAvailable() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

setIsdirectory(boolean) - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo

setIsdirectory(boolean) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

Auto generated setter method

setIsIPDConsensusDataAvailable() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

setIsSMRTGroup(String, boolean) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

Adds/removes host to list of systems requiring group-level access control

setJobTitle(String) - Method in class com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo

setKey(String) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the dockKey property.

setKineticsScaling(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setKineticsScalingMode(int) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

setLabel(String) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

Update the label to be displayed on the tab

setLane(int) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

setLane(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

setLanes(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setLanesSeparator(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setLastLocalDataFolderOpen(File, String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setLastLocalDataFolderSave(File, String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setLastRemoteDataFiles(String, String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setLastusedLayout(int) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setLength(long) - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo

setLength(long) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

Auto generated setter method

setLightweigthComponentEnabled(boolean) - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

A simple utility method to configure the docking framework to work properly with heavyweight component.

setLocation(FloatingDockableContainer, Point) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities

positions a detached dockable, regardless of its type (frame or dialog)

setLocation(DockableState.Location) - Method in class pub.vlsolutions.swing.docking.DockKey

updates the location property.

setLocationRelativeTo(FloatingDockableContainer, Component) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities

positions a detached dockable, regardless of its type (frame or dialog)

setLockGenomeRegionPanels(boolean) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setLockRangeExpand(boolean) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setLockRegionDetailsPanels(boolean) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setLocus(Locus) - Method in class com.pacbio.secondary.vis.data.queue.DetailsDataRequest

setLocus(Locus) - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage

setLogScaling(boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

call to turn visual filtering on or off updates region and whole genome view as needed

setLow_kin_threshold(double) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setLow_qv_threshold(double) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setM_contig_length(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo

setM_contig_length(int) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

Auto generated setter method

setM_contigs_info_array(WsContigInfo[]) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_contigs_info_array(VisServiceStub.WsContigInfo[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_data_file(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo

setM_data_file(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

Auto generated setter method

setM_file(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsTrackInfo

setM_file(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

Auto generated setter method

setM_header(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo

setM_header(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

Auto generated setter method

setM_id(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo

setM_id(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_id(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

Auto generated setter method

setM_id(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_ideogram_file(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_ideogram_file(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_image_file(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_image_file(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_info(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsFastaSequenceInfo

setM_info(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo

setM_ipd_ratio(int[]) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo

setM_job_title(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo

setM_job_title(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

Auto generated setter method

setM_max_contig_length(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_max_contig_length(int) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_name(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo

setM_name(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_name(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsTrackInfo

setM_name(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

Auto generated setter method

setM_name(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_name(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

Auto generated setter method

setM_num_contigs(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_num_contigs(int) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_path(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_path(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_reference_info(WsReferenceInfo) - Method in class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo

setM_reference_info(VisServiceStub.WsReferenceInfo) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

Auto generated setter method

setM_sequence(byte[]) - Method in class com.pacbio.secondary.vis.svc.server.data.WsFastaSequenceInfo

setM_sequence_file(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsContigInfo

setM_sequence_file(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_sequence_file(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo

Auto generated setter method

setM_sequence_file(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_sequence_index_file(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_sequence_index_file(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setM_tracks_info_array(WsTrackInfo[]) - Method in class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo

setM_tracks_info_array(VisServiceStub.WsTrackInfo[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo

Auto generated setter method

setM_web_search(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsTrackInfo

setM_web_search(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo

Auto generated setter method

setM_web_url(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo

setM_web_url(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo

Auto generated setter method

setMagnificationScaleFactor(double, double) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

setMapQVScalingMode(int) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

setMax(double) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

setMax_coverage(double) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue

setMax_details_coverage(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setMax_details_view_ordinate(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setMax_dynamic_range(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setMax_fixed_range(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setMax_norm_ipd_fwd(int, double) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue

setMax_norm_ipd_rev(int, double) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue

setMax_value(double) - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedDoubleInputVerifier

setMax_value(int) - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedFieldInputVerifier

setMax_variants(int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue

setMaxCoverage(int, double) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

setMaximizedDockable(WSDockKey) - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop

Sets the maximized dockable of this desktop, (or null if no dockable maximized).

setMaximizeEnabled(boolean) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the maximizeEnabled propety.

setMaxNormIPDFwd(int, int, double) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

setMaxNormIPDRev(int, int, double) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

setMaxReadLength(int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfoCalculator

setMaxSummaryCoverage(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

Called after summary file is first loaded (if available) to set max.

setMaxVariants(int, int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

setMean_coverage(double) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setMean_ipd(double) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setMean_score(double) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setMemoryInfoText(String, int) - Method in class com.pacbio.secondary.vis.gui.control.VioletStatusBar

setMin(double) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

setMin_value(double) - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedDoubleInputVerifier

setMin_value(int) - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedFieldInputVerifier

setMode(int) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

Auto generated setter method

setMode(int) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

Auto generated setter method

setMode(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setModels(List<IVariableResolutionDataModelServer>) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger

setModsFilterThreshold(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setMolID(int) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

setMolid(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

setMotif(String) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setMotif_group(String) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setMotif_partner(String) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setMultiChromosomesViewMagnification(double, boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

setMultisampleDataAvailable() - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

setN_detected(int) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setN_genome(int) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setName(String) - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo

setName(LinkedList<String>) - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection

setName(String) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

setName(String) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

setName(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo

setName(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

setName(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

Auto generated setter method

setName(String) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the name property.

setNodes(int[][]) - Method in class com.pacbio.secondary.vis.data.graph.GraphPrimitive

setNotification(boolean) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the notification propety.

setNumContigs(int) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

setObj_score(double) - Method in class com.pacbio.secondary.vis.data.db.MotifData

setOpaqueContents(boolean) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Set the desktop contents to be opaque or transparent.

setOptimumZoomFactors() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

setOpts(int) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

Auto generated setter method

setOrientation(int) - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripper

setOrientation(int) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanel

setOrientation(int) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Updates the orientation of this toolbar.

setPageFormat(PageFormat) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

setPainter(BackgroundPainter) - Method in class pub.vlsolutions.swing.toolbars.ToolBarPanel

Updates the optional background painter for this toolbar panel

setPaintShapes(boolean) - Method in class pub.vlsolutions.swing.docking.DragControlerGlassPane

Enables or disables shape painting

setPalette(Object) - Method in class com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer.EpiProPaletteDisplay

setParent(DockGroup) - Method in class pub.vlsolutions.swing.docking.DockGroup

Updates the parent of this group

setPath(String) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

setPattern(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation

Auto generated setter method

setPressed(boolean) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Update the pressed state

setPressed(boolean) - Method in class pub.vlsolutions.swing.toolbars.ToolBarButtonBorder

setPressedIcon(Icon) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Update the pressed icon property

setPrimaryInfo(int, long, long, int, int, int) - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo

setPrimitive(GraphPrimitive, int) - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure

setPrologInfo(int, long, long, int, int, int) - Method in class com.pacbio.secondary.vis.data.read.EpiProReadInfo

setProperDimension() - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog

setQV(byte[]) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

setQv(byte[]) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

setQVValue(WsRead, RawRead, int, int, float) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

setRangeSelection(Interval) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

setReadLenghtScalingMode(int) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

setReads(WsRead[]) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResults

setReads(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setRecords(ArrayList<VariableValuesDataRecord>) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel

setReference_data(byte[]) - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage

setReference_data(DataHandler) - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage

Deprecated.

setReference_locus(Locus) - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage

setReference_locus(Locus) - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage

setReferenceData(WsFastaSequenceInfo) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

setReferenceInfo(VisServiceStub.WsReferenceInfo) - Method in class com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo

setReferenceSequenceStorage(ReferenceSequenceStorage) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

setRefId(String) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

setRegionsOfInterestStorage(RegionsOfInterestStorage) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setRegionViewMagnification(double, double, boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

setResizeWeight(float) - Method in class pub.vlsolutions.swing.docking.DockKey

updates the resize weight of this dockable.

setResult(float[]) - Method in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesDataRecord

setResultsInfo(GenomicViewDetailsData, WsResults) - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage

setRollover(boolean) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Update the rollover state

setRolloverBorderPainted(boolean) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Updates the rolloverBorderPainted property.

setRolloverContentAreaFilled(boolean) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Updates the rolloverContentAreaFilled property.

setRolloverIcon(Icon) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Update the rollover icon property

setRolloverTriggerDelay(int) - Method in class pub.vlsolutions.swing.docking.AutoHidePolicy

Updates the rollover trigger delay

setRoot(Object) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel

setRowHeight(int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable

Overridden to pass the new rowHeight to the tree.

setRowHeight(int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable.TreeTableCellRenderer

Sets the row height of the tree, and forwards the row height to the table.

setRowIndex(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsReadEx

setScaledValue(double) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase.JDoubleSlider

setScor(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

setScore(int) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

setSelected(boolean) - Method in class pub.vlsolutions.swing.docking.AutoHideButton

Selects or unselects the button

setSelectedDims(long[]) - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo

Sets the dimension sizes of the selected subset

setSelectedDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane

Change the tab selection to display this dockable

setSelectedDockable(Dockable) - Method in interface pub.vlsolutions.swing.docking.TabbedDockableContainer

Change the tab selection to display this dockable

setSelectedGeneAndTrack(Marker, int, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Sets the currently selected gene to m.

setSelectedMarkerAndSlot(Marker, int, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Selects a marker/sample

setSeq(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

setSequence(String) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

setSequenceFile(String) - Method in class com.pacbio.secondary.vis.data.contig.ContigInfo

setSequenceFile(String) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

setSequenceIndexFile(String) - Method in class com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo

setShadowDesktopStyle() - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

Convenience method to use the VLDocking 1.0 layout and border style (with shadows around dockables)

setShowBaseModsInfo(boolean) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setShowGenes(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

setShowGenes(boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

setShowGraphStructureOnly(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setShowLabels(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Activates/Deactivates the chromosomal location label view (e.g.

setShowLabels(boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

Sets the visibility of the chromosomal labels for all ideograms.

setShowMarkerLabels(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Activates/Deactivates the tracks location label view (e.g.

setShowMarkerLabels(boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

setShowMarkers(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Show markers.

setShowMarkers(boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

setShowTooltips(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setSingleDockableTitleBarPopUpCustomizer(boolean) - Method in class pub.vlsolutions.swing.docking.DockableActionCustomizer

Updates the singleDockableTitleBar property.

setSingleHeavyWeightComponent(boolean) - Static method in class pub.vlsolutions.swing.docking.DockingPreferences

Notifies the framework that there is only one dockable that is heavyweight.

setSize(FloatingDockableContainer, Dimension) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities

resizes a detached dockable, regardless of its type (frame or dialog)

setSlotsDatasets(Vector<VariableResolutionDataSet>) - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase

setSmartButton(int, SmartIconJButton) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

setSorter() - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

setStar(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc

setStart(float) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo

setStart(long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

Auto generated setter method

setStart(long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

Auto generated setter method

setStart(long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

Auto generated setter method

setStart(long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

Auto generated setter method

setStart(long) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setStart(int) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure

setStart(long) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

Auto generated setter method

setStartBounds(Rectangle) - Method in class pub.vlsolutions.swing.docking.animation.ComponentAnimator

Sets the start bounds of the component for animation.

setStartDims(long[]) - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo

Sets the starting position of a selected subset

setStatus(TrackDataInfo.eTrackStatus) - Method in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

setStatus(String) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setStatusBarBusy(String, boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setStatusBarBusy(String, boolean) - Method in class com.pacbio.secondary.vis.gui.control.VioletStatusBar

setStatusBarBusy(String, boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

setStatusBarDataInfoText(String, boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setStatusBarDataInfoText(String, boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

setStatusBarProgress(String, int, int, int) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setStatusBarProgress(String, int, int, int) - Method in class com.pacbio.secondary.vis.gui.control.VioletStatusBar

setStatusBarProgress(String, int, int, int) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

setStatusBarSysInfoText(String, int) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

setStatusBarText(String) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setStatusBarText(String) - Method in class com.pacbio.secondary.vis.gui.control.VioletStatusBar

setStatusBarText(String) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

setStop(long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

Auto generated setter method

setStop(long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

Auto generated setter method

setStop(long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

Auto generated setter method

setStop(long) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

Auto generated setter method

setStride(long[]) - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo

Sets the selectedStride of the selected subset

setString(String, String) - Static method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setStrn(byte) - Method in class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc

setStrobe(boolean) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setStructID(int) - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

setStructid(int) - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

setSub_reads(ArrayList<WsRead>) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure

setSubBand(String) - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand

setSubSubBand(char) - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand

setSummaryKineticsScalingMode(int) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

setTableView(String) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

setTabName(String) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the tabname property.

setTabSelectorPopUpCustomizer(boolean) - Method in class pub.vlsolutions.swing.docking.DockableActionCustomizer

Updates the tabSelectorDockableTitleBar property

setText(String) - Method in class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog

Show a progress text in the StartDialog.

setText(String) - Method in interface com.pacbio.secondary.vis.gui.evt.IProgressNotifier

Sets the text in the progress bar.

setTime(double) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setTimestamp(long) - Method in class com.pacbio.secondary.vis.data.queue.DetailsDataRequest

setTimestamp(long) - Method in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo

setTimestamp(long) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo

Auto generated setter method

setTimestampFormat(String) - Method in class com.pacbio.secondary.vis.common.utils.SMRTHTMLLayout

Setter for timestamp format.

setTimeToAssemble(double) - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

setTipText(String) - Method in class com.pacbio.secondary.vis.gui.control.JHyperlinksHtmlTooltip

setTooltip(String) - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog.BookmarksEditorPane

setTooltip(String) - Method in class pub.vlsolutions.swing.docking.DockKey

Updates the tooltip property.

setTooltipText(String) - Method in class pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon

Update the tooltip of this icon

setTooltipText(String) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

setToolTipText(String) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Updates the tooltip of the toolbar, and propagates it to the toolbar gripper.

setTracksHeight(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal

set height of tracks

setTracksInfo(VisServiceStub.WsTrackInfo[]) - Method in class com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo

setType(int) - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure

setTypeAndNumContigs(BaseDataModel.eDataType, int) - Method in class com.pacbio.secondary.vis.data.base.BaseDataModel

setTypeAndNumContigs(BaseDataModel.eDataType, int) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

setUnmappedReadsCutoffThreshold(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions

Auto generated setter method

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults

Auto generated setter method

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence

Auto generated setter method

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames

Auto generated setter method

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader

Auto generated setter method

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus

Auto generated setter method

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence

Auto generated setter method

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo

Auto generated setter method

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo

Auto generated setter method

setUrl(String) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo

Auto generated setter method

setUseCustomUI(boolean) - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

Updates the useCustomUI property.

setUseEpiProReadsMode(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setUseEpiProReadsOnly(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setUseEventsCoverageFilter(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setUseLogScaling(boolean) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setUseMapQVFilter(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setUseModsFilter(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setUseQVFilter(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setUserData(String) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

setUseUnmappedReadsCutoffFilter(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setUseVariantsConfidenceFilter(boolean) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setUseVisualFilter(boolean) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setValidView(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

setValue(Object) - Method in class com.pacbio.secondary.vis.gui.table.renderer.IntegerRenderer

setValue(Object) - Method in class com.pacbio.secondary.vis.gui.table.renderer.IntervalRenderer

setValue(Object) - Method in class com.pacbio.secondary.vis.gui.table.renderer.LongRenderer

setValueAt(Object, Object, int) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel

setValueAt(Object, Object, int) - Method in interface com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel

Sets the value for node node, at column number column.

setVariantsConfFilterThreshold(int) - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

setViewContig(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData

Sets the currently shown contig.

setViewDataForCurrentContig(int, GenomicViewData, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData

setViewDataForCurrentContig(int, GenomicViewData, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData

setViewDataForCurrentContig(int, GenomicViewData, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion

setViewFilter(boolean, String) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

call to turn visual filtering on or off updates region and details view as needed

setViewSubreads(boolean) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setViewWithOrWithoutUpdate(Interval, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Sets the current genomic range for this view

setViewWithOrWithoutUpdate(Interval, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect

setVioletApp(Object) - Method in class com.pacbio.secondary.vis.gui.panels.base.DockableScrollPaneBase

setVioletFrame(VioletFrame) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

setVisible(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo

setVisible(FloatingDockableContainer, boolean) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities

shows a detached dockable, regardless of its type (frame or dialog)

setVisible(boolean) - Method in class pub.vlsolutions.swing.docking.TabbedDockView

setVisible(boolean) - Method in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Update the visible state

setVisibleGenomicRange(Interval, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Sets the genomic range for this view

setVisibleGenomicRegion(Locus, GenomicViewData, boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

setVisibleGenomicRegion(String[]) - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel

setVisibleGenomicRegion(String, String) - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel

setVisibleLocusDetailsPanel(Locus, boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

selects a new locus in details panel

setVisibleLocusGenomePanel(Locus, boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

selects a new locus in genome panel, eventually updates region and details

setVisibleLocusRegionPanel(Locus, boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletApp

selects a new locus in region panel, eventually updates details

setVisualFilter(String) - Method in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

setWidth(int, int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Sets the width-range of the ideogram graphic.

setWizardLabelText(String) - Method in class pub.vlsolutions.swing.docking.DockingSelectorDialog

Change the wizard label text (an explanation of the behaviour of this dialog).

setWorkspace(Workspace) - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceButton

updates the workspace to be used by this button

setWorkspace(Workspace) - Method in class pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem

updates the workspace to be used by this menu item

SEYMOUR_CONFIG_XML_FILE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

SEYMOUR_CONFIG_XML_JOBSROOT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_REFERENCE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SMRTVIEWINFO_HOST_TAG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SMRTVIEWINFO_PORT_TAG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SYSINFO_BUILD_TAG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SYSINFO_COMPONENTSNODE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SYSINFO_DIRECTORY_TAG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SYSINFO_FILENAME_TAG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SYSINFO_HOST_TAG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SYSINFO_HTTPPORT_TAG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SYSINFO_NODE_TAG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SYSINFO_SYSTEMNODE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_SYSINFO_VERSION_TAG - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_CONFIG_XML_VIOLET_CONTENT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

SEYMOUR_HOME_ENV - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

ShadowBorder - Class in pub.vlsolutions.swing.docking

A border using a shadow on right-bottom sides.

ShadowBorder() - Constructor for class pub.vlsolutions.swing.docking.ShadowBorder

ShadowBorder(boolean) - Constructor for class pub.vlsolutions.swing.docking.ShadowBorder

Constructs a full shadow border (if paintTopLeft is true) or a half shadow border (is false).

shouldCollapse() - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

Returns true if this panel agrees to beeing hidden.

shouldSelectCell(EventObject) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor

shouldYieldFocus(JComponent) - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedDoubleInputVerifier

shouldYieldFocus(JComponent) - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedFieldInputVerifier

SHOW_DETAILS_TOOLTIP - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

show_graph_structure_only - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

SHOW_GRAPH_STRUCTURE_ONLY_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

show_graph_structures_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

SHOW_IDEOGRAM_LABEL - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

SHOW_MARKER_LABEL - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

show_structures_only_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

show_tooltip_checkbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

show_tooltips - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

SHOW_WHATS_NEW_HELP - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

showAllAnnotations() - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

Shows all tracks of input view

showDataLabels() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

showDataLabels() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal

showDialog(VioletApp) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

showDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog

showDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog

showDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

showDialog(Component) - Method in class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog

show dialog centered on screen

showDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.PropertiesDialog

showDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog

showDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog

showDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog

showDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.SMRTViewDialog

showDragCursor() - Method in class pub.vlsolutions.swing.docking.DragControlerGlassPane

showErrorMessage(Component, String) - Static method in class com.pacbio.secondary.vis.common.utils.MessageUtils

showErrorMessageOnDataLoadFailure(int) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase

showFloatCursor() - Method in class pub.vlsolutions.swing.docking.DragControlerGlassPane

showGenes - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

showInterval(GenomicViewEvents) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

Shows all tracks of input view

showLabels - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

showMarkerLabels - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

showMarkers - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

showMemoryStats() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

showMessage(Component, String) - Static method in class com.pacbio.secondary.vis.common.utils.MessageUtils

showSelectJobDialog() - Method in class com.pacbio.secondary.vis.gui.dialogs.OpenRemoteDataHelper

showSelectTracksDialog(boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.OpenRemoteDataHelper

showStopDragCursor() - Method in class pub.vlsolutions.swing.docking.DragControlerGlassPane

showSwapDragCursor() - Method in class pub.vlsolutions.swing.docking.DragControlerGlassPane

showTrack(GenomicViewEvents) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

Shows selected track of input view

showURL(URL) - Static method in class com.pacbio.secondary.vis.common.utils.WebBrowserUtils

showUsage() - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileBuilder

showUsagev12() - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileBuilder

showUsagev13() - Method in class com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileBuilder

showWarningMessage(Component, String) - Static method in class com.pacbio.secondary.vis.common.utils.MessageUtils

sign(double) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

SingleDockableContainer - Interface in pub.vlsolutions.swing.docking

A SingleDockableContainer is a DockableContainer that can display a single Dockable component.

size() - Method in class com.pacbio.secondary.vis.common.collection.ByteArrayList

Returns the number of elements in this list.

size() - Method in class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet

size() - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet

size() - Method in class com.pacbio.secondary.vis.data.db.MotifsDB

size() - Method in class com.pacbio.secondary.vis.data.marker.MarkerCollection

size() - Method in class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage

size() - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage

size() - Method in class com.pacbio.secondary.vis.data.session.IPDConsensusStorage

size() - Method in class com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage

size() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage

size() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

size() - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer

Returns the overall number of markers.

size() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger

size() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

size() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel

size_disk_buffer - Static variable in class com.pacbio.secondary.vis.io.export.ExportRegionAsGFF

slot_index - Variable in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo

slots_colors - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper

slots_datasets - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase

slots_max_values - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper

slots_rows_cache - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations

smartIcon - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

smart icon used to display the title

SmartIconJButton - Class in pub.vlsolutions.swing.tabbedpane

A sub component of JTabbedPaneSmartIcon, used to describe a button included in a tabbedpane.

SmartIconJButton(Action) - Constructor for class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

Constructs a new button with an action.

SMRTGROUP_OPTION - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper

SMRTHTMLLayout - Class in com.pacbio.secondary.vis.common.utils

SMRTHTMLLayout() - Constructor for class com.pacbio.secondary.vis.common.utils.SMRTHTMLLayout

SMRTVIEW_ESCAPE_KEY - Static variable in class com.pacbio.secondary.vis.gui.dialogs.SMRTViewDialog

SMRTViewDialog - Class in com.pacbio.secondary.vis.gui.dialogs

SMRTViewDialog(Frame, String, boolean) - Constructor for class com.pacbio.secondary.vis.gui.dialogs.SMRTViewDialog

SMRTViewUpdater - Class in com.pacbio.secondary.vis.update

Wrapper smrtview updater called by install/update script

SMRTViewUpdater(String, String, boolean) - Constructor for class com.pacbio.secondary.vis.update.SMRTViewUpdater

sort() - Method in class com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage

sort(Object[]) - Method in class com.pacbio.secondary.vis.gui.control.treetable.MergeSort

SORT_ANNOTATION_DATA - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

SORT_DENOVO_CONTIGS - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

SortedMultiIterator<T extends java.lang.Comparable<T>> - Class in com.pacbio.secondary.vis.common.collection

Iterates over a set of sorted lists.

SortedMultiIterator(Collection<Iterator<T>>) - Constructor for class com.pacbio.secondary.vis.common.collection.SortedMultiIterator

All iterators of the input argument must be ascending

SortedRefIndexTable - Class in com.pacbio.secondary.vis.io.hdf.data

Simple extension class to store Sorted Ref Index table data.

SortedRefIndexTable(long, long, Object) - Constructor for class com.pacbio.secondary.vis.io.hdf.data.SortedRefIndexTable

sorter - Variable in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase

sortTableForBaseMods - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

sortViews(boolean) - Method in class com.pacbio.secondary.vis.gui.panels.WholeGenomePanel

source - Variable in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

source - Variable in class pub.vlsolutions.swing.docking.event.DockEvent

The drag source

sourceModels - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

split(DockDropEvent, Container, DockingConstants.Split) - Method in class pub.vlsolutions.swing.docking.BorderSplitter

This method should be overriden if the delegator doesn't belong to the docking containment hierarchy after drop acceptance.

split(Dockable, Dockable, DockingConstants.Split, double) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Splits a Dockable in 2 parts, if possible.

split(Dockable, Dockable, DockingConstants.Split) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Splits a Dockable in 2 parts, if possible.

split(Component, Component, DockingConstants.Split) - Method in class pub.vlsolutions.swing.docking.SplitContainer

Replaces the child component by a sub-split pane.

split(WSDockKey, WSDockKey, DockingConstants.Split, double) - Method in class pub.vlsolutions.swing.docking.ws.WSDesktop

Splits a dockable (with a given split location)

SPLIT_BOTTOM - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

A constant describing a VERTICAL splitting operation where the new component goes on the BOTTOM part

SPLIT_LEFT - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

A constant describing an HORIZONTAL splitting operation where the new component goes on the LEFT part

SPLIT_RIGHT - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

A constant describing an HORIZONTAL splitting operation where the new component goes on the RIGHT part

SPLIT_TOP - Static variable in class pub.vlsolutions.swing.docking.DockingConstants

A constant describing a VERTICAL splitting operation where the new component goes on the TOP part

splitComponent(Component, Dockable, DockingConstants.Split) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Replaces the base component by a split pane oriented according to position, and put dockable at position.

splitComponent(Component, Container, DockingConstants.Split) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Replaces the base component by a split pane oriented according to position, and put the dockablesContainer at position.

SplitContainer - Class in pub.vlsolutions.swing.docking

A Specialized JSplitPane which accepts drag and drop of DockableContainer.

SplitContainer() - Constructor for class pub.vlsolutions.swing.docking.SplitContainer

Constructs a vertically splitted SplitContainer

SplitContainer(int) - Constructor for class pub.vlsolutions.swing.docking.SplitContainer

Constructs a SplitContainer with the given JSplitPane orientation.

square(double) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility

start - Variable in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo

start - Variable in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo

start() - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper

start(VioletApp, InspectDataDialog, GenomicViewInspect, long) - Method in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper

start() - Method in class com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper

start() - Method in class com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper

start - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

start(OutputStream) - Method in class com.pacbio.secondary.vis.svc.server.threads.VisThreadPool

start() - Method in class pub.vlsolutions.swing.docking.animation.ComponentAnimator

Starts the animation.

start22() - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper

startBounds - Variable in class pub.vlsolutions.swing.docking.animation.ComponentAnimator

the component's start bounds

startDragComponent(Point) - Method in interface pub.vlsolutions.swing.docking.DockableDragSource

Notifies this source that a drag operation has begun.

startDragComponent(Point) - Method in class pub.vlsolutions.swing.docking.DockableStoreButton

startDragComponent(Point) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane

Notifies this source that a drag operation has begun.

startDragComponent(Point) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab.TabHeader

startDragComponent(Point) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

Notifies this source that a drag operation has begun.

startDragComponent(Point) - Method in class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab.MaximizedTabHeader

Notifies this source that a drag operation has begun.

startgetAnnotatedInsertions(HDFServiceStub.GetAnnotatedInsertions, HDFServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Auto generated method signature for Asynchronous Invocations

startgetAnnotatedResults(HDFServiceStub.GetAnnotatedResults, HDFServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Auto generated method signature for Asynchronous Invocations

startgetConsensusSequence(HDFServiceStub.GetConsensusSequence, HDFServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Auto generated method signature for Asynchronous Invocations

startgetContigNames(HDFServiceStub.GetContigNames, HDFServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Auto generated method signature for Asynchronous Invocations

startgetDefaultDirectory(VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startgetDirectoryList(VisServiceStub.GetDirectoryList, VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startgetFastaSequence(VisServiceStub.GetFastaSequence, VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startgetFile(VisServiceStub.GetFile, VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startgetFileHeader(HDFServiceStub.GetFileHeader, HDFServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Auto generated method signature for Asynchronous Invocations

startgetFilesInformation(VisServiceStub.GetFilesInformation, VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startgetGZippedFile(VisServiceStub.GetGZippedFile, VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startgetIPDConsensus(HDFServiceStub.GetIPDConsensus, HDFServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Auto generated method signature for Asynchronous Invocations

startgetMetadataInfo(VisServiceStub.GetMetadataInfo, VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startgetReferenceInfo(VisServiceStub.GetReferenceInfo, VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startgetServiceExperienceIndex(HDFServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Auto generated method signature for Asynchronous Invocations

startgetServiceInfo(HDFServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub

Auto generated method signature for Asynchronous Invocations

startgetServiceInfo(VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startgetTracksListInfo(VisServiceStub.GetTracksListInfo, VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startputFile(VisServiceStub.PutFile, VisServiceCallbackHandler) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub

Auto generated method signature for Asynchronous Invocations

startStreamingData(long, long, long) - Method in class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer

this method is called at the start of data transfer and receives the dimensions of the transfer, num_rows and num_columns, and number of chunks that will be streamed.

startStreamingData(long, long, long) - Method in class com.pacbio.secondary.vis.io.hdf.streaming.UCharStreamingDataConsumer

this method is called at the start of data transfer and receives the dimensions of the transfer, num_rows and num_columns, and number of chunks that will be streamed.

startStreamingData(long, long, long) - Method in class com.pacbio.secondary.vis.io.hdf.streaming.UIntStreamingDataConsumer

this method is called at the start of data transfer and receives the dimensions of the transfer, num_rows and num_columns, and number of chunks that will be streamed.

stateChanged(ChangeEvent) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger

stateChanged(ChangeEvent) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

stateChanged(ChangeEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

If a selection changed in one of the views

stateChanged(ChangeEvent) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel

status - Variable in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

status - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

statusBar - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

stop() - Method in class com.pacbio.secondary.vis.svc.server.threads.VisThreadPool

stopCellEditing() - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor

storage - Variable in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog

str_temp - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelBase

strand - Variable in class com.pacbio.secondary.vis.data.interval.Interval

StrandComparator - Class in com.pacbio.secondary.vis.svc.server.data

Specialized strand comparator for ccs+kinetics pileup

StrandComparator() - Constructor for class com.pacbio.secondary.vis.svc.server.data.StrandComparator

StreamingDataConsumer - Class in com.pacbio.secondary.vis.io.hdf.streaming

Abstract class representing a consumer of streaming chunks of data.

StreamingDataConsumer() - Constructor for class com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer

stride - Variable in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo

StringUtils - Class in com.pacbio.secondary.vis.common.utils

StringUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.StringUtils

strobe - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

structid - Variable in class com.pacbio.secondary.vis.data.read.ReadInfo

structid - Variable in class com.pacbio.secondary.vis.svc.server.data.WsRead

structures_close_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

structures_help_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

structures_listbox - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

structures_save_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

structures_tab - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

subband - Variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand

SUBREAD_COUNT - Static variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

subread_end - Variable in class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo

subread_length - Variable in class com.pacbio.secondary.vis.data.read.EpiProReadInfo

subread_start - Variable in class com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo

subSet(T, T) - Method in class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet

subSet(T, T) - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet

subsubband - Variable in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand

SUMMARY_BASEMODS_METRICS_COUNT - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_COVERAGE_AVG_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_COVERAGE_GAP_INTERVALS_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_COVERAGE_MAX_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_COVERAGE_MIN_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_COVERAGE_NUM_GAPS_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_DEL_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_DENOVO_QV_MAX_VALUE - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants

SUMMARY_INS_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_IPD_FWD_MODA_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_IPD_FWD_MODBASE_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_IPD_FWD_MODC_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_IPD_FWD_MODZ_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_IPD_REV_MODA_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_IPD_REV_MODBASE_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_IPD_REV_MODC_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_IPD_REV_MODZ_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_KINETIC_PALETTE_SIZE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

SUMMARY_QV_AVG_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_QV_MAX_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_QV_MIN_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_RESEQUENCING_QV_MAX_VALUE - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants

SUMMARY_RESEQUENCING_QV_MAX_VALUE_V1_2 - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants

SUMMARY_RESEQUENCING_QV_MAX_VALUE_V1_3_1 - Static variable in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants

SUMMARY_STD_METRICS_COUNT - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

SUMMARY_SUB_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs

summaryKineticsPalette - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorPalette

svc_wrapper - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel

svcexp_mode - Static variable in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex

swapComponents(Component, Component) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities

Swaps two toplevel DockableContainers (their parent must be a SplitContainer)

swapSpace - Variable in class com.pacbio.secondary.vis.gui.control.treetable.MergeSort

SweepLineIterator<T extends IntervalScale<T>> - Class in com.pacbio.secondary.vis.common.collection

Iterates over a set of sorted interval lists.

SweepLineIterator(Iterator<T>) - Constructor for class com.pacbio.secondary.vis.common.collection.SweepLineIterator

SweepLineIterator.CutLine - Class in com.pacbio.secondary.vis.common.collection

Represents a cut line of the line sweep.

SweepLineIterator.CutLine(int, int, SortedSet<T>) - Constructor for class com.pacbio.secondary.vis.common.collection.SweepLineIterator.CutLine

T

TAB_IDX_BASEMODS - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils

TAB_IDX_CDNA - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils

TAB_IDX_DETAILS - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils

TAB_IDX_EPIPRO - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils

TAB_IDX_GENERAL - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils

TAB_IDX_QV - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils

TAB_IDX_SINGLEMOLECULE - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils

TAB_IDX_VARIANTS - Static variable in class com.pacbio.secondary.vis.common.utils.ContextHelpUtils

tabbed_pane - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

TabbedContainerActions - Class in pub.vlsolutions.swing.docking

An utility class providing default implementation of usefull actions for pop-up menus in tab container selectors.

TabbedDockableContainer - Interface in pub.vlsolutions.swing.docking

Interface describing a container that can be used to display more than one Dockable in a Tabbed Pane fashion.

TabbedDockView - Class in pub.vlsolutions.swing.docking

A DockView that can be nested into a TabbedDockableContainer

TabbedDockView(Dockable) - Constructor for class pub.vlsolutions.swing.docking.TabbedDockView

tabbedGroups - Variable in class pub.vlsolutions.swing.docking.DockingDesktop

groups of tabs (used to re-tab autohidden dockable)

tabbedGroups - Variable in class pub.vlsolutions.swing.docking.ws.WSDesktop

groups of tabs (used to re-tab autohidden dockable)

TabFactory - Class in pub.vlsolutions.swing.docking

A factory that replaces DockViews (with title headers) by tabbed panes with a single tab.

TabFactory() - Constructor for class pub.vlsolutions.swing.docking.TabFactory

tabHeader - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

The tab container in which the components are added

table_menu - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

tableChanged(TableModelEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx

tableChanged(TableModelEvent) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

TableModelAnnotations - Class in com.pacbio.secondary.vis.data.table.model

TableModelAnnotations(VioletApp) - Constructor for class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations

TableModelBase - Class in com.pacbio.secondary.vis.data.table.model

TableModelBase(VioletApp) - Constructor for class com.pacbio.secondary.vis.data.table.model.TableModelBase

TableModelDeNovo - Class in com.pacbio.secondary.vis.data.table.model

TableModelDeNovo(VioletApp) - Constructor for class com.pacbio.secondary.vis.data.table.model.TableModelDeNovo

TableModelGenomicInterval - Class in com.pacbio.secondary.vis.data.table.model

TableModelGenomicInterval(VioletApp) - Constructor for class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval

TableModelTrack - Class in com.pacbio.secondary.vis.data.table.model

TableModelTrack(VioletApp) - Constructor for class com.pacbio.secondary.vis.data.table.model.TableModelTrack

TablePanelBase - Class in com.pacbio.secondary.vis.gui.panels.base

TablePanelBase(VioletApp, String, String, String, boolean) - Constructor for class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase

tag_gene_id - Static variable in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder

tailSet(T) - Method in class com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet

tailSet(T) - Method in class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet

TEMPLATE_INFO_TAG_TRACK - Static variable in class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants

TemplateInfo - Class in com.pacbio.secondary.vis.data.xmlinfo

TemplateInfo() - Constructor for class com.pacbio.secondary.vis.data.xmlinfo.TemplateInfo

TEST_EXTRA_GENE_TRACK - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants

test_no_indexer(String, long) - Static method in class com.pacbio.secondary.vis.io.fasta.FastaFileReader

test_start_with_indexer(String, int, String, long, long) - Static method in class com.pacbio.secondary.vis.io.fasta.FastaFileReader

testAllFiles() - Static method in class com.pacbio.secondary.vis.io.hdf.file.bash5.BaseH5FileBase

testAnalyzeFile(String, ArrayList<Integer>) - Static method in class com.pacbio.secondary.vis.io.importer.VioletFileAnalyzer

testDataStreaming(CMPH5File, H5ScalarDS, StreamingDataConsumer) - Static method in class com.pacbio.secondary.vis.io.hdf.test.HDFTest

Demo/Test method only.

testFastaIndexAndExtractMetadata(String) - Static method in class com.pacbio.secondary.vis.io.importer.VioletFileAnalyzer

testFile(HDFServiceWrapper, String, String, int, long, long, int) - Static method in class com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper

testFile(HDFService, String, String, int, long, long) - Static method in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest

testGetAlignmentIndexTableForInterval(CMPH5File, String, long, long) - Static method in class com.pacbio.secondary.vis.io.hdf.test.HDFTest

Demo/Test method.

testGFFIndexAndExtractMetadata(String, ArrayList<Integer>) - Static method in class com.pacbio.secondary.vis.io.importer.VioletFileAnalyzer

testH5BaseFile(String) - Static method in class com.pacbio.secondary.vis.io.hdf.file.bash5.BaseH5FileBase

testPrintDatasetInfo(H5ScalarDS) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

test only method, dumps dataset info

testReadCMPH5File(File, int) - Static method in class com.pacbio.secondary.vis.io.hdf.test.HDFTest

simple cmp.h5 file read access test

testStreamAlignmentIndexData(CMPH5File) - Static method in class com.pacbio.secondary.vis.io.hdf.test.HDFTest

Demo/Test method only.

testStreamFirstReadGroupData(CMPH5File) - Static method in class com.pacbio.secondary.vis.io.hdf.test.HDFTest

Demo/Test method only.

testWriteCMPH5File(File, int) - Static method in class com.pacbio.secondary.vis.io.hdf.test.HDFTest

simple cmp.h5 file write access test

testWriteDataSet(CMPH5File) - Static method in class com.pacbio.secondary.vis.io.hdf.test.HDFTest

Demo/Test method only.

textArea - Variable in class com.pacbio.secondary.vis.gui.control.VioletToolBarTest

TextFileIndexer - Class in com.pacbio.secondary.vis.io.indexer.text

TextFileIndexer() - Constructor for class com.pacbio.secondary.vis.io.indexer.text.TextFileIndexer

THICK_LINE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.GraphConstants

time_bld - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

time_io - Variable in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

time_started - Variable in class com.pacbio.secondary.vis.common.utils.PerformanceUtils

time_to_read - Variable in class com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics

timer - Variable in class com.pacbio.secondary.vis.data.session.timer.SessionDataTimer

timer - Variable in class com.pacbio.secondary.vis.data.session.timer.SessionDataTimerTask

timer - Variable in class com.pacbio.secondary.vis.smrtcloud.CloudTimer

timestamp - Variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFile

timestamp - Variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

timestamp - Variable in class com.pacbio.secondary.vis.svc.server.data.WsFileInfo

title - Variable in class pub.vlsolutions.swing.docking.DockView

titleBar - Variable in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI

titleHeight - Variable in class pub.vlsolutions.swing.docking.FloatingDialog

the drag header height

to - Variable in class com.pacbio.secondary.vis.common.collection.SweepLineIterator.CutLine

to() - Method in class com.pacbio.secondary.vis.common.collection.SweepLineIterator.CutLine

to() - Method in class com.pacbio.secondary.vis.data.base.BaseDataRecord

to - Variable in class com.pacbio.secondary.vis.data.interval.Interval

to() - Method in class com.pacbio.secondary.vis.data.interval.Interval

to() - Method in interface com.pacbio.secondary.vis.data.interval.IntervalScale

toArray() - Method in class com.pacbio.secondary.vis.common.collection.ByteArrayList

Returns an array containing all of the elements in this list in the correct order.

toCollection() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

toCollection() - Method in interface com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer

toCollection() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger

toCollection() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

toCollection() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel

toggleFilterByVariant - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

toggleMarker() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

Redraws the currently selected marker (blinking).

toggleShowDetails - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

toggleShowKinetics - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

toggleShowMapQV - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

toggleShowQV - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

toggleShowReads - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

toolBar - Variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

toolBar - Variable in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel

toolbar_items - Variable in class com.pacbio.secondary.vis.gui.control.VioletToolBar

ToolBarButtonBorder - Class in pub.vlsolutions.swing.toolbars

A border suitable for toolbar buttons.

ToolBarButtonBorder() - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarButtonBorder

ToolBarConstraints - Class in pub.vlsolutions.swing.toolbars

Constraints to be used with the ToolBarLayout.

ToolBarConstraints() - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarConstraints

Constructs a new ToolBarConstraints at (0,0)

ToolBarConstraints(int, int) - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarConstraints

Constructs a new ToolBarConstraints at (majorOrder,minorOrder).

ToolBarContainer - Class in pub.vlsolutions.swing.toolbars

The container for toolbar panels.

ToolBarContainer() - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarContainer

ToolBarGripper - Class in pub.vlsolutions.swing.toolbars

The component used to have a "grip" action on a toolbar (Drag and Drop support)

ToolBarGripper() - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarGripper

ToolBarGripper(int) - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarGripper

ToolBarGripperUI - Class in pub.vlsolutions.swing.toolbars

The default UI for the toolbar gripper.

ToolBarGripperUI() - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarGripperUI

Constructs a new gripper UI

ToolBarIO - Class in pub.vlsolutions.swing.toolbars

A utility class used to save and restore toolbars to/from an XML configuration.

ToolBarIO(ToolBarContainer) - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarIO

Constructs a new ToolBarIO utility based on the given container

ToolBarIOReadInfo - Class in pub.vlsolutions.swing.toolbars

Descriptor of the loading operation of toolbars.

ToolBarIOReadInfo() - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarIOReadInfo

ToolBarPanel - Class in pub.vlsolutions.swing.toolbars

The toolbar panel is able to receive multiple toolbars and arrange them in many columns or rows (depending on the horizontal/vertical orientation).

ToolBarPanel() - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarPanel

Constructs a new toobar panel with a LEADING alignment.

ToolBarPanel(int) - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarPanel

Constructs a new ToolBarPanel with the specified alignment.

ToolBarPanel(int, BackgroundPainter) - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarPanel

Constructs a new ToolBarPanel with the specified alignment and background painter.

ToolBarPanelBorder - Class in pub.vlsolutions.swing.toolbars

This is an optional class that can be used as a border for toolbar panels.

ToolBarPanelBorder() - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarPanelBorder

ToolBarPanelBorder(int) - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarPanelBorder

ToolBarPanelLayout - Class in pub.vlsolutions.swing.toolbars

The layout of a VLToolBarPanel

ToolBarPanelLayout(ToolBarPanel, int) - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout

ToolBarPanelLayout(ToolBarPanel) - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarPanelLayout

ToolBarPersistence - Class in pub.vlsolutions.swing.toolbars

This class contains methods to keep a set of toolbars persistent.

ToolBarPersistence(Object, ToolBarContainer) - Constructor for class pub.vlsolutions.swing.toolbars.ToolBarPersistence

Construct a new set of persistent toolbars.

TOOLTIP_IMAGE_SIZE - Static variable in class com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder

tooltipTableShowAll - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

tooltipTableShowDetails - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

tooltipTableShowRegion - Static variable in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions

tooltipText - Variable in class pub.vlsolutions.swing.tabbedpane.SmartIconJButton

the tooltip associated with the button

TOP - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition

convenience field referencing the TOP border of the DockingDesktop

TOP_CENTER - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition

convenience field referencing the CENTER part of TOP border of the DockingDesktop

TOP_LEFT - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition

convenience field referencing the TOP-LEFT corner of the DockingDesktop

TOP_PANEL - Static variable in class pub.vlsolutions.swing.toolbars.ToolBarPanelBorder

TOP_RIGHT - Static variable in class pub.vlsolutions.swing.docking.RelativeDockablePosition

convenience field referencing the TOP-RIGHT corner of the DockingDesktop

topBorderPane - Variable in class pub.vlsolutions.swing.docking.DockingDesktop

panel used to display autohide buttons

toSort - Variable in class com.pacbio.secondary.vis.gui.control.treetable.MergeSort

toString() - Method in class com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand

toString() - Method in class com.pacbio.secondary.vis.data.filesystem.LocalFileNode

Returns the the string to be used to display this leaf in the JTree.

toString() - Method in class com.pacbio.secondary.vis.data.filesystem.RemoteFileNode

Returns the the string to be used to display this leaf in the JTree.

toString() - Method in class com.pacbio.secondary.vis.data.gene.GeneInfo

toString() - Method in class com.pacbio.secondary.vis.data.graph.GraphStructure

toString() - Method in class com.pacbio.secondary.vis.data.interval.Interval

toString() - Method in class com.pacbio.secondary.vis.data.locus.Locus

toString() - Method in class com.pacbio.secondary.vis.data.marker.Marker

toString() - Method in class com.pacbio.secondary.vis.data.read.ReadInfo

toString() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions

toString() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest

toString() - Method in class com.pacbio.secondary.vis.io.hdf.data.UCharMatrixArray

toString() - Method in class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray

toString() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase

toString() - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File

toString() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo

toString() - Method in class com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo

toString() - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo

toString() - Method in class com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo

toString() - Method in class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo

toString() - Method in class com.pacbio.secondary.vis.svc.server.data.WsRead

toString() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResults

toString() - Method in class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo

toString() - Method in class pub.vlsolutions.swing.docking.DetachedDockView

toString() - Method in class pub.vlsolutions.swing.docking.DockableState

toString() - Method in class pub.vlsolutions.swing.docking.DockingPanel

toString() - Method in class pub.vlsolutions.swing.docking.DockKey

toString() - Method in class pub.vlsolutions.swing.docking.DockTabbedPane

toString() - Method in class pub.vlsolutions.swing.docking.DockView

toString() - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar

Returns a readeable String representing this title bar

toString() - Method in class pub.vlsolutions.swing.docking.event.DockingActionAddDockableEvent

toString() - Method in class pub.vlsolutions.swing.docking.event.DockingActionCloseEvent

toString() - Method in class pub.vlsolutions.swing.docking.event.DockingActionCreateTabEvent

toString() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSimpleStateChangeEvent

toString() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitComponentEvent

toString() - Method in class pub.vlsolutions.swing.docking.event.DockingActionSplitDockableEvent

toString() - Method in class pub.vlsolutions.swing.docking.RelativeDockablePosition

Returns a meaningfull string representation of this RelativeDockablePosition

toString() - Method in class pub.vlsolutions.swing.docking.SplitContainer

Returns a readable String representing this SplitContainer

toString() - Method in class pub.vlsolutions.swing.docking.ws.WSDockKey

toString() - Method in class pub.vlsolutions.swing.toolbars.ToolBarConstraints

Returns a description of these constraints.

toString() - Method in class pub.vlsolutions.swing.toolbars.VLToolBar

total_tracks - Variable in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo

tpManager - Variable in class pub.vlsolutions.swing.docking.DockViewAsTab

smart icon manager

track_area - Variable in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo

TRACK_BORDER - Static variable in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo

track_height - Variable in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo

track_index - Variable in class com.pacbio.secondary.vis.data.table.model.TableModelTrack

track_index - Variable in class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo

track_indexes - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

trackColor - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet

TrackDataInfo - Class in com.pacbio.secondary.vis.data.session.tracks

TrackDataInfo(String, String, String, TrackDataInfo.eTrackSource, DataFileInfo.eFileType) - Constructor for class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

TrackDataInfo(TrackDataInfo) - Constructor for class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

TrackDataInfo.eTrackSource - Enum in com.pacbio.secondary.vis.data.session.tracks

TrackDataInfo.eTrackStatus - Enum in com.pacbio.secondary.vis.data.session.tracks

TrackDrawInfo - Class in com.pacbio.secondary.vis.gui.draw.track

TrackDrawInfo() - Constructor for class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo

TrackDrawInfo(int, int, int, int, int, int) - Constructor for class com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo

trackIndexToXCoord(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

Compute the x-coordinate of a marker position.

trackIndexToYBaseline(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo

trackIndexToYCenter(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo

trackIndexToYTop(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo

TrackInfoParser - Class in com.pacbio.secondary.vis.svc.server.data.parser

TrackInfoParser(String) - Constructor for class com.pacbio.secondary.vis.svc.server.data.parser.TrackInfoParser

trackName - Variable in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo

tracks_info - Variable in class com.pacbio.secondary.vis.data.session.DataStorageBase

tracks_info - Variable in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo

TracksDataInfoList - Class in com.pacbio.secondary.vis.data.session.tracks

TracksDataInfoList() - Constructor for class com.pacbio.secondary.vis.data.session.tracks.TracksDataInfoList

trackToYCoord(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

Compute the y-coordinate of a track.

TRANSLATE_READ_4BITS - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants

Translates a 4-bit compressed base into a letter

TRANSLATE_REVERSE_READ_4BITS - Static variable in class com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants

Translates a 4-bit compressed complemented base into a letter

translateInPlace() - Method in class com.pacbio.secondary.vis.io.hdf.data.ConsensusCallsTable

Fast and lightweight method to convert compressed consensus sequence in place.

transparent(Color, double) - Static method in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants

tree - Variable in class com.pacbio.secondary.vis.data.db.IdeogramDB

tree - Variable in class com.pacbio.secondary.vis.data.interval.IntervalTreeQuery

tree - Variable in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable

TreeSortedMultiSet<T extends java.lang.Comparable<T>> - Class in com.pacbio.secondary.vis.common.collection

A sorted container which can contain more equal objects.

TreeSortedMultiSet() - Constructor for class com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet

TreeTableModel - Interface in com.pacbio.secondary.vis.gui.control.treetable

TreeTableModel is the model used by a JTreeTable.

trim(String, String) - Static method in class com.pacbio.secondary.vis.common.utils.StringUtils

trims a string of a single occurrence of the search string

type - Variable in class com.pacbio.secondary.vis.data.graph.GraphStructure

type - Variable in class com.pacbio.secondary.vis.io.importer.DataFileInfo

U

UCharMatrixArray - Class in com.pacbio.secondary.vis.io.hdf.data

Mmemory-space-saving unsigned char array wrapper.

UCharMatrixArray(Object) - Constructor for class com.pacbio.secondary.vis.io.hdf.data.UCharMatrixArray

set the data into this matrix array

UCharStreamingDataConsumer - Class in com.pacbio.secondary.vis.io.hdf.streaming

Specialized class representing a consumer of streaming chunks of UChar data.

UCharStreamingDataConsumer() - Constructor for class com.pacbio.secondary.vis.io.hdf.streaming.UCharStreamingDataConsumer

UCSCGTFReader - Class in com.pacbio.secondary.vis.io.ucsc.gtf.reader

UCSCGTFReader() - Constructor for class com.pacbio.secondary.vis.io.ucsc.gtf.reader.UCSCGTFReader

uiClassID - Static variable in class com.pacbio.secondary.vis.gui.control.JMultiLineHtmlToolTip

uiClassID - Static variable in class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip

uiClassID - Static variable in class pub.vlsolutions.swing.docking.AutoHideButton

uiClassID - Static variable in class pub.vlsolutions.swing.docking.AutoHideButtonPanel

uiClassID - Static variable in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

UIntMatrixArray - Class in com.pacbio.secondary.vis.io.hdf.data

Mmemory-space-saving unsigned integer array wrapper.

UIntMatrixArray(long, long, Object) - Constructor for class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray

creates a matrix array that holds unsigned integers

UIntStreamingDataConsumer - Class in com.pacbio.secondary.vis.io.hdf.streaming

Specialized class representing a consumer of streaming chunks of UInt data.

UIntStreamingDataConsumer() - Constructor for class com.pacbio.secondary.vis.io.hdf.streaming.UIntStreamingDataConsumer

UM_EPILOG_END - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_EPILOG_MAPQV - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_EPILOG_PCT_SIMILARITY - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_EPILOG_REF_ID - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_EPILOG_SCORE - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_EPILOG_START - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_EPILOG_STRAND - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_EPILOG_SUBREAD_END - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_EPILOG_SUBREAD_START - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_NO_DATA - Static variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PRIMARY_END - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PRIMARY_MAPQV - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PRIMARY_PCT_SIMILARITY - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PRIMARY_REF_ID - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PRIMARY_SCORE - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PRIMARY_START - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PRIMARY_STRAND - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PRIMARY_SUBREAD_END - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PRIMARY_SUBREAD_START - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PROLOG_END - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PROLOG_MAPQV - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PROLOG_PCT_SIMILARITY - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PROLOG_REF_ID - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PROLOG_SCORE - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PROLOG_START - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PROLOG_STRAND - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PROLOG_SUBREAD_END - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_PROLOG_SUBREAD_START - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_READ_ID - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_SBR_LENGTH - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_SEPARATOR - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

UM_TOTAL_COLUMNS - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

undo() - Method in class com.pacbio.secondary.vis.common.collection.UndoIterator

UndoIterator<T> - Class in com.pacbio.secondary.vis.common.collection

Iterator which can step back a single step with the method UndoIterator.undo()

UndoIterator(Iterator<T>) - Constructor for class com.pacbio.secondary.vis.common.collection.UndoIterator

uninstallDockableDragSource(DockableDragSource) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

This method is used by DockableContainers in order to unregister their DockableDragSource(s) to the OldDragControler.

uninstallDockableDragSources(DockableDragSource[]) - Method in class pub.vlsolutions.swing.docking.DockingDesktop

Uninstalls multiple drag sources.

uninstallDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.AutoHideExpandPanel

uninstallDocking(DockingDesktop) - Method in interface pub.vlsolutions.swing.docking.DockableContainer

Called once, when the dockablecontainer is no longer used by the desktop, in order to releases resources and listeners taken on installDocking().
uninstallDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockTabbedPane Called once, when the dockablecontainer is no longer used by the desktop, in order to releases resources and listeners taken on installDocking(). uninstallDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockView Called once, when the dockablecontainer is no longer used by the desktop, in order to releases resources and listeners taken on installDocking(). uninstallDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockViewAsTab Called once, when the dockablecontainer is no longer used by the desktop, in order to releases resources and listeners taken on installDocking(). uninstallDocking(DockingDesktop) - Method in class pub.vlsolutions.swing.docking.DockViewTitleBar uninstallTitleBorder(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI uninstalls the icons and tooltip suitable for a close button uninstallUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonPanelUI uninstallUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideButtonUI uninstallUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.AutoHideExpandPanelUI uninstallUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DetachedDockViewUI Uninstalls the component's UI uninstallUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI uninstallUI(JComponent) - Method in class pub.vlsolutions.swing.docking.ui.DockViewUI union(Interval) - Method in class com.pacbio.secondary.vis.data.interval.Interval unitMatrix(double[][]) - Static method in class com.pacbio.secondary.vis.common.collection.MathUtility unregisterDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingContext Unregisters the dockable, which can be garbage collected (no longer used by docking desktops. unregisterDockable(Dockable) - Method in class pub.vlsolutions.swing.docking.DockingDesktop Unregisters the dockable, which can be garbage collected (no longer used by the docking desktop. unregisterToolBar(VLToolBar) - Method in class pub.vlsolutions.swing.toolbars.ToolBarContainer Unregisters a ToolBar. updateAutoResizeMode() - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel updateAutoResizeMode() - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel updateButtonText() - Method in class pub.vlsolutions.swing.docking.DockableStoreButton Override this method if you want to change the display (text and icon) of this button and the default settings don't suit your needs. updateCircularView() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges updateColumnWidths() - Method in class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog default column widths updateColumnWidths() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase default column widths updateConsensusQVLimits() - Method in class com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader updateContigPalette(int) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette updateControlsFromApp(boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog updateData(boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase updateDataDoNotClear(GenomicViewDetailsData, Interval, WsResults, Locus) - Method in class com.pacbio.secondary.vis.data.session.DetailsStorage updateDataSet(TrackDataInfo) - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper updateDataSet(TrackDataInfo) - Method in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper updateDataSet(VariableResolutionDataSet) - Method in class com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper.ThreadHelper updateDataSet(VariableResolutionDataSet) - Method in class com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper.ThreadHelper updateDeNovoTablePanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges updateDetailsControls(int) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase updates status of details controls updateDetailsData() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase UpdateDetailsDataHelper - Class in com.pacbio.secondary.vis.io.update UpdateDetailsDataHelper(VioletApp) - Constructor for class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper UpdateDetailsDataHelper.UpdateDetailsThreadHelper - Class in com.pacbio.secondary.vis.io.update UpdateDetailsDataHelper.UpdateDetailsThreadHelper(VioletApp) - Constructor for class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper updateDetailsView(boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges updateEpiProDataSet(String) - Method in class com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper updateFilter() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase Update the row filter regular expression from the expression in the text box. updateHistory() - Method in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserEditorPane updateHTMLText() - Method in class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog updateInfo() - Method in class com.pacbio.secondary.vis.svc.server.threads.JobInfo UpdateInsertionsDataHelper - Class in com.pacbio.secondary.vis.io.update UpdateInsertionsDataHelper() - Constructor for class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper - Class in com.pacbio.secondary.vis.io.update UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper(VioletApp, InspectDataDialog, GenomicViewInspect, long) - Constructor for class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper updateIOTimeStats(WsResults, long) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder updateJNLPFile(File) - Method in class com.pacbio.secondary.vis.update.SMRTViewUpdater Processes single vis.jnlp file updateJNLPTemplateHostTags(String) - Method in class com.pacbio.secondary.vis.update.SMRTViewUpdater Updates hostname, httpport and version tags updateKineticsControls(boolean) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase updates status of kinetics controls updateLaneOffset() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions updateLayout() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails updateLayout() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw updateLayout() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion updateLayoutOnDemand() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData this method can be called concurrently updateLockedPanels(String, boolean) - Method in class com.pacbio.secondary.vis.gui.app.VioletAppBase updateMaxRange(int) - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel updates max range after changing contig updateMetricsFromRawRead(WsRead, RawRead, float) - Method in class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures must report right or left insertion... updateMinMaxValues(IVariableResolutionDataModelServer) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger updateMinMaxValues(IVariableResolutionDataModelServer) - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet updateModel() - Method in class com.pacbio.secondary.vis.gui.dialogs.EpiProColorOptionsPane updateModel() - Method in class com.pacbio.secondary.vis.gui.dialogs.QVThresholdOptionsPane updateModificationsData() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase UpdateModificationsDataHelper - Class in com.pacbio.secondary.vis.io.update UpdateModificationsDataHelper(VioletApp) - Constructor for class com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper UpdateModificationsDataHelper.ThreadHelper - Class in com.pacbio.secondary.vis.io.update UpdateModificationsDataHelper.ThreadHelper(VioletApp) - Constructor for class com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper.ThreadHelper updateMovieInfoFromMovieIDs() - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase reads movie ids and eventually update table of movie names and frame rates updatePacBioLookAndFeel() - Static method in class com.pacbio.secondary.vis.common.utils.GUIUtils method to update some aspects of l&f of the app updatePanel(GenomicViewEvents) - Method in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel updatePanel(String) - Method in class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel updatePanelFromApp() - Method in class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel updatePanelStatus() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase Updates panel header text updatePopupMenuStatus(Component[]) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel Updates selection state of popup menu UpdateProgressBar(VioletApp, double) - Method in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader updateQueryCriteria(boolean, String) - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase updateReferenceData() - Method in class com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper loads fasta reference or consensus data depending on job type e.g. updateRegionView(boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges updateRegionViewDetailsRange() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges updateResizeWeights(DockingPanel) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities Invoked every time the layout is changed, to rebuild the weighting of split containers UpdaterUtils - Class in com.pacbio.secondary.vis.update Generic utilities to update smrtview UpdaterUtils() - Constructor for class com.pacbio.secondary.vis.update.UpdaterUtils updateScrollbarsLAF() - Static method in class com.pacbio.secondary.vis.common.utils.GUIUtils sets scrollbar width to half standard updateSelectionPanel(GenomicViewEvents) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges updateSingleRawReadUsingCache(RawRead, H5ScalarDS, AlignmentIndexTable, int) - Method in class com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileData updateSize(boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData updateSize(boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails updateSize(boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw updateSize(boolean, boolean) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal updateStates() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase updateTableMenus() - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel Called by main frame when users change table options using main menu updateTablePanel() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges updateTablePanel() - Method in class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel Called after summary file is updated for denovo experiments updateTablePanel(boolean) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel called by listener frame in event thread... updateTitle() - Method in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog updateTitle() - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel updateTitle(GenomicViewEvents) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel updateTitle(GenomicViewEvents, int) - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel updateToggleButtons() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase called by mainframe after toggle buttons in toolbar change state updateToggleButtonsInGoToDialog() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions Updates status of toggle buttons in preferences dialog updateToggleButtonsInPrefDialog() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions Updates status of toggle buttons in preferences dialog updateToggleButtonsInToolbar() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions Updates selection status of toolbar toggle buttons updateToggleMenuItems() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameActions updateTracksListAfterRemovingSlot(String) - Method in class com.pacbio.secondary.vis.data.session.DataStorageBase Called after user removes a track, updates trackslist and tracks indexes in remaining slots updateUI() - Method in class com.pacbio.secondary.vis.gui.control.JHyperlinksHtmlTooltip updateUI() - Method in class com.pacbio.secondary.vis.gui.control.JMultiLineHtmlToolTip updateUI() - Method in class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip updateUI() - Method in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable.TreeTableCellRenderer updateUI is overridden to set the colors of the Tree's renderer to match that of the table. updateUI() - Method in class com.pacbio.secondary.vis.gui.control.VioletStatusBar updateUI() - Method in class pub.vlsolutions.swing.docking.ui.DockingUISettings Allows updating of the ui after a look and feel change. updateUI() - Method in class pub.vlsolutions.swing.toolbars.ToolBarGripper Resets the UI property to a value from the current look and feel. updateUnMappedReadsPalette(int) - Method in class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette updateVariantsData() - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase UpdateVariantsDataHelper - Class in com.pacbio.secondary.vis.io.update UpdateVariantsDataHelper(VioletApp) - Constructor for class com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper UpdateVariantsDataHelper.ThreadHelper - Class in com.pacbio.secondary.vis.io.update UpdateVariantsDataHelper.ThreadHelper(VioletApp) - Constructor for class com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper.ThreadHelper updateViews() - Method in class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase updateVisibility() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData Finds for each MarkerCollection if it is empty or not and updates the two BitSets leftVisible and rightVisible. updateWholeGenomeView() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase URL_SEPARATOR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants USE_EPIPRO_CUTOFF_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper use_epipro_cutoff_filter - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions use_epipro_cutoff_threshold - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions use_epipro_mode - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions use_epipro_mode - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader USE_EPIPRO_ONLY - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper use_epipro_only - Variable in class com.pacbio.secondary.vis.io.epipro.EpiProReadsReader use_epipro_only_reads - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions USE_EPIPRO_UNFOLDED - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper use_events_coverage_filter - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions use_external_browser - Variable in class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel USE_FOR_TESTING_WHEN_NEEDED - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper use_frank_style - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase use_local_autoscale - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions USE_MAPQV_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper use_mapqv_filter - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions USE_MODS_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper use_mods_filter - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions use_monochrome_kinetic_palette - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions USE_NEW_COLORS_FOR_PANEL_TITLE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ColorConstants USE_QV_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper use_qv_filter - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions USE_VARIANT_COV_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper USE_VARIANTS_CONF_FILTER - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper use_variants_confidence_filter - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions useLogScaling - Variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper user_data - Variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest USER_DEFAULT_DATA_DIRECTORY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants USER_DEFAULT_GRAPHICS_DIRECTORY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants USER_DEFAULT_PROJECTS_DIRECTORY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants USER_DEFAULT_ROIS_DIRECTORY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants USER_HOME_ENV - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants useTableViewFilter - Variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper
V valid - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel valid - Variable in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet validate() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel validate() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger validate(FloatingDockableContainer) - Static method in class pub.vlsolutions.swing.docking.DockingUtilities validates a detached dockable, regardless of its type (frame or dialog) validate_return(String[]) - Method in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse validate the array for _return validate_return(String[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse validate the array for _return validate_return(VisServiceStub.WsFileInfo[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse validate the array for _return validate_return(VisServiceStub.WsTrackInfo[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse validate the array for _return validateFilename(String) - Static method in class com.pacbio.secondary.vis.common.utils.FileUtils validateM_contigs_info_array(VisServiceStub.WsContigInfo[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo validate the array for M_contigs_info_array validateM_tracks_info_array(VisServiceStub.WsTrackInfo[]) - Method in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo validate the array for M_tracks_info_array validateold() - Method in class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger Deprecated. value() - Method in class pub.vlsolutions.swing.docking.DockingConstants.Hide value() - Method in class pub.vlsolutions.swing.docking.DockingConstants.Split valueChanged(ListSelectionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx This is called when kinetics list changes valueChanged(ListSelectionEvent) - Method in class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog valueForPathChanged(TreePath, Object) - Method in class com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel valueOf(String) - Static method in enum com.pacbio.secondary.vis.data.base.BaseDataModel.eDataType Returns the enum constant of this type with the specified name. valueOf(String) - Static method in enum com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo.eTrackSource Returns the enum constant of this type with the specified name. valueOf(String) - Static method in enum com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo.eTrackStatus Returns the enum constant of this type with the specified name. valueOf(String) - Static method in enum com.pacbio.secondary.vis.gui.app.VioletAppBase.APP_TYPE Returns the enum constant of this type with the specified name. valueOf(String) - Static method in enum com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent.GenomicViewEventType Returns the enum constant of this type with the specified name. valueOf(String) - Static method in enum com.pacbio.secondary.vis.io.importer.DataFileInfo.eFileType Returns the enum constant of this type with the specified name. valueOf(String) - Static method in enum com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader.vcf_version Returns the enum constant of this type with the specified name. valueOf(String) - Static method in enum pub.vlsolutions.swing.docking.AutoHidePolicy.ExpandMode Returns the enum constant of this type with the specified name. valueOf(String) - Static method in enum pub.vlsolutions.swing.docking.DockableContainerFactory.ParentType Returns the enum constant of this type with the specified name. valueOf(String) - Static method in enum pub.vlsolutions.swing.docking.DockableState.Location Returns the enum constant of this type with the specified name. values() - Static method in enum com.pacbio.secondary.vis.data.base.BaseDataModel.eDataType Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo.eTrackSource Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo.eTrackStatus Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum com.pacbio.secondary.vis.gui.app.VioletAppBase.APP_TYPE Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent.GenomicViewEventType Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum com.pacbio.secondary.vis.io.importer.DataFileInfo.eFileType Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader.vcf_version Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum pub.vlsolutions.swing.docking.AutoHidePolicy.ExpandMode Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum pub.vlsolutions.swing.docking.DockableContainerFactory.ParentType Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum pub.vlsolutions.swing.docking.DockableState.Location Returns an array containing the constants of this enum type, in the order they are declared. VariableResolutionDataModel - Class in com.pacbio.secondary.vis.data.variableresolution.model VariableResolutionDataModel() - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel VariableResolutionDataModel(BaseDataModel.eDataType, int) - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel VariableResolutionDataModelsMerger - Class in com.pacbio.secondary.vis.data.variableresolution.model Merges an array of VariableResolutionDataModelsMerger VariableResolutionDataModelsMerger() - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger VariableResolutionDataSet - Class in com.pacbio.secondary.vis.data.variableresolution.model A DataSlot encapsulates one or more GenericDataModel datasets with all configurations. VariableResolutionDataSet(BaseDataModel.eDataType, int) - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet VariableResolutionDataSetValues - Class in com.pacbio.secondary.vis.data.variableresolution.model.gff VariableResolutionDataSetValues() - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues VariableResolutionDataSetValues(int) - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues VariableResolutionDataSetValues(int, int) - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues VariableResolutionDataSetValues.VariableResolutionDataSetValue - Class in com.pacbio.secondary.vis.data.variableresolution.model.gff VariableResolutionDataSetValues.VariableResolutionDataSetValue(int) - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue VariableResolutionMemoryDataModel - Class in com.pacbio.secondary.vis.data.variableresolution.model VariableResolutionMemoryDataModel() - Constructor for class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel VariableValuesDataRecord - Class in com.pacbio.secondary.vis.data.variableresolution.record VariableValuesDataRecord() - Constructor for class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesDataRecord VariableValuesDataRecord(float[]) - Constructor for class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesDataRecord VariableValuesDataRecord(VariableValuesDataRecord) - Constructor for class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesDataRecord VariableValuesTypeDefs - Class in com.pacbio.secondary.vis.data.variableresolution.record VariableValuesTypeDefs() - Constructor for class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs VARIANT_DEF_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_DELETION_TYPE - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_INSERTION_TYPE - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_SUBST_TYPE - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_TYPES_LABELS - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_V12_GENOTYPE_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_V131_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_V133_FREQUENCY_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_V133_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_V13_GENOTYPE_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_V13_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_V140_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_V200_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANT_V210_TAG - Static variable in class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader VARIANTS_BIT_LEFT_INSERTION - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs VARIANTS_BIT_POS_INSERTION - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs VARIANTS_BIT_RIGHT_INSERTION - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs VARIANTS_BITMASK_RIGHT_INSERTION - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs variants_close_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase VARIANTS_CONF_FILTER_VALUE - Static variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper VARIANTS_CONFIDENCE_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs VARIANTS_COVERAGE_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs variants_filter_threshold - Variable in class com.pacbio.secondary.vis.data.session.options.DetailsOptions variants_help_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase variants_save_btn - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase variants_tab - Variable in class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase VARIANTS_TYPE_DELETION - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs VARIANTS_TYPE_INSERTION - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs VARIANTS_TYPE_OFFSET - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs VARIANTS_TYPE_SUBSTITUTION - Static variable in class com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs variations_splitter - Static variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal VCF_AD_RSLT - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_ALT_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_CHROM_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_COVERAGE_TAG - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_COVERAGE_TAG - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFReader VCF_DP_RSLT - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_FILTER_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_FORMAT_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_FORMATS_GENOTYPE_SEPARATOR - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_FORMATS_RSLT_SEPARATOR - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_FORMATS_SEPARATOR - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_GQ_RSLT - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_GT_RSLT - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_ID_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_INFO_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_NO_SAMPLE_DATA - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_PACBIO_TAG - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFReader VCF_PL_RSLT - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_POS_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_QUAL_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_REF_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_START_SAMPLE_COL - Variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCF_VERSION_TAG - Static variable in class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCFMultiSampleReader - Class in com.pacbio.secondary.vis.io.vcf VCFMultiSampleReader() - Constructor for class com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader VCFMultiSampleReader.vcf_version - Enum in com.pacbio.secondary.vis.io.vcf VCFReader - Class in com.pacbio.secondary.vis.io.vcf VCFReader() - Constructor for class com.pacbio.secondary.vis.io.vcf.VCFReader verify(JComponent) - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedDoubleInputVerifier verify(JComponent) - Method in class com.pacbio.secondary.vis.gui.dialogs.FormattedFieldInputVerifier VERSION_DATE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants VERSION_STRING - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants VersionService - Class in com.pacbio.secondary.vis.svc.server VersionService() - Constructor for class com.pacbio.secondary.vis.svc.server.VersionService view - Variable in class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog view_intervals - Variable in class com.pacbio.secondary.vis.data.session.SessionDataHelper viewEvent() - Method in class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel viewHistory - Variable in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase ViewLayoutInfo - Class in com.pacbio.secondary.vis.gui.draw.views ViewLayoutInfo() - Constructor for class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo viewPushpin(VioletApp, int) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage viewSubReadsData - Variable in class com.pacbio.secondary.vis.common.utils.PropertiesHelper VIOLET_HTML_HREF_TAG_NAVIGATE - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants violet_toolbar_items - Static variable in class com.pacbio.secondary.vis.gui.control.VioletToolBar VIOLET_USER_DATA_DIRECTORY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants VioletApp - Class in com.pacbio.secondary.vis.gui.app VioletApp(String[], VioletAppBase.APP_TYPE) - Constructor for class com.pacbio.secondary.vis.gui.app.VioletApp VioletAppBase - Class in com.pacbio.secondary.vis.gui.app Base class of main application VioletAppBase() - Constructor for class com.pacbio.secondary.vis.gui.app.VioletAppBase VioletAppBase.APP_TYPE - Enum in com.pacbio.secondary.vis.gui.app VioletFileAnalyzer - Class in com.pacbio.secondary.vis.io.importer VioletFileAnalyzer() - Constructor for class com.pacbio.secondary.vis.io.importer.VioletFileAnalyzer VioletFrame - Class in com.pacbio.secondary.vis.gui.frame Main application frame. VioletFrame(VioletApp, String) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrame Entry point VioletFrame(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrame Used by desktop mode VioletFrameActions - Class in com.pacbio.secondary.vis.gui.frame VioletFrameActions(String) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrameActions VioletFrameBase - Class in com.pacbio.secondary.vis.gui.frame VioletFrameBase(String) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrameBase VioletFrameChanges - Class in com.pacbio.secondary.vis.gui.frame VioletFrameChanges(String) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges VioletFrameChanges.setOptimumZoomFactorsThreaded - Class in com.pacbio.secondary.vis.gui.frame VioletFrameChanges.setOptimumZoomFactorsThreaded(boolean, int) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges.setOptimumZoomFactorsThreaded VioletFrameCreate - Class in com.pacbio.secondary.vis.gui.frame VioletFrameCreate(String) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate VioletFrameDesktop - Class in com.pacbio.secondary.vis.gui.frame VioletFrameDesktop(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrameDesktop VioletFrameIO - Class in com.pacbio.secondary.vis.gui.frame VioletFrameIO(String) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrameIO VioletFrameSummary - Class in com.pacbio.secondary.vis.gui.frame VioletFrameSummary(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.frame.VioletFrameSummary VioletStatusBar - Class in com.pacbio.secondary.vis.gui.control This is a statusbar component with a text control for messages. VioletStatusBar() - Constructor for class com.pacbio.secondary.vis.gui.control.VioletStatusBar VioletToolBar - Class in com.pacbio.secondary.vis.gui.control VioletToolBar() - Constructor for class com.pacbio.secondary.vis.gui.control.VioletToolBar not used VioletToolBar(ActionListener, String) - Constructor for class com.pacbio.secondary.vis.gui.control.VioletToolBar VioletToolBar(ActionListener) - Constructor for class com.pacbio.secondary.vis.gui.control.VioletToolBar Used by summary frame only VioletToolBarTest - Class in com.pacbio.secondary.vis.gui.control Local test of app toolbar VioletToolBarTest() - Constructor for class com.pacbio.secondary.vis.gui.control.VioletToolBarTest VIS_SERVICE_PROGRAM_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants VIS_SERVICE_URL - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants visibleRow - Variable in class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable.TreeTableCellRenderer Last table/tree row asked to renderer. visit(int, IntervalTreeNode) - Method in class com.pacbio.secondary.vis.data.interval.IntervalTreeQuery.FilterVisitor visit(int, IntervalTreeNode) - Method in interface com.pacbio.secondary.vis.data.interval.IntervalTreeVisitor visitAllDirs(File) - Static method in class com.pacbio.secondary.vis.common.utils.FileUtils visitAllFiles(File) - Static method in class com.pacbio.secondary.vis.common.utils.FileUtils visitAllFiles(File, HDFService, String, int, long, long) - Static method in class com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest visitAllFiles(File) - Method in class com.pacbio.secondary.vis.update.SMRTViewUpdater Processes all vis.jnlp files under directory visitSingleDockableTitleBarPopUp(JPopupMenu, Dockable) - Method in class pub.vlsolutions.swing.docking.DockableActionCustomizer Override this method to add contextual items at the end of the pop-up menu which can be triggered on the title bar of a single dockable. visitTabSelectorPopUp(JPopupMenu, Dockable) - Method in class pub.vlsolutions.swing.docking.DockableActionCustomizer Override this method to add contextual items at the end of the pop-up menu which can be triggered on a tab selector. VisService - Class in com.pacbio.secondary.vis.svc.server VisService() - Constructor for class com.pacbio.secondary.vis.svc.server.VisService VisServiceCallbackHandler - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceCallbackHandler Callback class, Users can extend this class and implement their own receiveResult and receiveError methods. VisServiceCallbackHandler(Object) - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler User can pass in any object that needs to be accessed once the NonBlocking Web service call is finished and appropriate method of this CallBack is called. VisServiceCallbackHandler() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler Please use this constructor if you don't want to set any clientData VisServiceCallbackImpl - Class in com.pacbio.secondary.vis.svc.vis.client Class to receive callbacks for asynchronous axis2 web service calls Overrides auto-generated stubs, implements desired specialization VisServiceCallbackImpl(VioletApp, Object) - Constructor for class com.pacbio.secondary.vis.svc.vis.client.VisServiceCallbackImpl VisServiceLocalTest - Class in com.pacbio.secondary.vis.svc.server.test VisServiceLocalTest() - Constructor for class com.pacbio.secondary.vis.svc.server.test.VisServiceLocalTest VisServiceStub - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub(org.apache.axis2.context.ConfigurationContext, String) - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub Constructor that takes in a configContext VisServiceStub(org.apache.axis2.context.ConfigurationContext, String, boolean) - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub Constructor that takes in a configContext and useseperate listner VisServiceStub(org.apache.axis2.context.ConfigurationContext) - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub Default Constructor VisServiceStub() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub Default Constructor VisServiceStub.ExtensionMapper - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.ExtensionMapper() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.ExtensionMapper VisServiceStub.GetDefaultDirectoryResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetDefaultDirectoryResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse VisServiceStub.GetDefaultDirectoryResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetDefaultDirectoryResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse.Factory VisServiceStub.GetDirectoryList - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetDirectoryList() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList VisServiceStub.GetDirectoryList.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetDirectoryList.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList.Factory VisServiceStub.GetDirectoryListResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetDirectoryListResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse VisServiceStub.GetDirectoryListResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetDirectoryListResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse.Factory VisServiceStub.GetFastaSequence - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetFastaSequence() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence VisServiceStub.GetFastaSequence.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetFastaSequence.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence.Factory VisServiceStub.GetFastaSequenceResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetFastaSequenceResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse VisServiceStub.GetFastaSequenceResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetFastaSequenceResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse.Factory VisServiceStub.GetFile - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetFile() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile VisServiceStub.GetFile.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetFile.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile.Factory VisServiceStub.GetFileResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetFileResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse VisServiceStub.GetFileResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetFileResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse.Factory VisServiceStub.GetFilesInformation - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetFilesInformation() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation VisServiceStub.GetFilesInformation.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetFilesInformation.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation.Factory VisServiceStub.GetFilesInformationResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetFilesInformationResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse VisServiceStub.GetFilesInformationResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetFilesInformationResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse.Factory VisServiceStub.GetGZippedFile - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetGZippedFile() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile VisServiceStub.GetGZippedFile.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetGZippedFile.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile.Factory VisServiceStub.GetGZippedFileResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetGZippedFileResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse VisServiceStub.GetGZippedFileResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetGZippedFileResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse.Factory VisServiceStub.GetMetadataInfo - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetMetadataInfo() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo VisServiceStub.GetMetadataInfo.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetMetadataInfo.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo.Factory VisServiceStub.GetMetadataInfoResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetMetadataInfoResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse VisServiceStub.GetMetadataInfoResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetMetadataInfoResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse.Factory VisServiceStub.GetReferenceInfo - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetReferenceInfo() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo VisServiceStub.GetReferenceInfo.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetReferenceInfo.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo.Factory VisServiceStub.GetReferenceInfoResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetReferenceInfoResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse VisServiceStub.GetReferenceInfoResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetReferenceInfoResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse.Factory VisServiceStub.GetServiceInfoResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetServiceInfoResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse VisServiceStub.GetServiceInfoResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetServiceInfoResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse.Factory VisServiceStub.GetTracksListInfo - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetTracksListInfo() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo VisServiceStub.GetTracksListInfo.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetTracksListInfo.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo.Factory VisServiceStub.GetTracksListInfoResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.GetTracksListInfoResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse VisServiceStub.GetTracksListInfoResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.GetTracksListInfoResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse.Factory VisServiceStub.PutFile - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.PutFile() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile VisServiceStub.PutFile.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.PutFile.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile.Factory VisServiceStub.PutFileResponse - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.PutFileResponse() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse VisServiceStub.PutFileResponse.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.PutFileResponse.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse.Factory VisServiceStub.WsContigInfo - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.WsContigInfo() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo VisServiceStub.WsContigInfo.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.WsContigInfo.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo.Factory VisServiceStub.WsFileInfo - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.WsFileInfo() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo VisServiceStub.WsFileInfo.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.WsFileInfo.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo.Factory VisServiceStub.WsJobMetadataInfo - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.WsJobMetadataInfo() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo VisServiceStub.WsJobMetadataInfo.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.WsJobMetadataInfo.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo.Factory VisServiceStub.WsReferenceInfo - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.WsReferenceInfo() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo VisServiceStub.WsReferenceInfo.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.WsReferenceInfo.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo.Factory VisServiceStub.WsTrackInfo - Class in com.pacbio.secondary.vis.svc.vis.client.auto VisServiceStub.WsTrackInfo() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo VisServiceStub.WsTrackInfo.Factory - Class in com.pacbio.secondary.vis.svc.vis.client.auto Factory class that keeps the parse method VisServiceStub.WsTrackInfo.Factory() - Constructor for class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo.Factory VisServiceWrapper - Class in com.pacbio.secondary.vis.svc.vis.client VisServiceWrapper(String, VioletApp) - Constructor for class com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper VisThreadPool - Class in com.pacbio.secondary.vis.svc.server.threads VisThreadPool(VisWorkToDoQueue) - Constructor for class com.pacbio.secondary.vis.svc.server.threads.VisThreadPool VisWorkDoneQueue - Class in com.pacbio.secondary.vis.svc.server.threads VisWorkDoneQueue() - Constructor for class com.pacbio.secondary.vis.svc.server.threads.VisWorkDoneQueue VisWorkerThread - Class in com.pacbio.secondary.vis.svc.server.threads VisWorkerThread(VisWorkToDoQueue, VisWorkDoneQueue) - Constructor for class com.pacbio.secondary.vis.svc.server.threads.VisWorkerThread VisWorkSenderThread - Class in com.pacbio.secondary.vis.svc.server.threads VisWorkSenderThread(VisWorkDoneQueue, OutputStream) - Constructor for class com.pacbio.secondary.vis.svc.server.threads.VisWorkSenderThread VisWorkToDoQueue - Class in com.pacbio.secondary.vis.svc.server.threads VisWorkToDoQueue() - Constructor for class com.pacbio.secondary.vis.svc.server.threads.VisWorkToDoQueue VLButtonUI - Class in pub.vlsolutions.swing.toolbars A UI for toolbar buttons : replaces the look and feel default UI to have a unified toolbar rendering. VLButtonUI() - Constructor for class pub.vlsolutions.swing.toolbars.VLButtonUI VLToolBar - Class in pub.vlsolutions.swing.toolbars A JToolbar suitable for drag and drop purposes. VLToolBar() - Constructor for class pub.vlsolutions.swing.toolbars.VLToolBar Constructs a toolbar with a null name (this toolbar will not be able to write its structure in a XML encoder, unless you call setName(String) with a non null name before saving). VLToolBar(String) - Constructor for class pub.vlsolutions.swing.toolbars.VLToolBar Constructs a toolbar with the given name. VLToolBarLayout - Class in pub.vlsolutions.swing.toolbars The layout for VLToolBar (supports horizontal and vertical orientation). VLToolBarLayout() - Constructor for class pub.vlsolutions.swing.toolbars.VLToolBarLayout VLToolBarLayout(boolean) - Constructor for class pub.vlsolutions.swing.toolbars.VLToolBarLayout Constructs a new Layout. VLToolBarLayout(boolean, int) - Constructor for class pub.vlsolutions.swing.toolbars.VLToolBarLayout Constructs a new Layout. W waitCursor() - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameBase Sets the current mouse cursor to a waiting cursor (e.g. WEB_BROWSER_PANEL_KEY - Static variable in class com.pacbio.secondary.vis.common.utils.constants.PanelConstants WEB_SERVICES_CLIENT_TIMEOUT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants WEB_SERVICES_DEFAULT_PORT - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants WebBrowserPanel - Class in com.pacbio.secondary.vis.gui.panels WebBrowserPanel(VioletApp, String, String, boolean, boolean) - Constructor for class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel creates a web browser with toolbar, opens specified url WebBrowserPanel(VioletApp, String, String, String, String) - Constructor for class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel creates a web browser with toolbar, opens specified html string WebBrowserPanel(VioletApp, JFrame) - Constructor for class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel creates webbrowser with no toolbar, open html text passed in WebBrowserPanel.WebBrowserEditorPane - Class in com.pacbio.secondary.vis.gui.panels WebBrowserPanel.WebBrowserEditorPane(WebBrowserPanel, URL) - Constructor for class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserEditorPane WebBrowserPanel.WebBrowserEditorPane(WebBrowserPanel, String) - Constructor for class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserEditorPane WebBrowserPanel.WebBrowserToolBar - Class in com.pacbio.secondary.vis.gui.panels WebBrowserPanel.WebBrowserToolBar(boolean) - Constructor for class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserToolBar WebBrowserUtils - Class in com.pacbio.secondary.vis.common.utils WebBrowserUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.WebBrowserUtils websearchURL - Variable in class com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo WebStartApp - Class in com.pacbio.secondary.vis.gui.app WebStartApp(String[]) - Constructor for class com.pacbio.secondary.vis.gui.app.WebStartApp WholeGenomePanel - Class in com.pacbio.secondary.vis.gui.panels WholeGenomePanel(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.panels.WholeGenomePanel WholeGenomePanel.CtgInfo - Class in com.pacbio.secondary.vis.gui.panels WholeGenomePanel.CtgInfo(int, long) - Constructor for class com.pacbio.secondary.vis.gui.panels.WholeGenomePanel.CtgInfo WIN_FLAG - Static variable in class com.pacbio.secondary.vis.common.utils.WebBrowserUtils WIN_PATH - Static variable in class com.pacbio.secondary.vis.common.utils.WebBrowserUtils WINDOWS_FILE_SEPARATOR - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants workspace - Variable in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest Workspace - Class in pub.vlsolutions.swing.docking.ws A logical organization of dockables. Workspace() - Constructor for class pub.vlsolutions.swing.docking.ws.Workspace Creates a workspace with a single default WSDesktop WorkspaceButton - Class in pub.vlsolutions.swing.docking.ws A simple button that applies a workspace to a given Docking context when pressed . WorkspaceButton() - Constructor for class pub.vlsolutions.swing.docking.ws.WorkspaceButton default constructor WorkspaceButton(String) - Constructor for class pub.vlsolutions.swing.docking.ws.WorkspaceButton constructor with a menu text WorkspaceButton(String, Icon) - Constructor for class pub.vlsolutions.swing.docking.ws.WorkspaceButton constructor with a menu text and an icon WorkspaceException - Exception in pub.vlsolutions.swing.docking.ws An exception raised when a workspace operation has gone wrong (can encapsulate another exception). WorkspaceException(String) - Constructor for exception pub.vlsolutions.swing.docking.ws.WorkspaceException WorkspaceException(Exception) - Constructor for exception pub.vlsolutions.swing.docking.ws.WorkspaceException WorkspaceException(String, Exception) - Constructor for exception pub.vlsolutions.swing.docking.ws.WorkspaceException WorkspaceManager - Class in com.pacbio.secondary.vis.gui.desktop WorkspaceManager(VioletApp) - Constructor for class com.pacbio.secondary.vis.gui.desktop.WorkspaceManager WorkspaceMenuItem - Class in pub.vlsolutions.swing.docking.ws A simple menu item that applies a workspace to a given Docking context when selected . WorkspaceMenuItem() - Constructor for class pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem Default constructor WorkspaceMenuItem(String) - Constructor for class pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem constructor with a menu text WorkspaceMenuItem(String, Icon) - Constructor for class pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem constructor with a menu text and an icon writeAllViewsToPDFFile(String, Boolean[]) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO writeAllViewsToPNGFile(String, Boolean[]) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO writeBytesToFile(String, byte[]) - Static method in class com.pacbio.secondary.vis.svc.server.utils.ServiceUtils writeChunkToDataset(H5ScalarDS, HDF5HyperslabInfo, Object) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File Writes a block of data to the selected dataset. writeDetailsOptionsToPropertiesFile() - Method in class com.pacbio.secondary.vis.data.session.options.DetailsOptions writeFileInfoToCacheFile(String, int, int) - Method in class com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer writeImageToByteArray(BufferedImage, String) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils writeImageToFile(BufferedImage, String) - Static method in class com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils Write a BufferedImage to a File. writeJNLP(File) - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper writePDFFile(OutputStream, IdeogramViewPrintingHelper) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO writePNGFile(FileOutputStream, IdeogramViewPrintingHelper) - Method in class com.pacbio.secondary.vis.gui.frame.VioletFrameIO writeROIsDataToByteArray() - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage writeROIsToFile(Component, VioletApp, File) - Method in class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage writeSessionData(File) - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper writeSessionDataToByteArray() - Method in class com.pacbio.secondary.vis.data.session.SessionDataHelper writeStringAttribute(HObject, String, String) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File Creates a new String attribute in the specified group or dataset and writes the passed in value. writeUIntAttribute(HObject, String, long) - Method in class com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File Creates a new UInt attribute in the specified group or dataset and writes the passed in value writeXML(OutputStream) - Method in class pub.vlsolutions.swing.docking.DockingContext Saves the current desktop configuration into an XML stream. writeXML(OutputStream) - Method in class pub.vlsolutions.swing.docking.DockingDesktop Saves the current desktop configuration into an XML stream. writeXML(OutputStream) - Method in class pub.vlsolutions.swing.docking.ws.Workspace Saves the workspace layout into an XML stream. writeXML(OutputStream) - Method in class pub.vlsolutions.swing.toolbars.ToolBarIO Saves the current toolbar configuration into an XML stream. writeXMLObject(Object, File) - Static method in class com.pacbio.secondary.vis.common.utils.XMLObjectSerializerUtils Writes an object to an XML file writeXMLObject(Object) - Static method in class com.pacbio.secondary.vis.common.utils.XMLObjectSerializerUtils Writes an object to a byte array WsContigInfo - Class in com.pacbio.secondary.vis.svc.server.data WsContigInfo() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsContigInfo WsContigInfo(String, String, String, int) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsContigInfo WsContigInfo(WsContigInfo) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsContigInfo WSDesktop - Class in pub.vlsolutions.swing.docking.ws A desktop part of a workspace. WSDesktop() - Constructor for class pub.vlsolutions.swing.docking.ws.WSDesktop Constructs a WSDesktop with "default" as name WSDesktop(String) - Constructor for class pub.vlsolutions.swing.docking.ws.WSDesktop Constructs a WSDesktop with a given name WSDockKey - Class in pub.vlsolutions.swing.docking.ws Defines a key associated to a dockable in a workspace. WSDockKey(String) - Constructor for class pub.vlsolutions.swing.docking.ws.WSDockKey WsFastaSequenceInfo - Class in com.pacbio.secondary.vis.svc.server.data WsFastaSequenceInfo() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsFastaSequenceInfo WsFileInfo - Class in com.pacbio.secondary.vis.svc.server.data WsFileInfo() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsFileInfo WsFileInfo(WsFileInfo) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsFileInfo WsIntervalSvc - Class in com.pacbio.secondary.vis.svc.server.data WsIntervalSvc() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc WsIntervalSvc(int, int, int, byte) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc WsIPDConsensusInfo - Class in com.pacbio.secondary.vis.svc.server.data WsIPDConsensusInfo() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo WsIPDConsensusInfo(String, int[]) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo WsJobMetadataInfo - Class in com.pacbio.secondary.vis.svc.server.data WsJobMetadataInfo() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo WsRead - Class in com.pacbio.secondary.vis.svc.server.data WsRead() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsRead WsRead(String, int, int, int, byte, String, double, byte[], byte[], int, int) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsRead called by CMPH5FileWrapper::getAlignedResultsFromFile WsRead(String, int, int, int, byte, double, int, boolean, int, int) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsRead called by CMPH5FileWrapper::getAnnotatedResultsFromFile WsReadEx - Class in com.pacbio.secondary.vis.svc.server.data WsReadEx() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsReadEx serialization only WsReadEx(int, String, int, int, int, byte, double, int, int) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsReadEx WsReferenceInfo - Class in com.pacbio.secondary.vis.svc.server.data WsReferenceInfo() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo WsReferenceInfo(String) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo WsResults - Class in com.pacbio.secondary.vis.svc.server.data This is an abstraction to represent a set of results and associated detailed metadata WsResults(String) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsResults WsResults(WsResultsInfo) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsResults WsResults() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsResults de-serialization only WsResultsInfo - Class in com.pacbio.secondary.vis.svc.server.data WsResultsInfo(String, boolean, int, long, long, int, long, double) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo WsResultsInfo(String) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo No data, error code only WsResultsInfo() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo de-serialization only WsTrackInfo - Class in com.pacbio.secondary.vis.svc.server.data WsTrackInfo() - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsTrackInfo WsTrackInfo(String, String, String) - Constructor for class com.pacbio.secondary.vis.svc.server.data.WsTrackInfo X XCoordToBase(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw Transforms a canvas x coordinate to basepairs. xCoordToTrackIndex(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw Converts a x-coordinate in this panel into a track index value. XML_INFO_REFERENCE_MARKER - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants XML_REFERENCE_INFO_NAME - Static variable in class com.pacbio.secondary.vis.common.utils.constants.ProgramConstants XMLInfoBaseParser - Class in com.pacbio.secondary.vis.svc.server.data.parser XMLInfoBaseParser() - Constructor for class com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser XMLInfoConstants - Class in com.pacbio.secondary.vis.common.utils.constants XMLInfoConstants() - Constructor for class com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants XMLObjectSerializerUtils - Class in com.pacbio.secondary.vis.common.utils XMLObjectSerializerUtils() - Constructor for class com.pacbio.secondary.vis.common.utils.XMLObjectSerializerUtils xsin(double) - Static method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular Y YCoordToBase(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw Transforms a canvas y coordinate to basepairs. yCoordToMarkerCollectionIndex(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw returns index of markercollection for this y coordinate yCoordToMarkerCollectionIndexNew(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw yCoordToMarkerCollectionIndexOrg(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw returns index of markercollection for this y coordinate yCoordToSlotIndex(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo returns slot index from y coordinate yCoordToTrackIndex(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw returns index of track in graph, e.g. yCoordToTrackIndex(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo returns non-absolute track index from Y coord... Z ZERO - Static variable in class com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel ZERO - Static variable in class com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel zoomToBases() - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData zoom to single base level at once zoomVisibleGenomicRange(int) - Method in class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents Zooms in (for dy < 0) or out (for dy > 0). _ _operations - Variable in class com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub _operations - Variable in class com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _