Uses of Class
com.pacbio.secondary.vis.gui.app.VioletApp

Packages that use VioletApp

Package	Description
com.pacbio.secondary.vis.common.utils	Client/Server common utilities
com.pacbio.secondary.vis.common.utils.constants	Client/Server common constants
com.pacbio.secondary.vis.data.db	Ideogram and genes collections support
com.pacbio.secondary.vis.data.filesystem	Abstraction layer for local and remote filesystem access
com.pacbio.secondary.vis.data.session	Client side user session data models
com.pacbio.secondary.vis.data.session.timer	Timer and timer task for restoring user session
com.pacbio.secondary.vis.data.table.model	Genomic tables data models
com.pacbio.secondary.vis.data.variableresolution.model.gff	GFF3 variable resolution data model
com.pacbio.secondary.vis.gui.app	Main application classes, support local, remote, webstart based deployment
com.pacbio.secondary.vis.gui.desktop	Support for dockable windows based desktop
com.pacbio.secondary.vis.gui.dialogs	Application dialogs
com.pacbio.secondary.vis.gui.draw.utils	Drawing utilities
com.pacbio.secondary.vis.gui.draw.views	Genomic views
com.pacbio.secondary.vis.gui.frame	Client application main frame
com.pacbio.secondary.vis.gui.panels	Specialized dockable genomic panels
com.pacbio.secondary.vis.gui.panels.base	Generic dockable genomic panels
com.pacbio.secondary.vis.io.epipro	Parser for epipro/unmapped reads data
com.pacbio.secondary.vis.io.export	GFF3 export support
com.pacbio.secondary.vis.io.gff	GFF3 reader support
com.pacbio.secondary.vis.io.gff.modifications	GFF3 Base Modifications Info support
com.pacbio.secondary.vis.io.gff.summary	GFF3 Summary Info support
com.pacbio.secondary.vis.io.gff.variants	GFF3 variants support
com.pacbio.secondary.vis.io.importer	Local and remote data files import support
com.pacbio.secondary.vis.io.motifs	Parser for Motifs files
com.pacbio.secondary.vis.io.ucsc.gtf.reader	Parser for UCSC generated gtf (gene transfer format) files
com.pacbio.secondary.vis.io.update	Support for interactive data updates after user preferences changes
com.pacbio.secondary.vis.io.vcf	Parser for VCF (variants) files
com.pacbio.secondary.vis.smrtcloud	SMRT Cloud deployment support
com.pacbio.secondary.vis.svc.hdf.client	HDFService client support
com.pacbio.secondary.vis.svc.vis.client	VisService client support

Uses of VioletApp in com.pacbio.secondary.vis.common.utils

Fields in com.pacbio.secondary.vis.common.utils declared as VioletApp

Modifier and Type	Field and Description
static VioletApp	ProgramGlobals.main_app

Methods in com.pacbio.secondary.vis.common.utils with parameters of type VioletApp

Modifier and Type	Method and Description
static boolean	FileUtils.acceptOverwriteExistingServerFile(VioletApp app, java.lang.String directory, java.lang.String filename)
static int	GenomicUtils.getModeFromOptions(VioletApp app, boolean updateData) Creates mode value for results web services from runtime options

Uses of VioletApp in com.pacbio.secondary.vis.common.utils.constants

Constructors in com.pacbio.secondary.vis.common.utils.constants with parameters of type VioletApp

Constructor and Description
EpiProPalette(VioletApp app)

Uses of VioletApp in com.pacbio.secondary.vis.data.db

Methods in com.pacbio.secondary.vis.data.db with parameters of type VioletApp

Modifier and Type	Method and Description
boolean	MotifsDB.readMotifsFile(VioletApp app, java.lang.String filename)

Uses of VioletApp in com.pacbio.secondary.vis.data.filesystem

Constructors in com.pacbio.secondary.vis.data.filesystem with parameters of type VioletApp

Constructor and Description
RemoteFileSystemModel(VioletApp main_app, java.lang.String svc_url, java.lang.String pattern)

Uses of VioletApp in com.pacbio.secondary.vis.data.session

Fields in com.pacbio.secondary.vis.data.session declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	DataStorageBase.app
protected VioletApp	SessionDataHelper.main_app

Methods in com.pacbio.secondary.vis.data.session with parameters of type VioletApp

Modifier and Type	Method and Description
boolean	RegionsOfInterestStorage.addNewPushpin(VioletApp main_app, java.lang.String user_data, byte[] image)
boolean	RegionsOfInterestStorage.addNewPushpinInteractive(java.awt.Component parent, VioletApp main_app)
protected java.lang.String	RegionsOfInterestStorage.getButtonImageHtml(VioletApp main_app, java.lang.String tag, java.lang.String imagename, int index)
java.lang.String	RegionsOfInterestStorage.getHtmlText(VioletApp main_app)
protected java.lang.String	RegionsOfInterestStorage.getNewPushpinInfo(VioletApp main_app)
boolean	RegionsOfInterestStorage.readROIsFromFile(java.awt.Component parent, VioletApp main_app, java.io.File file)
void	SessionDataHelper.restoreAppOptions(VioletApp app) Restores app options into app
void	RegionsOfInterestStorage.showDialog(VioletApp main_app)
void	RegionsOfInterestStorage.viewPushpin(VioletApp main_app, int index)
boolean	RegionsOfInterestStorage.writeROIsToFile(java.awt.Component parent, VioletApp main_app, java.io.File file)

Constructors in com.pacbio.secondary.vis.data.session with parameters of type VioletApp

Constructor and Description
DataStorage(VioletApp app)
DataStorageBase(VioletApp app)
SessionDataHelper(VioletApp app) Save session data from app into this class

Uses of VioletApp in com.pacbio.secondary.vis.data.session.timer

Fields in com.pacbio.secondary.vis.data.session.timer declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	SessionDataTimer.main_app

Methods in com.pacbio.secondary.vis.data.session.timer that return VioletApp

Modifier and Type	Method and Description
VioletApp	SessionDataTimer.getVioletApp()
protected VioletApp	SessionDataTimerTask.getVioletApp()

Constructors in com.pacbio.secondary.vis.data.session.timer with parameters of type VioletApp

Constructor and Description
SessionDataTimer(VioletApp app)

Uses of VioletApp in com.pacbio.secondary.vis.data.table.model

Fields in com.pacbio.secondary.vis.data.table.model declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	TableModelBase.main_app

Methods in com.pacbio.secondary.vis.data.table.model that return VioletApp

Modifier and Type	Method and Description
VioletApp	TableModelBase.getVioletApp() return the app

Constructors in com.pacbio.secondary.vis.data.table.model with parameters of type VioletApp

Constructor and Description
TableModelAnnotations(VioletApp app)
TableModelBase(VioletApp app)
TableModelDeNovo(VioletApp app)
TableModelGenomicInterval(VioletApp app)
TableModelTrack(VioletApp app)

Uses of VioletApp in com.pacbio.secondary.vis.data.variableresolution.model.gff

Methods in com.pacbio.secondary.vis.data.variableresolution.model.gff with parameters of type VioletApp

Modifier and Type	Method and Description
abstract int	GFFDataModel.readElements(VioletApp app, java.io.Reader reader)

Uses of VioletApp in com.pacbio.secondary.vis.gui.app

Subclasses of VioletApp in com.pacbio.secondary.vis.gui.app

Modifier and Type	Class and Description
class	DesktopApp
class	LocalTestApp
class	WebStartApp

Uses of VioletApp in com.pacbio.secondary.vis.gui.desktop

Fields in com.pacbio.secondary.vis.gui.desktop declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	WorkspaceManager.main_app

Methods in com.pacbio.secondary.vis.gui.desktop with parameters of type VioletApp

Modifier and Type	Method and Description
static java.lang.String	WorkspaceManager.getLoadUserWorkspaceFilename(java.awt.Component frame, VioletApp app)

Constructors in com.pacbio.secondary.vis.gui.desktop with parameters of type VioletApp

Constructor and Description
WorkspaceManager(VioletApp main_app)

Uses of VioletApp in com.pacbio.secondary.vis.gui.dialogs

Fields in com.pacbio.secondary.vis.gui.dialogs declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	GoToDialog.app
protected VioletApp	PreferencesDialogBase.app
protected VioletApp	InspectDataDialog.main_app
protected VioletApp	RegionsOfInterestDialog.main_app

Methods in com.pacbio.secondary.vis.gui.dialogs with parameters of type VioletApp

Modifier and Type	Method and Description
protected java.lang.String	AboutDialog.getServicesInfo(VioletApp app)

Constructors in com.pacbio.secondary.vis.gui.dialogs with parameters of type VioletApp

Constructor and Description
AboutDialog(java.awt.Frame owner, VioletApp app)
EpiProColorOptionsPane(VioletApp app, javax.swing.event.TableModelListener listener, int table_width)
GoToDialog(VioletApp app, java.lang.String[] contigs, java.lang.String contig)
InspectDataDialog(VioletApp app, long location)
OpenRemoteDataHelper(VioletApp main_app, java.lang.String svc_url)
PreferencesDialogEx(VioletApp violet)
RegionsOfInterestDialog(VioletApp main_app, RegionsOfInterestStorage storage)
RemoveTrackDialog(VioletApp app, java.awt.Frame owner)
SelectFileDialog(VioletApp app, java.awt.Frame owner, java.lang.String svc_url, java.lang.String title, java.lang.String pattern, boolean remote, boolean showHelpButton)

Uses of VioletApp in com.pacbio.secondary.vis.gui.draw.utils

Methods in com.pacbio.secondary.vis.gui.draw.utils with parameters of type VioletApp

Modifier and Type	Method and Description
static java.lang.String	InfoBuilder.getSessionProperties(VioletApp app) creates html info of all loaded data

Uses of VioletApp in com.pacbio.secondary.vis.gui.draw.views

Fields in com.pacbio.secondary.vis.gui.draw.views declared as VioletApp

Modifier and Type	Field and Description
protected static VioletApp	GenomicViewBase.main_app
protected VioletApp	GenomicViewCircular.main_app

Methods in com.pacbio.secondary.vis.gui.draw.views that return VioletApp

Modifier and Type	Method and Description
VioletApp	GenomicViewBase.getVioletApp()

Constructors in com.pacbio.secondary.vis.gui.draw.views with parameters of type VioletApp

Constructor and Description
GenomicViewBase(VioletApp app)
GenomicViewCircular(VioletApp mainApp)
GenomicViewData(VioletApp main_app)
GenomicViewDetails(VioletApp mainApp)
GenomicViewDetailsData(VioletApp mainApp)
GenomicViewDetailsDraw(VioletApp mainApp)
GenomicViewDraw(VioletApp main_app)
GenomicViewEvents(VioletApp main_app)
GenomicViewHorizontal(VioletApp mainApp)
GenomicViewInspect(VioletApp mainApp)
GenomicViewRegion(VioletApp main_app)
GenomicViewSingleContig(VioletApp main_app, int contig)
GenomicViewVertical(VioletApp mainApp)

Uses of VioletApp in com.pacbio.secondary.vis.gui.frame

Fields in com.pacbio.secondary.vis.gui.frame declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	VioletFrameBase.main_app

Methods in com.pacbio.secondary.vis.gui.frame that return VioletApp

Modifier and Type	Method and Description
VioletApp	VioletFrameBase.getVioletApp()

Constructors in com.pacbio.secondary.vis.gui.frame with parameters of type VioletApp

Constructor and Description
VioletFrame(VioletApp app) Used by desktop mode
VioletFrame(VioletApp app, java.lang.String title) Entry point
VioletFrameDesktop(VioletApp app)
VioletFrameSummary(VioletApp app)

Uses of VioletApp in com.pacbio.secondary.vis.gui.panels

Fields in com.pacbio.secondary.vis.gui.panels declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	WebBrowserPanel.main_app

Constructors in com.pacbio.secondary.vis.gui.panels with parameters of type VioletApp

Constructor and Description
DeNovoTablePanel(VioletApp main_app, java.lang.String dockkey, java.lang.String name, java.lang.String tooltip, boolean enable_filter)
GenomicTablePanel(VioletApp main_app, java.lang.String dockkey, java.lang.String name, java.lang.String tooltip, boolean enable_filter)
SelectionInfoPanel(VioletApp main_app)
WebBrowserPanel(VioletApp main_app, javax.swing.JFrame frame) creates webbrowser with no toolbar, open html text passed in
WebBrowserPanel(VioletApp main_app, java.lang.String dockey, java.lang.String url, boolean use_external_browser, boolean url_editable) creates a web browser with toolbar, opens specified url
WebBrowserPanel(VioletApp main_app, java.lang.String dockey, java.lang.String title, java.lang.String tooltip, java.lang.String html) creates a web browser with toolbar, opens specified html string
WholeGenomePanel(VioletApp app)

Uses of VioletApp in com.pacbio.secondary.vis.gui.panels.base

Fields in com.pacbio.secondary.vis.gui.panels.base declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	TablePanelBase.main_app

Constructors in com.pacbio.secondary.vis.gui.panels.base with parameters of type VioletApp

Constructor and Description
TablePanelBase(VioletApp main_app, java.lang.String dockkey, java.lang.String name, java.lang.String tooltip, boolean enable_filter)

Uses of VioletApp in com.pacbio.secondary.vis.io.epipro

Methods in com.pacbio.secondary.vis.io.epipro with parameters of type VioletApp

Modifier and Type	Method and Description
protected void	EpiProReadsReader.initContigInfo(VioletApp app)
void	EpiProReadsReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
protected Marker	EpiProReadsReader.processReadRecord(VioletApp app, java.lang.String[] ar, int contig_idx)
void	EpiProReadsReader.readElements(VioletApp app, java.io.Reader reader)
protected void	EpiProReadsReader.UpdateProgressBar(VioletApp app, double pct)

Uses of VioletApp in com.pacbio.secondary.vis.io.export

Fields in com.pacbio.secondary.vis.io.export declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	ExportDataUtils.main_app

Methods in com.pacbio.secondary.vis.io.export with parameters of type VioletApp

Modifier and Type	Method and Description
protected void	ExportRegionAsGFF.exportDetailsAsGFF(VioletApp app, java.lang.String path)
void	ExportRegionAsGFF.exportDetailsViewDataAsGFF(VioletApp app)
protected void	ExportDataUtils.exportTableAsGFF(VioletApp app, java.lang.String path) exports table view as gff
protected void	ExportDataUtils.exportViewAsGFF(VioletApp app, java.lang.String path, boolean isDetails) exports region or details view as gff
java.lang.String	ExportRegionAsGFF.getDefaultDataFilename(VioletApp app)

Constructors in com.pacbio.secondary.vis.io.export with parameters of type VioletApp

Constructor and Description
ExportDataUtils(VioletApp app)

Uses of VioletApp in com.pacbio.secondary.vis.io.gff

Methods in com.pacbio.secondary.vis.io.gff with parameters of type VioletApp

Modifier and Type	Method and Description
void	GFF3Reader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	GFF3Reader.readElements(VioletApp app, java.io.Reader reader) Loads a marker collection from a stream.

Uses of VioletApp in com.pacbio.secondary.vis.io.gff.modifications

Methods in com.pacbio.secondary.vis.io.gff.modifications with parameters of type VioletApp

Modifier and Type	Method and Description
void	GFFModificationsReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	GFFModificationsReader.readElements(VioletApp app, java.io.Reader reader) Loads base mods or motifs info

Uses of VioletApp in com.pacbio.secondary.vis.io.gff.summary

Methods in com.pacbio.secondary.vis.io.gff.summary with parameters of type VioletApp

Modifier and Type	Method and Description
void	GFFSummaryReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	GFFSummaryReader.readElements(VioletApp app, java.io.Reader reader) Loads summary information

Uses of VioletApp in com.pacbio.secondary.vis.io.gff.variants

Methods in com.pacbio.secondary.vis.io.gff.variants with parameters of type VioletApp

Modifier and Type	Method and Description
void	GFFVariantsReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	GFFVariantsReader.readElements(VioletApp app, java.io.Reader reader) Loads variants info

Uses of VioletApp in com.pacbio.secondary.vis.io.importer

Fields in com.pacbio.secondary.vis.io.importer declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	ImportDataHelper.app

Methods in com.pacbio.secondary.vis.io.importer with parameters of type VioletApp

Modifier and Type	Method and Description
protected void	DataFileInfo.lookIntoFile(java.lang.String file_name, VioletApp app)

Constructors in com.pacbio.secondary.vis.io.importer with parameters of type VioletApp

Constructor and Description
DataFileInfo(java.io.File file, VioletApp app)
DataFileInfo(java.lang.String file_name, VioletApp app) Open and analyze file to find out what type it is and if it requires sub-sampling Called by background (from server) loader
ImportDataHelper(VioletApp app) constructor

Uses of VioletApp in com.pacbio.secondary.vis.io.motifs

Methods in com.pacbio.secondary.vis.io.motifs with parameters of type VioletApp

Modifier and Type	Method and Description
int	MotifsReader.loadFromFile(java.io.File file, VioletApp app)
int	MotifsReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	MotifsReader.readElements(VioletApp app, java.io.Reader reader)

Uses of VioletApp in com.pacbio.secondary.vis.io.ucsc.gtf.reader

Methods in com.pacbio.secondary.vis.io.ucsc.gtf.reader with parameters of type VioletApp

Modifier and Type	Method and Description
void	UCSCGTFReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	UCSCGTFReader.readElements(VioletApp app, java.io.Reader reader) Loads a marker collection from a stream.

Uses of VioletApp in com.pacbio.secondary.vis.io.update

Methods in com.pacbio.secondary.vis.io.update with parameters of type VioletApp

Modifier and Type	Method and Description
void	UpdateInsertionsDataHelper.start(VioletApp app, InspectDataDialog dlg, GenomicViewInspect view, long location)

Constructors in com.pacbio.secondary.vis.io.update with parameters of type VioletApp

Constructor and Description
UpdateDetailsDataHelper.UpdateDetailsThreadHelper(VioletApp main_app)
UpdateDetailsDataHelper(VioletApp violet)
UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper(VioletApp app, InspectDataDialog dlg, GenomicViewInspect view, long location)
UpdateModificationsDataHelper.ThreadHelper(VioletApp main_app)
UpdateModificationsDataHelper(VioletApp violet)
UpdateVariantsDataHelper.ThreadHelper(VioletApp main_app)
UpdateVariantsDataHelper(VioletApp violet)

Uses of VioletApp in com.pacbio.secondary.vis.io.vcf

Methods in com.pacbio.secondary.vis.io.vcf with parameters of type VioletApp

Modifier and Type	Method and Description
void	VCFMultiSampleReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
void	VCFReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	VCFMultiSampleReader.readElements(VioletApp app, java.io.Reader reader)
int	VCFReader.readElements(VioletApp app, java.io.Reader reader)

Uses of VioletApp in com.pacbio.secondary.vis.smrtcloud

Fields in com.pacbio.secondary.vis.smrtcloud declared as VioletApp

Modifier and Type	Field and Description
protected VioletApp	CloudTimer.main_app

Methods in com.pacbio.secondary.vis.smrtcloud that return VioletApp

Modifier and Type	Method and Description
VioletApp	CloudTimer.getVioletApp()

Methods in com.pacbio.secondary.vis.smrtcloud with parameters of type VioletApp

Modifier and Type	Method and Description
static long	CloudUtils.getSMRTCloudDataFileInfo(VioletApp app) returns negative value if file is found positive value with size in byte of directory if not found
static boolean	CloudUtils.isVisJnlpPresent(VioletApp app, java.lang.String job_metadata)

Constructors in com.pacbio.secondary.vis.smrtcloud with parameters of type VioletApp

Constructor and Description
CloudTimer(VioletApp app)

Uses of VioletApp in com.pacbio.secondary.vis.svc.hdf.client

Constructors in com.pacbio.secondary.vis.svc.hdf.client with parameters of type VioletApp

Constructor and Description
HDFServiceCallbackImpl(VioletApp app, java.lang.Object clientData)
HDFServiceWrapper(java.lang.String url, VioletApp app)

Uses of VioletApp in com.pacbio.secondary.vis.svc.vis.client

Constructors in com.pacbio.secondary.vis.svc.vis.client with parameters of type VioletApp

Constructor and Description
VisServiceCallbackImpl(VioletApp app, java.lang.Object clientData)
VisServiceWrapper(java.lang.String url, VioletApp app)