com.pacbio.secondary.vis.gui.frame

Class VioletFrameActions

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Frame

javax.swing.JFrame

com.pacbio.secondary.vis.gui.frame.VioletFrameBase

com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

com.pacbio.secondary.vis.gui.frame.VioletFrameIO

com.pacbio.secondary.vis.gui.frame.VioletFrameActions

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.ComponentListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.ChangeListener, javax.swing.event.TableModelListener, javax.swing.RootPaneContainer, javax.swing.WindowConstants, DockableSelectionListener, DockableStateChangeListener

Direct Known Subclasses:

VioletFrameCreate

public class VioletFrameActions
extends VioletFrameIO
implements java.awt.event.ActionListener

Author:

mmilletti

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

VioletFrameChanges.setOptimumZoomFactorsThreaded

Nested classes/interfaces inherited from class javax.swing.JFrame

javax.swing.JFrame.AccessibleJFrame

Nested classes/interfaces inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Nested classes/interfaces inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
protected GoToDialog	goto_dlg
static java.lang.String	menuAddTracks
static java.lang.String	menuAddTracksFromServer
static java.lang.String	menuAutoFitTableView
static java.lang.String	menuBookmarks
static java.lang.String	menuDecreaseDNASize
static java.lang.String	menuDecreaseKinetogramSize
static java.lang.String	menuDecreaseTrackSize
static java.lang.String	menuDefaultScale
static java.lang.String	menuExit
static java.lang.String	menuExportMarkers
static java.lang.String	menuFitViewsToPanels
static java.lang.String	menuGoToDevnet
static java.lang.String	menuGoToLocation
static java.lang.String	menuGoToPacBio
static java.lang.String	menuGroupFile
static java.lang.String	menuGroupHelp
static java.lang.String	menuGroupTools
static java.lang.String	menuGroupView
static java.lang.String	menuGroupWindow
static java.lang.String	menuHelpAbout
static java.lang.String	menuHelpContent
static java.lang.String	menuIncreaseDNASize
static java.lang.String	menuIncreaseKinetogramSize
static java.lang.String	menuIncreaseTrackSize
static java.lang.String	menuInstallShortcut
static java.lang.String	menuLayoutAnnotate
static java.lang.String	menuLayoutDefault
static java.lang.String	menuLayoutDetails
static java.lang.String	menuLayoutOverview
static java.lang.String	menuLinkGenomeRegionPanels
static java.lang.String	menuLinkRegionDetailsPanels
static java.lang.String	menuLockRegionGenomicRangeM
static java.lang.String	menuLockRegionGenomicRangeS
static java.lang.String	menuNew
static java.lang.String	menuOpenJobDataFromServer
static java.lang.String	menuPanLeft
static java.lang.String	menuPanRight
static java.lang.String	menuPreviousScale
static java.lang.String	menuPrint
static java.lang.String	menuPrintSettings
static java.lang.String	menuProgramOptions
static java.lang.String	menuRemoveTrack
static java.lang.String	menuResetView
static java.lang.String	menuSaveAsGraphics
static java.lang.String	menuSaveSession
static java.lang.String	menuSelectNext
static java.lang.String	menuSelectPrevious
static java.lang.String	menuSessionInfo
static java.lang.String	menuShowAllInTableView
static java.lang.String	menuShowContigLabels
static java.lang.String	menuShowDetailsInTableView
static java.lang.String	menuShowMarkerLabels
static java.lang.String	menuShowRegionInTableView
static java.lang.String	menuShowTracks
static java.lang.String	menuViewInsertions
static java.lang.String	menuZoomBases
static java.lang.String	menuZoomIn
static java.lang.String	menuZoomOut
protected PreferencesDialogEx	preferences_dlg
protected boolean	sortTableForBaseMods
protected VioletStatusBar	statusBar
protected javax.swing.JMenu	table_menu
static java.lang.String	toggleFilterByVariant
static java.lang.String	toggleShowDetails
static java.lang.String	toggleShowKinetics
static java.lang.String	toggleShowMapQV
static java.lang.String	toggleShowQV
static java.lang.String	toggleShowReads
protected VioletToolBar	toolBar
static java.lang.String	tooltipTableShowAll
static java.lang.String	tooltipTableShowDetails
static java.lang.String	tooltipTableShowRegion

Fields inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

last_selected_dockable_view

Fields inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

bFitRegionViewToWindowHeight, bFitToWindow, browser_panel, chromosomes_panel, chromosomes_scroller, chromosomes_views, circular_scroller, circular_view, currentMainFrameContig, default_workspace_layout, denovo_table_panel, details_scroller, details_view, docking_desktop, genomic_table_panel, heartbeat_timer, main_app, pageFormat, popmenu, printerJob, region_scroller, region_view, selection_panel

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Constructor and Description
VioletFrameActions(java.lang.String str)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	actionFileNew()
protected void	actionGoToLocation()
protected void	actionInstallSMRTView()
protected void	actionLayout(java.lang.String cmd)
protected void	actionMagnification(java.lang.String cmd) set magnification of active view
void	actionPerformed(java.awt.event.ActionEvent event)
protected void	actionProgramOptions()
protected void	actionToggleFilterAnnotationsByVariants(java.awt.event.ActionEvent event)
protected void	actionToggleKinetics(java.awt.event.ActionEvent event)
protected void	actionToggleLinkPanels(java.awt.event.ActionEvent event)
protected void	actionToggleLockRegionGenomicRange(java.awt.event.ActionEvent event)
protected void	actionToggleRetrieveDetailedAnnotations(java.awt.event.ActionEvent event)
protected void	actionToggleShowMapQV(java.awt.event.ActionEvent event)
protected void	actionToggleShowQV(java.awt.event.ActionEvent event)
protected void	actionToggleShowReads(java.awt.event.ActionEvent event)
protected void	actionViewInsertions(java.lang.String cmd)
protected javax.swing.JMenu	createFileMenu()
protected javax.swing.JMenu	createHelpMenu()
protected void	createMenuBar()
protected void	createPopupMenu()
protected void	createStatusbar()
protected void	createToolbar()
protected javax.swing.JMenu	createToolsMenu()
protected javax.swing.JMenu	createViewMenu()
protected javax.swing.JMenu	createWindowMenu()
protected GenomicViewEvents	getActiveView(boolean toolbar)
VioletStatusBar	getStatusBar()
javax.swing.JMenu	getTableMenu()
VioletToolBar	getToolBar()
protected void	onFrameClosing()
protected void	onFrameCreated()
protected void	onFrameStateChanged(int oldState, int newState)
void	setGoToDialog(GoToDialog dlg)
void	setStatusBarBusy(java.lang.String msg, boolean busy_state)
void	setStatusBarDataInfoText(java.lang.String msg, boolean bWarning)
void	setStatusBarProgress(java.lang.String msg, int min, int max, int value)
void	setStatusBarSysInfoText(java.lang.String msg, int warningLevel)
void	setStatusBarText(java.lang.String msg)
void	showMemoryStats()
void	updateToggleButtonsInGoToDialog() Updates status of toggle buttons in preferences dialog
void	updateToggleButtonsInPrefDialog() Updates status of toggle buttons in preferences dialog
void	updateToggleButtonsInToolbar() Updates selection status of toolbar toggle buttons
protected void	updateToggleMenuItems()

Methods inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameIO

actionFileAddTracksFromServer, actionFileExportAsGraphics, actionFileExportDataAsGFF, actionFileOpenData, actionFileOpenJobFromServer, actionFilePrint, actionFilePrinterSettings, actionFileRemoveTrack, actionFileSaveSession, actionSessionProperties, readDetailsOptionsFromSession, readProperties, rebuildAllViewsMarkerCollectionsAndUpdateViews, saveGraphicsFile, saveProperties, writeAllViewsToPDFFile, writeAllViewsToPNGFile, writePDFFile, writePNGFile

Methods inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

componentHidden, componentMoved, componentResized, componentShown, dockableStateChanged, getActiveGenomicView, invalidateAndRepaintAllViews, selectionChanged, setOptimumZoomFactors, stateChanged, tableChanged, updateCircularView, updateDeNovoTablePanel, updateDetailsView, updateRegionView, updateRegionViewDetailsRange, updateSelectionPanel, updateTablePanel

Methods inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

clearAllSlots, clearMarkersFromAllViews, getCircularScrollPanel, getCurrentMainFrameContig, getDataStorage, getDefaultWorkspaceLayout, getDeNovoTablePanel, getDetailsPanel, getDetailsView, getDockingDesktop, getGeneDB, getGenomePanel, getGenomeScrollPanel, getGenomicTablePanel, getIdeogramDB, getNumChromosomes, getPageFormat, getPrinterJob, getReferenceInfo, getRegionPanel, getRegionView, getSelectedSingleContigView, getSelectionPanel, getShowLabels, getShowMarkerLabels, getShowMarkers, getSingleContigsViews, getSlots, getVioletApp, getWebBrowserPanel, initLocals, normalCursor, resetVisibleGenomicRangeOfViews, saveDefaultLayout, setCurrentMainFrameContig, setDetailsViewMagnification, setFitRegionViewToWindowHeight, setMultiChromosomesViewMagnification, setPageFormat, setRegionViewMagnification, setShowGenes, setShowLabels, setShowMarkerLabels, setShowMarkers, updateWholeGenomeView, waitCursor

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.awt.Frame

addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

menuGroupFile

public static final java.lang.String menuGroupFile

See Also:

Constant Field Values

menuGroupView

public static final java.lang.String menuGroupView

See Also:

Constant Field Values

menuGroupTools

public static final java.lang.String menuGroupTools

See Also:

Constant Field Values

menuGroupWindow

public static final java.lang.String menuGroupWindow

See Also:

Constant Field Values

menuGroupHelp

public static final java.lang.String menuGroupHelp

See Also:

Constant Field Values

menuNew

public static final java.lang.String menuNew

See Also:

Constant Field Values

menuOpenJobDataFromServer

public static final java.lang.String menuOpenJobDataFromServer

See Also:

Constant Field Values

menuAddTracks

public static final java.lang.String menuAddTracks

See Also:

Constant Field Values

menuAddTracksFromServer

public static final java.lang.String menuAddTracksFromServer

See Also:

Constant Field Values

menuRemoveTrack

public static final java.lang.String menuRemoveTrack

See Also:

Constant Field Values

menuSaveSession

public static final java.lang.String menuSaveSession

See Also:

Constant Field Values

menuSessionInfo

public static final java.lang.String menuSessionInfo

See Also:

Constant Field Values

menuExportMarkers

public static final java.lang.String menuExportMarkers

See Also:

Constant Field Values

menuSaveAsGraphics

public static final java.lang.String menuSaveAsGraphics

See Also:

Constant Field Values

menuGoToLocation

public static final java.lang.String menuGoToLocation

See Also:

Constant Field Values

menuShowTracks

public static final java.lang.String menuShowTracks

See Also:

Constant Field Values

menuShowContigLabels

public static final java.lang.String menuShowContigLabels

See Also:

Constant Field Values

menuShowMarkerLabels

public static final java.lang.String menuShowMarkerLabels

See Also:

Constant Field Values

menuProgramOptions

public static final java.lang.String menuProgramOptions

See Also:

Constant Field Values

menuLinkGenomeRegionPanels

public static final java.lang.String menuLinkGenomeRegionPanels

See Also:

Constant Field Values

menuLinkRegionDetailsPanels

public static final java.lang.String menuLinkRegionDetailsPanels

See Also:

Constant Field Values

menuLockRegionGenomicRangeM

public static final java.lang.String menuLockRegionGenomicRangeM

See Also:

Constant Field Values

menuLockRegionGenomicRangeS

public static final java.lang.String menuLockRegionGenomicRangeS

See Also:

Constant Field Values

menuLayoutDefault

public static final java.lang.String menuLayoutDefault

See Also:

Constant Field Values

menuLayoutOverview

public static final java.lang.String menuLayoutOverview

See Also:

Constant Field Values

menuLayoutDetails

public static final java.lang.String menuLayoutDetails

See Also:

Constant Field Values

menuLayoutAnnotate

public static final java.lang.String menuLayoutAnnotate

See Also:

Constant Field Values

menuBookmarks

public static final java.lang.String menuBookmarks

See Also:

Constant Field Values

menuHelpContent

public static final java.lang.String menuHelpContent

See Also:

Constant Field Values

menuGoToPacBio

public static final java.lang.String menuGoToPacBio

See Also:

Constant Field Values

menuGoToDevnet

public static final java.lang.String menuGoToDevnet

See Also:

Constant Field Values

menuInstallShortcut

public static final java.lang.String menuInstallShortcut

See Also:

Constant Field Values

menuHelpAbout

public static final java.lang.String menuHelpAbout

See Also:

Constant Field Values

menuPrintSettings

public static final java.lang.String menuPrintSettings

See Also:

Constant Field Values

menuPrint

public static final java.lang.String menuPrint

See Also:

Constant Field Values

menuExit

public static final java.lang.String menuExit

See Also:

Constant Field Values

menuResetView

public static final java.lang.String menuResetView

See Also:

Constant Field Values

menuFitViewsToPanels

public static final java.lang.String menuFitViewsToPanels

See Also:

Constant Field Values

menuZoomIn

public static final java.lang.String menuZoomIn

See Also:

Constant Field Values

menuZoomOut

public static final java.lang.String menuZoomOut

See Also:

Constant Field Values

menuZoomBases

public static final java.lang.String menuZoomBases

See Also:

Constant Field Values

menuPreviousScale

public static final java.lang.String menuPreviousScale

See Also:

Constant Field Values

menuDefaultScale

public static final java.lang.String menuDefaultScale

See Also:

Constant Field Values

menuPanRight

public static final java.lang.String menuPanRight

See Also:

Constant Field Values

menuPanLeft

public static final java.lang.String menuPanLeft

See Also:

Constant Field Values

menuSelectNext

public static final java.lang.String menuSelectNext

See Also:

Constant Field Values

menuSelectPrevious

public static final java.lang.String menuSelectPrevious

See Also:

Constant Field Values

menuShowAllInTableView

public static final java.lang.String menuShowAllInTableView

See Also:

Constant Field Values

menuShowRegionInTableView

public static final java.lang.String menuShowRegionInTableView

See Also:

Constant Field Values

menuShowDetailsInTableView

public static final java.lang.String menuShowDetailsInTableView

See Also:

Constant Field Values

menuAutoFitTableView

public static final java.lang.String menuAutoFitTableView

See Also:

Constant Field Values

menuViewInsertions

public static final java.lang.String menuViewInsertions

See Also:

Constant Field Values

menuDecreaseDNASize

public static final java.lang.String menuDecreaseDNASize

See Also:

Constant Field Values

menuIncreaseDNASize

public static final java.lang.String menuIncreaseDNASize

See Also:

Constant Field Values

menuDecreaseTrackSize

public static final java.lang.String menuDecreaseTrackSize

See Also:

Constant Field Values

menuIncreaseTrackSize

public static final java.lang.String menuIncreaseTrackSize

See Also:

Constant Field Values

menuDecreaseKinetogramSize

public static final java.lang.String menuDecreaseKinetogramSize

See Also:

Constant Field Values

menuIncreaseKinetogramSize

public static final java.lang.String menuIncreaseKinetogramSize

See Also:

Constant Field Values

tooltipTableShowAll

public static final java.lang.String tooltipTableShowAll

See Also:

Constant Field Values

tooltipTableShowRegion

public static final java.lang.String tooltipTableShowRegion

See Also:

Constant Field Values

tooltipTableShowDetails

public static final java.lang.String tooltipTableShowDetails

See Also:

Constant Field Values

toggleShowDetails

public static final java.lang.String toggleShowDetails

See Also:

Constant Field Values

toggleShowQV

public static final java.lang.String toggleShowQV

See Also:

Constant Field Values

toggleShowMapQV

public static final java.lang.String toggleShowMapQV

See Also:

Constant Field Values

toggleShowReads

public static final java.lang.String toggleShowReads

See Also:

Constant Field Values

toggleFilterByVariant

public static final java.lang.String toggleFilterByVariant

See Also:

Constant Field Values

toggleShowKinetics

public static final java.lang.String toggleShowKinetics

See Also:

Constant Field Values

sortTableForBaseMods

protected transient boolean sortTableForBaseMods

table_menu

protected javax.swing.JMenu table_menu

statusBar

protected VioletStatusBar statusBar

toolBar

protected VioletToolBar toolBar

preferences_dlg

protected PreferencesDialogEx preferences_dlg

goto_dlg

protected GoToDialog goto_dlg

Constructor Detail

VioletFrameActions

public VioletFrameActions(java.lang.String str)

Method Detail

createToolbar

protected void createToolbar()

createStatusbar

protected void createStatusbar()

setStatusBarText

public void setStatusBarText(java.lang.String msg)

setStatusBarSysInfoText

public void setStatusBarSysInfoText(java.lang.String msg,
                           int warningLevel)

setStatusBarDataInfoText

public void setStatusBarDataInfoText(java.lang.String msg,
                            boolean bWarning)

setStatusBarProgress

public void setStatusBarProgress(java.lang.String msg,
                        int min,
                        int max,
                        int value)

setStatusBarBusy

public void setStatusBarBusy(java.lang.String msg,
                    boolean busy_state)

getStatusBar

public VioletStatusBar getStatusBar()

getToolBar

public VioletToolBar getToolBar()

getTableMenu

public javax.swing.JMenu getTableMenu()

createMenuBar

protected void createMenuBar()

createPopupMenu

protected void createPopupMenu()

createFileMenu

protected javax.swing.JMenu createFileMenu()

createViewMenu

protected javax.swing.JMenu createViewMenu()

Returns:

createToolsMenu

protected javax.swing.JMenu createToolsMenu()

createWindowMenu

protected javax.swing.JMenu createWindowMenu()

createHelpMenu

protected javax.swing.JMenu createHelpMenu()

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent event)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

getActiveView

protected GenomicViewEvents getActiveView(boolean toolbar)

Parameters:

toolbar -

Returns:

showMemoryStats

public void showMemoryStats()

updateToggleButtonsInToolbar

public void updateToggleButtonsInToolbar()

Updates selection status of toolbar toggle buttons

updateToggleMenuItems

protected void updateToggleMenuItems()

updateToggleButtonsInPrefDialog

public void updateToggleButtonsInPrefDialog()

Updates status of toggle buttons in preferences dialog

updateToggleButtonsInGoToDialog

public void updateToggleButtonsInGoToDialog()

Updates status of toggle buttons in preferences dialog

setGoToDialog

public void setGoToDialog(GoToDialog dlg)

actionToggleShowQV

protected void actionToggleShowQV(java.awt.event.ActionEvent event)

actionToggleShowMapQV

protected void actionToggleShowMapQV(java.awt.event.ActionEvent event)

actionToggleLinkPanels

protected void actionToggleLinkPanels(java.awt.event.ActionEvent event)

actionToggleLockRegionGenomicRange

protected void actionToggleLockRegionGenomicRange(java.awt.event.ActionEvent event)

actionToggleShowReads

protected void actionToggleShowReads(java.awt.event.ActionEvent event)

actionToggleFilterAnnotationsByVariants

protected void actionToggleFilterAnnotationsByVariants(java.awt.event.ActionEvent event)

Parameters:

event -

actionToggleRetrieveDetailedAnnotations

protected void actionToggleRetrieveDetailedAnnotations(java.awt.event.ActionEvent event)

Parameters:

event -

actionToggleKinetics

protected void actionToggleKinetics(java.awt.event.ActionEvent event)

Parameters:

event -

actionLayout

protected void actionLayout(java.lang.String cmd)

Parameters:

cmd -

actionFileNew

protected void actionFileNew()

actionMagnification

protected void actionMagnification(java.lang.String cmd)

set magnification of active view

Parameters:

cmd -

actionProgramOptions

protected void actionProgramOptions()

actionInstallSMRTView

protected void actionInstallSMRTView()

actionViewInsertions

protected void actionViewInsertions(java.lang.String cmd)

actionGoToLocation

protected void actionGoToLocation()

onFrameCreated

protected void onFrameCreated()

onFrameClosing

protected void onFrameClosing()

onFrameStateChanged

protected void onFrameStateChanged(int oldState,
                       int newState)