com.pacbio.secondary.vis.gui.frame

Class VioletFrameBase

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

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

Direct Known Subclasses:

VioletFrameChanges

public class VioletFrameBase
extends javax.swing.JFrame

Author:

mmilletti

See Also:

Serialized Form

Nested Class Summary

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 boolean	bFitRegionViewToWindowHeight
protected boolean	bFitToWindow
protected WebBrowserPanel	browser_panel
protected WholeGenomePanel	chromosomes_panel
protected DockableScrollPaneBase	chromosomes_scroller
protected GenomicViewSingleContig[]	chromosomes_views
protected DockableScrollPaneBase	circular_scroller
protected GenomicViewCircular	circular_view
protected int	currentMainFrameContig
protected java.lang.String	default_workspace_layout
protected DeNovoTablePanel	denovo_table_panel
protected DockableScrollPaneBase	details_scroller
protected GenomicViewDetails	details_view
protected DockingDesktop	docking_desktop
protected GenomicTablePanel	genomic_table_panel
protected javax.swing.Timer	heartbeat_timer
protected VioletApp	main_app
protected java.awt.print.PageFormat	pageFormat
javax.swing.JPopupMenu	popmenu
protected java.awt.print.PrinterJob	printerJob
protected DockableScrollPaneBase	region_scroller
protected GenomicViewRegion	region_view
protected SelectionInfoPanel	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
VioletFrameBase(java.lang.String str)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	clearAllSlots()
protected void	clearMarkersFromAllViews(boolean forceClearDetails)
DockableScrollPaneBase	getCircularScrollPanel()
int	getCurrentMainFrameContig()
DataStorage	getDataStorage()
java.lang.String	getDefaultWorkspaceLayout()
DeNovoTablePanel	getDeNovoTablePanel()
DockableScrollPaneBase	getDetailsPanel()
GenomicViewDetails	getDetailsView()
DockingDesktop	getDockingDesktop()
GeneDB	getGeneDB()
WholeGenomePanel	getGenomePanel()
DockableScrollPaneBase	getGenomeScrollPanel()
GenomicTablePanel	getGenomicTablePanel()
IdeogramDB	getIdeogramDB()
int	getNumChromosomes()
java.awt.print.PageFormat	getPageFormat()
java.awt.print.PrinterJob	getPrinterJob()
ReferenceInfo	getReferenceInfo()
DockableScrollPaneBase	getRegionPanel()
GenomicViewEvents	getRegionView()
GenomicViewSingleContig	getSelectedSingleContigView()
SelectionInfoPanel	getSelectionPanel()
boolean	getShowLabels()
boolean	getShowMarkerLabels()
boolean	getShowMarkers()
GenomicViewEvents[]	getSingleContigsViews()
java.util.Vector<VariableResolutionDataSet>	getSlots()
VioletApp	getVioletApp()
WebBrowserPanel	getWebBrowserPanel()
protected void	initLocals()
void	normalCursor() Sets the current mouse cursor to a normal cursor.
void	resetVisibleGenomicRangeOfViews()
void	saveDefaultLayout()
void	setCurrentMainFrameContig(int contig)
protected void	setDetailsViewMagnification(double zoom_x, double zoom_y, boolean repaint)
void	setFitRegionViewToWindowHeight(boolean b)
protected void	setMultiChromosomesViewMagnification(double zoom, boolean repaint)
void	setPageFormat(java.awt.print.PageFormat format)
protected void	setRegionViewMagnification(double zoom_x, double zoom_y, boolean repaint)
void	setShowGenes(boolean b)
void	setShowLabels(boolean show) Sets the visibility of the chromosomal labels for all ideograms.
void	setShowMarkerLabels(boolean show)
void	setShowMarkers(boolean show)
protected void	updateWholeGenomeView()
void	waitCursor() Sets the current mouse cursor to a waiting cursor (e.g.

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

pageFormat

protected java.awt.print.PageFormat pageFormat

printerJob

protected java.awt.print.PrinterJob printerJob

popmenu

public javax.swing.JPopupMenu popmenu

heartbeat_timer

protected transient javax.swing.Timer heartbeat_timer

main_app

protected VioletApp main_app

currentMainFrameContig

protected int currentMainFrameContig

bFitToWindow

protected boolean bFitToWindow

bFitRegionViewToWindowHeight

protected boolean bFitRegionViewToWindowHeight

docking_desktop

protected DockingDesktop docking_desktop

default_workspace_layout

protected java.lang.String default_workspace_layout

chromosomes_views

protected GenomicViewSingleContig[] chromosomes_views

chromosomes_panel

protected WholeGenomePanel chromosomes_panel

chromosomes_scroller

protected DockableScrollPaneBase chromosomes_scroller

region_view

protected GenomicViewRegion region_view

region_scroller

protected DockableScrollPaneBase region_scroller

details_view

protected GenomicViewDetails details_view

details_scroller

protected DockableScrollPaneBase details_scroller

circular_view

protected GenomicViewCircular circular_view

circular_scroller

protected DockableScrollPaneBase circular_scroller

denovo_table_panel

protected DeNovoTablePanel denovo_table_panel

genomic_table_panel

protected GenomicTablePanel genomic_table_panel

browser_panel

protected WebBrowserPanel browser_panel

selection_panel

protected SelectionInfoPanel selection_panel

Constructor Detail

VioletFrameBase

public VioletFrameBase(java.lang.String str)

Parameters:

str -

Method Detail

initLocals

protected void initLocals()

setMultiChromosomesViewMagnification

protected void setMultiChromosomesViewMagnification(double zoom,
                                        boolean repaint)

Parameters:

zoom -

setRegionViewMagnification

protected void setRegionViewMagnification(double zoom_x,
                              double zoom_y,
                              boolean repaint)

Parameters:

zoom -

setDetailsViewMagnification

protected void setDetailsViewMagnification(double zoom_x,
                               double zoom_y,
                               boolean repaint)

Parameters:

zoom -

getSelectedSingleContigView

public GenomicViewSingleContig getSelectedSingleContigView()

getNumChromosomes

public int getNumChromosomes()

getDefaultWorkspaceLayout

public java.lang.String getDefaultWorkspaceLayout()

saveDefaultLayout

public void saveDefaultLayout()

setCurrentMainFrameContig

public void setCurrentMainFrameContig(int contig)

getCurrentMainFrameContig

public int getCurrentMainFrameContig()

getDataStorage

public DataStorage getDataStorage()

getReferenceInfo

public ReferenceInfo getReferenceInfo()

getSlots

public java.util.Vector<VariableResolutionDataSet> getSlots()

getIdeogramDB

public IdeogramDB getIdeogramDB()

getGeneDB

public GeneDB getGeneDB()

setFitRegionViewToWindowHeight

public void setFitRegionViewToWindowHeight(boolean b)

getPageFormat

public java.awt.print.PageFormat getPageFormat()

setPageFormat

public void setPageFormat(java.awt.print.PageFormat format)

getPrinterJob

public java.awt.print.PrinterJob getPrinterJob()

getVioletApp

public VioletApp getVioletApp()

getRegionView

public GenomicViewEvents getRegionView()

getRegionPanel

public DockableScrollPaneBase getRegionPanel()

getDetailsView

public GenomicViewDetails getDetailsView()

getDetailsPanel

public DockableScrollPaneBase getDetailsPanel()

getSingleContigsViews

public GenomicViewEvents[] getSingleContigsViews()

getGenomicTablePanel

public GenomicTablePanel getGenomicTablePanel()

getDeNovoTablePanel

public DeNovoTablePanel getDeNovoTablePanel()

getGenomeScrollPanel

public DockableScrollPaneBase getGenomeScrollPanel()

getGenomePanel

public WholeGenomePanel getGenomePanel()

getDockingDesktop

public DockingDesktop getDockingDesktop()

getWebBrowserPanel

public WebBrowserPanel getWebBrowserPanel()

getSelectionPanel

public SelectionInfoPanel getSelectionPanel()

getCircularScrollPanel

public DockableScrollPaneBase getCircularScrollPanel()

setShowGenes

public void setShowGenes(boolean b)

getShowMarkerLabels

public boolean getShowMarkerLabels()

Returns:

True if chromosomal labels (bands) are shown in the diagrams.

setShowMarkerLabels

public void setShowMarkerLabels(boolean show)

Parameters:

show -

getShowLabels

public boolean getShowLabels()

Returns:

True if chromosomal labels (bands) are shown in the diagrams.

setShowLabels

public void setShowLabels(boolean show)

Sets the visibility of the chromosomal labels for all ideograms.

Parameters:

show -

getShowMarkers

public boolean getShowMarkers()

Returns:

setShowMarkers

public void setShowMarkers(boolean show)

Parameters:

show -

normalCursor

public void normalCursor()

Sets the current mouse cursor to a normal cursor.

See Also:

waitCursor()

waitCursor

public void waitCursor()

Sets the current mouse cursor to a waiting cursor (e.g. hourglass).

See Also:

normalCursor()

resetVisibleGenomicRangeOfViews

public void resetVisibleGenomicRangeOfViews()

clearAllSlots

protected void clearAllSlots()

updateWholeGenomeView

protected void updateWholeGenomeView()

clearMarkersFromAllViews

protected void clearMarkersFromAllViews(boolean forceClearDetails)