com.pacbio.secondary.vis.gui.draw.views

Class GenomicViewEvents

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

com.pacbio.secondary.vis.gui.draw.views.GenomicViewData

com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.print.Printable, java.io.Serializable

Direct Known Subclasses:

GenomicViewCircular, GenomicViewHorizontal, GenomicViewVertical

public abstract class GenomicViewEvents
extends GenomicViewDraw

Handles mouse and keyboards events of genomic view

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	GenomicViewEvents.GenomicViewKeyListener
protected class	GenomicViewEvents.GenomicViewMouseListener
protected class	GenomicViewEvents.GenomicViewMouseMotionListener

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

javax.swing.JComponent.AccessibleJComponent

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 inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

end_last_lower_label_x, end_last_upper_label_x

Fields inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

active, bCircular, bDetails, beginPoint, bHorizontal, bInspection, bottomMarkerBounds, bottomPileUpBounds, bottomReferenceBounds, contigLength, currentViewContig, default_border_width, default_feature_size, default_height_top_axis, default_ideogram_height, default_ideogram_label_width, default_ideogram_width, default_left_info_width, default_tracks_width, default_view_height, default_view_width, default_y_bottom_ideogram, default_y_top_ideogram, dim_ideogramview, endPoint, ideogramBounds, ideogramLabelBounds, int_visible_range, isDragging, layout_info, leftLegendBounds, leftMarkerBounds, leftVisible, main_app, marker_state, markers, maxWidth, minViewGenomicRange, minWidth, paintBuffer, paintBufferValid, rangeSelection, rightLegendBounds, rightMarkerBounds, rightVisible, scaleX, scaleY, selected_gene, selectedMarker, selectedSlotIndex, selectedTrackIndex, selectionChangedListeners, showGenes, showLabels, showMarkerLabels, showMarkers, viewHistory

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.print.Printable

NO_SUCH_PAGE, PAGE_EXISTS

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

Constructors

Constructor and Description
GenomicViewEvents(VioletApp main_app)

Method Summary

Methods

Modifier and Type	Method and Description
void	addGenomicRangeToDetailsViewDataRequestsQueue(Interval interval, boolean updateGenomicRange)
void	addSelectionChangedListener(javax.swing.event.ChangeListener obj)
protected void	beginSelection(java.awt.Point point)
void	center(long pos) Scroll to the given basepair (such that the position is centered)
void	changeDNAFontSize(boolean bIncrement)
void	changeIPDConsensusHeight(boolean bIncrement)
void	changeTrackSize(boolean bIncrement)
protected boolean	clearSelections()
javax.swing.JToolTip	createToolTip()
protected void	endSelection(java.awt.Point point)
Marker	findVariantByPositionAndYCoordinate(MarkerCollection track, long bp, int y)
protected void	fireSelectionChanged(GenomicViewChangeEvent.GenomicViewEventType event_type)
protected GenomicViewEvents	getActiveViewForKeyEvents()
DetailsStorage	getDetailsDataStorage()
int	getScaledHeight()
int	getScaledWidth()
Marker	getSelectedGene()
Marker	getSelectedMarker()
int	getSelectedSlotIndex()
java.lang.String	getSelectionInfo()
boolean	getShowLabels()
boolean	getShowMarkerLabels()
boolean	getShowMarkers()
java.lang.String	getToolTipText(java.awt.event.MouseEvent e)
double	getZoom()
protected double	getZoom(long max_range)
boolean	hasViewHistoryItems()
protected void	initTransientState()
boolean	isSelection()
Interval	popView()
void	pushView()
void	resetVisibleGenomicRange(boolean firechangeevent) Zoom fully out.
void	scroll(int dy)
void	scrollVisibleGenomicRangeToTopOrBottom(boolean top)
protected void	selectNextPreviousContig(int trackIndex, boolean next)
protected void	selectNextPreviousGeneContig(boolean next) Selects gene in next or previous contig
void	selectNextPreviousMarker(boolean next)
void	selectPoint(java.awt.Point pt) Selects a feature in the view
boolean	setActive(boolean active, boolean firechangeevent) Shows an activation frame around the ideogram.
void	setRangeSelection(Interval selection)
protected boolean	setSelectedGeneAndTrack(Marker m, int trackIndex, boolean bFireEvent) Sets the currently selected gene to m.
protected boolean	setSelectedMarkerAndSlot(Marker marker, int slotIndex, boolean bFireEvent) Selects a marker/sample
void	setShowGenes(boolean showGenes)
void	setShowLabels(boolean showLabels) Activates/Deactivates the chromosomal location label view (e.g.
void	setShowMarkerLabels(boolean bshowMarkerLabels) Activates/Deactivates the tracks location label view (e.g.
void	setShowMarkers(boolean showMarkers) Show markers.
void	setViewWithOrWithoutUpdate(Interval interval, boolean bredraw) Sets the current genomic range for this view
void	setVisibleGenomicRange(Interval interval, boolean firechangeevent) Sets the genomic range for this view
void	setVisibleGenomicRegion(Locus locus, GenomicViewData contig_data, boolean firechangeevent, boolean updateTablePanel)
void	setWidth(int minWidth, int maxWidth) Sets the width-range of the ideogram graphic.
void	toggleMarker() Redraws the currently selected marker (blinking).
void	zoomVisibleGenomicRange(int dy) Zooms in (for dy < 0) or out (for dy > 0).

Methods inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

autofitLabelWidth, BaseRangeToXExtent, BaseToXCoord, BaseToYCoord, drawAxisHeaderlabel, drawBackgroundSelections, drawEpiProIdeogram, drawForegroundSelections, drawGene, drawGenes, drawGenomicViewDoubleBuffered, drawGenomicViewToGraphicsContext, drawGenomicViewToPaintBuffer, drawHeaderFooter, drawHorizontalTracksHeader, drawIdeogram, drawInfoLabel, drawInfoLabelJustified, drawLabelWithOffsetAndWidth, drawMarker, drawMarkerInterval, drawMarkers, drawMinMaxLabel, drawModification, drawModificationInterval, drawRangeSelection, drawRotatedLabel, drawSummary, drawSummaryInterval, drawSummaryRegion, drawTrackMetricLabel, drawVariant, drawVariantInterval, getContigLength, getContigMaxRange, getDim, getExtraRefTrackDistance, getGenesBounds, getIdeogramBounds, getLabelBounds, getLegendBounds, getMarkersBounds, getMaxMagnification, getMinMagnification, getNumLeft, getNumRight, getPanelTitle, getPileupBounds, getRangeSelection, getReferenceBounds, getSelectedRangeColor, getVisibleGenomicRange, invalidatePaintBuffer, isCircular, isDetails, isHorizontal, isInspection, paintActiveBorder, paintComponent, paintLegendBackground, prepareDrawVariant, print, scaleX, scaleY, setMagnificationScaleFactor, showDataLabels, trackIndexToXCoord, trackToYCoord, updateLayout, updateSize, XCoordToBase, xCoordToTrackIndex, YCoordToBase, yCoordToMarkerCollectionIndex, yCoordToMarkerCollectionIndexNew, yCoordToMarkerCollectionIndexOrg, yCoordToTrackIndex

Methods inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData

addTrackDataToViewAndUpdateLayout, clearMarkers, getContigLabel, getGenesOfCurrentContig, getIdeogramTreeOfCurrentContig, getMarkerCollection, getMarkers, getNumMarkerCollections, getSlotColor, getSlotMaxCoverage, getSlotMaxVariants, getSlots, markerToSampleIndex, sampleToMarkerIndex, sampleToMarkerIndex, setViewContig, setViewDataForCurrentContig, updateVisibility

Methods inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

getAbsMaxGenomicRange, getBorderWidth, getDataStorage, getGeneDB, getIdeogramDB, getMainWindow, getMaxGenomicRange, getMinGenomicRange, getReferenceInfo, getViewContig, getViewContigName, getVioletApp, initializeViewBase, isActive, isDNABaseShown, isIdeogramDBLoaded

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getTopLevelAncestor, getTransferHandler, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, paramString, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update, updateUI

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, 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, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomicViewEvents

public GenomicViewEvents(VioletApp main_app)

Method Detail

setVisibleGenomicRegion

public void setVisibleGenomicRegion(Locus locus,
                           GenomicViewData contig_data,
                           boolean firechangeevent,
                           boolean updateTablePanel)

resetVisibleGenomicRange

public void resetVisibleGenomicRange(boolean firechangeevent)

Zoom fully out.

setVisibleGenomicRange

public void setVisibleGenomicRange(Interval interval,
                          boolean firechangeevent)

Sets the genomic range for this view

Parameters:

interval -

setViewWithOrWithoutUpdate

public void setViewWithOrWithoutUpdate(Interval interval,
                              boolean bredraw)

Sets the current genomic range for this view

Parameters:

interval -

fireSelectionChanged

protected void fireSelectionChanged(GenomicViewChangeEvent.GenomicViewEventType event_type)

isSelection

public boolean isSelection()

Returns:

True if an item is selected (marker, gene etc.)

toggleMarker

public void toggleMarker()

Redraws the currently selected marker (blinking).

getSelectedSlotIndex

public int getSelectedSlotIndex()

hasViewHistoryItems

public boolean hasViewHistoryItems()

Returns:

true if this view has history items

pushView

public void pushView()

popView

public Interval popView()

getZoom

public double getZoom()

Returns:

Current zoom factor 1.0 = 1:1, 20.0 = 20:1

getScaledWidth

public int getScaledWidth()

getScaledHeight

public int getScaledHeight()

getShowMarkerLabels

public boolean getShowMarkerLabels()

Returns:

True if the contig labels are shown.

setShowMarkerLabels

public void setShowMarkerLabels(boolean bshowMarkerLabels)

Activates/Deactivates the tracks location label view (e.g. "1p22")

Parameters:

bshowMarkerLabels -

getShowLabels

public boolean getShowLabels()

Returns:

True if the chromosomal labels are shown.

setShowLabels

public void setShowLabels(boolean showLabels)

Activates/Deactivates the chromosomal location label view (e.g. "1p22")

Parameters:

showLabels -

setShowGenes

public void setShowGenes(boolean showGenes)

getShowMarkers

public boolean getShowMarkers()

Returns:

True if the markers are shown.

See Also:

setShowMarkers(boolean)

setShowMarkers

public void setShowMarkers(boolean showMarkers)

Show markers.

Parameters:

showMarkers -

getZoom

protected double getZoom(long max_range)

Returns:

Current zoom factor 1.0 = 1:1, 20.0 = 20:1

setWidth

public void setWidth(int minWidth,
            int maxWidth)

Sets the width-range of the ideogram graphic. So if the size of the panel changes the graphic will not exceed the given boundary.

Parameters:

minWidth - Minimum width of the ideogram graphic.

maxWidth - Maximum width of the ideogram graphic.

zoomVisibleGenomicRange

public void zoomVisibleGenomicRange(int dy)

Zooms in (for dy < 0) or out (for dy > 0). Zooms in into a range selection (if it exists).

Parameters:

dy - Zoom step directly proportional to 1/5th of the current field of view.

scroll

public void scroll(int dy)

scrollVisibleGenomicRangeToTopOrBottom

public void scrollVisibleGenomicRangeToTopOrBottom(boolean top)

selectNextPreviousContig

protected void selectNextPreviousContig(int trackIndex,
                            boolean next)

Parameters:

marker -

sampleIndex -

next -

selectNextPreviousGeneContig

protected void selectNextPreviousGeneContig(boolean next)

Selects gene in next or previous contig

Parameters:

next -

selectNextPreviousMarker

public void selectNextPreviousMarker(boolean next)

getSelectedMarker

public Marker getSelectedMarker()

getSelectedGene

public Marker getSelectedGene()

addSelectionChangedListener

public void addSelectionChangedListener(javax.swing.event.ChangeListener obj)

center

public void center(long pos)

Scroll to the given basepair (such that the position is centered)

Parameters:

pos -

getDetailsDataStorage

public DetailsStorage getDetailsDataStorage()

getSelectionInfo

public java.lang.String getSelectionInfo()

Returns:

A string describing information for the currently selected marker(s)/gene(s).

createToolTip

public javax.swing.JToolTip createToolTip()

Overrides:

createToolTip in class javax.swing.JComponent

getToolTipText

public java.lang.String getToolTipText(java.awt.event.MouseEvent e)

Overrides:

getToolTipText in class javax.swing.JComponent

setRangeSelection

public void setRangeSelection(Interval selection)

beginSelection

protected void beginSelection(java.awt.Point point)

endSelection

protected void endSelection(java.awt.Point point)

initTransientState

protected void initTransientState()

changeDNAFontSize

public void changeDNAFontSize(boolean bIncrement)

changeIPDConsensusHeight

public void changeIPDConsensusHeight(boolean bIncrement)

changeTrackSize

public void changeTrackSize(boolean bIncrement)

addGenomicRangeToDetailsViewDataRequestsQueue

public void addGenomicRangeToDetailsViewDataRequestsQueue(Interval interval,
                                                 boolean updateGenomicRange)

selectPoint

public void selectPoint(java.awt.Point pt)

Selects a feature in the view

Parameters:

pt - Point in component coordinates.

findVariantByPositionAndYCoordinate

public Marker findVariantByPositionAndYCoordinate(MarkerCollection track,
                                         long bp,
                                         int y)

setSelectedMarkerAndSlot

protected boolean setSelectedMarkerAndSlot(Marker marker,
                               int slotIndex,
                               boolean bFireEvent)

Selects a marker/sample

Parameters:

marker -

slotIndex - Which marker collection 0..n-1

Returns:

True if the selection changed

setSelectedGeneAndTrack

protected boolean setSelectedGeneAndTrack(Marker m,
                              int trackIndex,
                              boolean bFireEvent)

Sets the currently selected gene to m. To deselect choose null as parameter.

Parameters:

m - The marker which should be highlighted.

Returns:

True if the selection changed

clearSelections

protected boolean clearSelections()

Returns:

True if at least one selections changed.

setActive

public boolean setActive(boolean active,
                boolean firechangeevent)

Shows an activation frame around the ideogram.

Parameters:

active - Set true if frame should be shown.

Returns:

True if something changed

getActiveViewForKeyEvents

protected GenomicViewEvents getActiveViewForKeyEvents()

Parameters:

toolbar -

Returns: