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

Class GenomicViewRegion

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

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

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

All Implemented Interfaces:

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

public class GenomicViewRegion
extends GenomicViewHorizontal
implements java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

GenomicViewEvents.GenomicViewKeyListener, GenomicViewEvents.GenomicViewMouseListener, 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

Modifier and Type	Field and Description
protected static int	MAX_TRACK_HEIGHT
protected static int	MIN_TRACK_HEIGHT

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

default_tracks_height, variations_splitter

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

Modifier	Constructor and Description
protected	GenomicViewRegion() de-serialization only
	GenomicViewRegion(VioletApp main_app)

Method Summary

Methods

Modifier and Type	Method and Description
void	changeTrackSize(boolean bIncrement)
int	getScaledHeight()
int	getScaledWidth()
protected void	initLocals()
void	reflectUpdatedDetailsRange()
boolean	setViewDataForCurrentContig(int contig, GenomicViewData contig_data, boolean updateTablePanel)
java.awt.Dimension	updateLayout()

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

calcSize, canDrawIPDConsensus, drawBackgroundSelections, drawCrossLines, drawFilteredTrack, drawFilteredTracks, drawForegroundSelections, drawGene, drawGenomicViewToGraphicsContext, drawHorizontalTracksHeader, drawIdeogram, drawLabelWithoutCollision, drawMarkerHorizontal, drawMarkerInterval, drawMarkers, drawMarkersLegend, drawModification, drawModificationInterval, drawModificationsLegend, drawModificationSummaryHeatmap, drawModificationSummaryHistogram, drawMotifLegend, drawRangeSelection, drawReferenceSequenceOutline, drawSummaryLegends, drawSummaryTracks, drawUnFilteredTracks, drawVariant, drawVariantInterval, drawVariantIntervalOrg, drawVariantsLegend, drawVariantsLegendOrg, getLegendLabelsWidth, getMaxCoverageInInterval, getMaxCoverageInInterval, getMaxMagnification, getMinMagnification, getTracksHeight, isIdeogramDBLoaded, resetVisibleGenomicRange, selectPoint, setTracksHeight, showDataLabels, updateSize

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

addGenomicRangeToDetailsViewDataRequestsQueue, addSelectionChangedListener, beginSelection, center, changeDNAFontSize, changeIPDConsensusHeight, clearSelections, createToolTip, endSelection, findVariantByPositionAndYCoordinate, fireSelectionChanged, getActiveViewForKeyEvents, getDetailsDataStorage, getSelectedGene, getSelectedMarker, getSelectedSlotIndex, getSelectionInfo, getShowLabels, getShowMarkerLabels, getShowMarkers, getToolTipText, getZoom, getZoom, hasViewHistoryItems, initTransientState, isSelection, popView, pushView, scroll, scrollVisibleGenomicRangeToTopOrBottom, selectNextPreviousContig, selectNextPreviousGeneContig, selectNextPreviousMarker, setActive, setRangeSelection, setSelectedGeneAndTrack, setSelectedMarkerAndSlot, setShowGenes, setShowLabels, setShowMarkerLabels, setShowMarkers, setViewWithOrWithoutUpdate, setVisibleGenomicRange, setVisibleGenomicRegion, setWidth, toggleMarker, zoomVisibleGenomicRange

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

autofitLabelWidth, BaseRangeToXExtent, BaseToXCoord, BaseToYCoord, drawAxisHeaderlabel, drawEpiProIdeogram, drawGenes, drawGenomicViewDoubleBuffered, drawGenomicViewToPaintBuffer, drawHeaderFooter, drawInfoLabel, drawInfoLabelJustified, drawLabelWithOffsetAndWidth, drawMarker, drawMinMaxLabel, drawModification, drawRotatedLabel, drawSummary, drawSummaryInterval, drawSummaryRegion, drawTrackMetricLabel, drawVariant, getContigLength, getContigMaxRange, getDim, getExtraRefTrackDistance, getGenesBounds, getIdeogramBounds, getLabelBounds, getLegendBounds, getMarkersBounds, getNumLeft, getNumRight, getPanelTitle, getPileupBounds, getRangeSelection, getReferenceBounds, getSelectedRangeColor, getVisibleGenomicRange, invalidatePaintBuffer, isCircular, isDetails, isHorizontal, isInspection, paintActiveBorder, paintComponent, paintLegendBackground, prepareDrawVariant, print, scaleX, scaleY, setMagnificationScaleFactor, trackIndexToXCoord, trackToYCoord, 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, 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

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

Field Detail

MAX_TRACK_HEIGHT

protected static final int MAX_TRACK_HEIGHT

See Also:

Constant Field Values

MIN_TRACK_HEIGHT

protected static final int MIN_TRACK_HEIGHT

See Also:

Constant Field Values

Constructor Detail

GenomicViewRegion

public GenomicViewRegion(VioletApp main_app)

GenomicViewRegion

protected GenomicViewRegion()

de-serialization only

Method Detail

initLocals

protected void initLocals()

Specified by:

initLocals in class GenomicViewHorizontal

updateLayout

public java.awt.Dimension updateLayout()

Overrides:

updateLayout in class GenomicViewDraw

getScaledWidth

public int getScaledWidth()

Overrides:

getScaledWidth in class GenomicViewEvents

getScaledHeight

public int getScaledHeight()

Overrides:

getScaledHeight in class GenomicViewEvents

reflectUpdatedDetailsRange

public void reflectUpdatedDetailsRange()

setViewDataForCurrentContig

public boolean setViewDataForCurrentContig(int contig,
                                  GenomicViewData contig_data,
                                  boolean updateTablePanel)

Overrides:

setViewDataForCurrentContig in class GenomicViewData

changeTrackSize

public void changeTrackSize(boolean bIncrement)

Overrides:

changeTrackSize in class GenomicViewEvents