public abstract class GenomicViewDetailsDraw extends GenomicViewDetailsData
GenomicViewEvents.GenomicViewKeyListener, GenomicViewEvents.GenomicViewMouseListener, GenomicViewEvents.GenomicViewMouseMotionListenerjavax.swing.JComponent.AccessibleJComponentdata_on_demand_queue, data_on_demand_timer, data_request_queue, details_data, details_options, gappedDNAAnnotation, ipd_consensus_data, ipd_consensus_request_queue, MIN_EXTRA_DELTA_ADD_RANGE_REQUEST, MIN_HALF_DATA_ON_DEMAND_REQUEST, MIN_RANGE_REFERENCE_OR_IPD_REQUEST, noDNAAnnotation, reference_data, reference_request_queuedefault_tracks_height, variations_splitterend_last_lower_label_x, end_last_upper_label_xactive, 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, viewHistoryaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
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GenomicViewDetailsDraw(VioletApp mainApp) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
drawEpiProFoldedRead(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width) |
protected void |
drawEpiProUnfoldedReadMappedCoord(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width) |
protected void |
drawEpiProUnfoldedReadSubreadCoord(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width) |
protected void |
drawEpiProUnfoldedReadSubreadCoordOrg(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width)
Deprecated.
|
protected void |
drawReadShape(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width) |
actionPerformed, addGenomicRangeToDetailsViewDataRequestsQueue, addGenomicRangeToDetailsViewIPDConsensusRequestQueue, addGenomicRangeToDetailsViewReferenceRequestQueue, canDrawIPDConsensus, clearAllDetailsData, findReadByPositionAndLane, getDetailsDataLocus, getDetailsDataStorage, getDetailsOptions, getEmptyCharArray, getIPDConsensusDataLocus, getIPDConsensusStorage, getReferenceDataLocus, getReferenceSequenceStorage, isCDNADataAvailable, isDNABaseShown, isDrawIPDConsensus, isIPDConsensusDataAvailable, retrieveDataOnDemand, setConsensusData, setDetailsOptions, setDetailsViewData, setIPDConsensusData, setReferenceData, setReferenceSequenceStorage, setViewDataForCurrentContig, updateLayoutOnDemand, zoomToBasescalcSize, 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, initLocals, isIdeogramDBLoaded, resetVisibleGenomicRange, selectPoint, setTracksHeight, showDataLabels, updateSizeaddSelectionChangedListener, beginSelection, center, changeDNAFontSize, changeIPDConsensusHeight, changeTrackSize, clearSelections, createToolTip, endSelection, findVariantByPositionAndYCoordinate, fireSelectionChanged, getActiveViewForKeyEvents, getScaledHeight, getScaledWidth, 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, zoomVisibleGenomicRangeautofitLabelWidth, 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, updateLayout, XCoordToBase, xCoordToTrackIndex, YCoordToBase, yCoordToMarkerCollectionIndex, yCoordToMarkerCollectionIndexNew, yCoordToMarkerCollectionIndexOrg, yCoordToTrackIndexaddTrackDataToViewAndUpdateLayout, clearMarkers, getContigLabel, getGenesOfCurrentContig, getIdeogramTreeOfCurrentContig, getMarkerCollection, getMarkers, getNumMarkerCollections, getSlotColor, getSlotMaxCoverage, getSlotMaxVariants, getSlots, markerToSampleIndex, sampleToMarkerIndex, sampleToMarkerIndex, setViewContig, updateVisibilitygetAbsMaxGenomicRange, getBorderWidth, getDataStorage, getGeneDB, getIdeogramDB, getMainWindow, getMaxGenomicRange, getMinGenomicRange, getReferenceInfo, getViewContig, getViewContigName, getVioletApp, initializeViewBase, isActiveaddAncestorListener, 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, updateUIadd, 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, validateTreeaction, 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, transferFocusUpCyclepublic GenomicViewDetailsDraw(VioletApp mainApp)
protected void drawReadShape(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width)
g - marker - x - y - width - protected void drawEpiProFoldedRead(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width)
g - marker - x - y - width - protected void drawEpiProUnfoldedReadSubreadCoord(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width)
g - marker - x - y - width - protected void drawEpiProUnfoldedReadMappedCoord(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width)
g - marker - x - y - width - @Deprecated
protected void drawEpiProUnfoldedReadSubreadCoordOrg(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width)
g - marker - x - y - width - Copyright © 2010-2014 Pacific Biosciences. All Rights Reserved.