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

Class GenomicViewInspect

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.GenomicViewDetailsData

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

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

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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.print.Printable, java.io.Serializable, java.util.EventListener

public class GenomicViewInspect
extends GenomicViewDetails

Author:

mmilletti

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	GenomicViewInspect.GenomicViewInspectMouseMotionListener

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 int	end_first_insertion
protected int	end_insertion_reference
protected int	insertion_width
protected boolean	is_valid
protected static java.lang.String	no_data_msg

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

ipd_baseline, ipd_nan_marker, MAX_TRACK_HEIGHT, min_ipdratio_plot, MIN_TRACK_HEIGHT

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

data_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_queue

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

Constructor and Description
GenomicViewInspect(VioletApp mainApp)

Method Summary

Methods

Modifier and Type	Method and Description
void	assembleReadsWithGappedInsertions() Creates pseudo-reads with added gaps so we can construct and view an MSA
protected int	calcRequiredGapsForRead(ReadInfo read, int read_idx_start, int read_idx_end, int gaps_to_add) count total gaps to add to this read
protected void	calculateInsertionExtent() two pass to determine insertion range and start-stop ref coordinates
boolean	calculateInsertionInfo() Determines insertion genomic range and start-stop coordinates
void	drawBackgroundSelections(java.awt.Graphics g) draw header area and reference sequence outline
void	drawForegroundSelections(java.awt.Graphics g)
protected void	drawGenomicViewDoubleBuffered(java.awt.Graphics graphics) Main draw function for class
void	drawGenomicViewToGraphicsContext(java.awt.Graphics g) Paints the ideogram into the given graphical context.
protected void	drawHeaderFooter(java.awt.Graphics g)
protected void	drawHorizontalTracksHeader(java.awt.Graphics g) Draws the labels for each track
protected void	drawReadKinetic(java.awt.Graphics g, Marker marker, int y_start, boolean bDrawDNABases, int mode)
protected void	drawReadUnfiltered(java.awt.Graphics g, Marker marker, int y_start, boolean bDrawDNABases, boolean bDrawQV)
protected void	drawReferenceSequence(java.awt.Graphics g)
protected void	drawTargetInDetailsView() draw selection in region panel
int	getCenterLocation()
long	getEndFirstInsertion()
long	getEndInsertionReference()
int	getInsertionWidth()
int	getMaxGenomicRange()
protected double	getMinMagnification()
java.lang.String	getToolTipText(java.awt.event.MouseEvent e)
protected void	initLocals()
protected void	initTransientState()
protected boolean	isDrawIPDConsensus() should we draw consensus ipd based on user options, etc.
boolean	isValidView()
void	noDataFound()
void	setEndInsertions(int l)
void	setValidView(boolean b)
void	setViewWithOrWithoutUpdate(Interval interval, boolean bredraw) Sets the current genomic range for this view

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

center, changeDNAFontSize, changeIPDConsensusHeight, changeTrackSize, drawDetailsLegend, drawGraphStructures, drawIPDConsensusPlot, drawIPDConsensusRevRefAndBases, drawKineticsLegendToDeviceContext, drawLineStructures, drawLinkStructures, drawMapQVLegendToDeviceContext, drawMinMaxIPDRatioLabel, drawNodeStructures, drawReadFiltered, drawReadLengthLegendToDeviceContext, drawReadsFiltered, drawReadsKinetics, drawReadsUnfiltered, drawReferenceBases, drawReferenceBasesOutline, drawStructureLegend, drawSubReads, drawTruncatedEndsOfLink, drawTruncatedEndsOfRead, getDefaultVisibleRange, getListOfReadsToDraw, getMaxIPDToPlot, getScaledWidth, resetVisibleGenomicRange, saveLastPosition, updateLayout, updateSize

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

drawEpiProFoldedRead, drawEpiProUnfoldedReadMappedCoord, drawEpiProUnfoldedReadSubreadCoord, drawEpiProUnfoldedReadSubreadCoordOrg, drawReadShape

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

actionPerformed, addGenomicRangeToDetailsViewDataRequestsQueue, addGenomicRangeToDetailsViewIPDConsensusRequestQueue, addGenomicRangeToDetailsViewReferenceRequestQueue, canDrawIPDConsensus, clearAllDetailsData, findReadByPositionAndLane, getDetailsDataLocus, getDetailsDataStorage, getDetailsOptions, getEmptyCharArray, getIPDConsensusDataLocus, getIPDConsensusStorage, getReferenceDataLocus, getReferenceSequenceStorage, isCDNADataAvailable, isDNABaseShown, isIPDConsensusDataAvailable, retrieveDataOnDemand, setConsensusData, setDetailsOptions, setDetailsViewData, setIPDConsensusData, setReferenceData, setReferenceSequenceStorage, setViewDataForCurrentContig, updateLayoutOnDemand, zoomToBases

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

calcSize, drawCrossLines, drawFilteredTrack, drawFilteredTracks, drawGene, 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, getTracksHeight, isIdeogramDBLoaded, selectPoint, setTracksHeight, showDataLabels, updateSize

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

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

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

autofitLabelWidth, BaseRangeToXExtent, BaseToXCoord, BaseToYCoord, drawAxisHeaderlabel, drawEpiProIdeogram, drawGenes, drawGenomicViewToPaintBuffer, 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, getMinGenomicRange, getReferenceInfo, getViewContig, getViewContigName, getVioletApp, initializeViewBase, isActive

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

no_data_msg

protected static java.lang.String no_data_msg

is_valid

protected transient boolean is_valid

end_first_insertion

protected int end_first_insertion

end_insertion_reference

protected int end_insertion_reference

insertion_width

protected int insertion_width

Constructor Detail

GenomicViewInspect

public GenomicViewInspect(VioletApp mainApp)

Method Detail

getEndFirstInsertion

public long getEndFirstInsertion()

getEndInsertionReference

public long getEndInsertionReference()

getInsertionWidth

public int getInsertionWidth()

calculateInsertionInfo

public boolean calculateInsertionInfo()

Determines insertion genomic range and start-stop coordinates

initLocals

protected void initLocals()

Overrides:

initLocals in class GenomicViewDetails

initTransientState

protected void initTransientState()

Overrides:

initTransientState in class GenomicViewDetails

isDrawIPDConsensus

protected boolean isDrawIPDConsensus()

should we draw consensus ipd based on user options, etc.

Overrides:

isDrawIPDConsensus in class GenomicViewDetailsData

Returns:

drawGenomicViewDoubleBuffered

protected void drawGenomicViewDoubleBuffered(java.awt.Graphics graphics)

Description copied from class: GenomicViewDraw

Main draw function for class

Overrides:

drawGenomicViewDoubleBuffered in class GenomicViewDraw

drawGenomicViewToGraphicsContext

public void drawGenomicViewToGraphicsContext(java.awt.Graphics g)

Description copied from class: GenomicViewHorizontal

Paints the ideogram into the given graphical context.

Overrides:

drawGenomicViewToGraphicsContext in class GenomicViewDetails

drawHeaderFooter

protected void drawHeaderFooter(java.awt.Graphics g)

Overrides:

drawHeaderFooter in class GenomicViewDetails

drawHorizontalTracksHeader

protected void drawHorizontalTracksHeader(java.awt.Graphics g)

Description copied from class: GenomicViewHorizontal

Draws the labels for each track

Overrides:

drawHorizontalTracksHeader in class GenomicViewDetails

drawReadUnfiltered

protected void drawReadUnfiltered(java.awt.Graphics g,
                      Marker marker,
                      int y_start,
                      boolean bDrawDNABases,
                      boolean bDrawQV)

Overrides:

drawReadUnfiltered in class GenomicViewDetails

drawReadKinetic

protected void drawReadKinetic(java.awt.Graphics g,
                   Marker marker,
                   int y_start,
                   boolean bDrawDNABases,
                   int mode)

Overrides:

drawReadKinetic in class GenomicViewDetails

drawReferenceSequence

protected void drawReferenceSequence(java.awt.Graphics g)

Overrides:

drawReferenceSequence in class GenomicViewDetails

drawBackgroundSelections

public void drawBackgroundSelections(java.awt.Graphics g)

draw header area and reference sequence outline

Overrides:

drawBackgroundSelections in class GenomicViewHorizontal

drawForegroundSelections

public void drawForegroundSelections(java.awt.Graphics g)

Overrides:

drawForegroundSelections in class GenomicViewHorizontal

drawTargetInDetailsView

protected void drawTargetInDetailsView()

draw selection in region panel

getMaxGenomicRange

public int getMaxGenomicRange()

Overrides:

getMaxGenomicRange in class GenomicViewDetails

getMinMagnification

protected double getMinMagnification()

Overrides:

getMinMagnification in class GenomicViewHorizontal

setValidView

public void setValidView(boolean b)

isValidView

public boolean isValidView()

setEndInsertions

public void setEndInsertions(int l)

setViewWithOrWithoutUpdate

public void setViewWithOrWithoutUpdate(Interval interval,
                              boolean bredraw)

Description copied from class: GenomicViewEvents

Sets the current genomic range for this view

Overrides:

setViewWithOrWithoutUpdate in class GenomicViewEvents

noDataFound

public void noDataFound()

getToolTipText

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

Overrides:

getToolTipText in class GenomicViewEvents

getCenterLocation

public int getCenterLocation()

Returns:

calculateInsertionExtent

protected void calculateInsertionExtent()

two pass to determine insertion range and start-stop ref coordinates

assembleReadsWithGappedInsertions

public void assembleReadsWithGappedInsertions()

Creates pseudo-reads with added gaps so we can construct and view an MSA

calcRequiredGapsForRead

protected int calcRequiredGapsForRead(ReadInfo read,
                          int read_idx_start,
                          int read_idx_end,
                          int gaps_to_add)

count total gaps to add to this read

Parameters:

read -

read_idx_start -

read_idx_end -

gaps_to_add - total gaps required

Returns: