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

Class GenomicViewDetails

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

All Implemented Interfaces:

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

Direct Known Subclasses:

GenomicViewInspect

public class GenomicViewDetails
extends GenomicViewDetailsDraw

GenomicViewDetailsData

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 double	ipd_baseline
protected static double	ipd_nan_marker
protected static int	MAX_TRACK_HEIGHT
protected static double	min_ipdratio_plot
protected static int	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
GenomicViewDetails(VioletApp mainApp)

Method Summary

Methods

Modifier and Type	Method and Description
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 int	drawDetailsLegend(java.awt.Graphics g)
void	drawGenomicViewToGraphicsContext(java.awt.Graphics g) Paints the ideogram into the given graphical context.
protected void	drawGraphStructures(java.awt.Graphics g) draws various types of graphs
protected void	drawHeaderFooter(java.awt.Graphics g)
protected void	drawHorizontalTracksHeader(java.awt.Graphics g) Draws the labels for each track
protected void	drawIPDConsensusPlot(java.awt.Graphics g, int y_location, int const_x_offset, int dna_letter_width)
protected void	drawIPDConsensusRevRefAndBases(java.awt.Graphics g, char[] dna_sequence, int const_x_offset, int y_location, int dna_letter_width)
protected void	drawKineticsLegendToDeviceContext(java.awt.Graphics g, int ctrl_x, int ctrl_y, int ctrl_height, int ctrl_width, int mode, int scaling) Draw kinetics palette in legend area *****version for dual palette for kinetics
protected void	drawLineStructures(java.awt.Graphics g) draws graphic structures created for strobes as lines
protected void	drawLinkStructures(java.awt.Graphics g) draws graphic structures created for standard reads
protected void	drawMapQVLegendToDeviceContext(java.awt.Graphics g, int ctrl_x, int ctrl_y, int ctrl_height, int ctrl_width) Draw mapqv palette in legend area
protected void	drawMinMaxIPDRatioLabel(java.awt.Graphics g, double min, double max, int y_offset, int vertical_height, double delta_extent, java.lang.String metric, boolean format_as_int)
protected void	drawNodeStructures(java.awt.Graphics g) draws all graphic structures for strobes as rectangles
protected void	drawReadFiltered(java.awt.Graphics g, java.util.List<Marker> variants, Marker marker, int y_start, boolean bDrawDNABases, boolean bDrawQV)
protected void	drawReadKinetic(java.awt.Graphics g, Marker marker, int y_start, boolean bDrawDNABases, int mode)
protected void	drawReadLengthLegendToDeviceContext(java.awt.Graphics g, int ctrl_x, int ctrl_y, int ctrl_height, int ctrl_width) Draw read length palette in legend area
protected void	drawReadsFiltered(java.awt.Graphics gContext)
protected void	drawReadsKinetics(java.awt.Graphics gContext)
protected void	drawReadsUnfiltered(java.awt.Graphics gContext)
protected void	drawReadUnfiltered(java.awt.Graphics g, Marker marker, int y_start, boolean bDrawDNABases, boolean bDrawQV)
protected void	drawReferenceBases(java.awt.Graphics g, char[] dna_sequence, int y_location, int const_x_offset, int dna_letter_width, boolean bw)
protected void	drawReferenceBasesOutline(java.awt.Graphics g, char[] dna_sequence, int y_location, int const_x_offset, int dna_letter_width, boolean bw)
protected void	drawReferenceSequence(java.awt.Graphics g)
protected void	drawStructureLegend(java.awt.Graphics g, int header_y, int header_width, int delta, int header_height) Draw legend for structure graphs
protected boolean	drawSubReads()
protected void	drawTruncatedEndsOfLink(java.awt.Graphics g, int x_from, int x_to, int y1, int y2)
protected void	drawTruncatedEndsOfRead(java.awt.Graphics g, int x_from, int x_to, int y)
protected Interval	getDefaultVisibleRange()
protected java.util.List<Marker>	getListOfReadsToDraw()
int	getMaxGenomicRange()
protected double	getMaxIPDToPlot()
int	getScaledWidth()
protected void	initLocals()
protected void	initTransientState()
void	resetVisibleGenomicRange(boolean firechangeevent) Zoom fully out.
protected boolean	saveLastPosition(int dna_letter_width)
java.awt.Dimension	updateLayout()
java.awt.Dimension	updateSize(boolean repaint)

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, isDrawIPDConsensus, isIPDConsensusDataAvailable, retrieveDataOnDemand, setConsensusData, setDetailsOptions, setDetailsViewData, setIPDConsensusData, setReferenceData, setReferenceSequenceStorage, setViewDataForCurrentContig, updateLayoutOnDemand, zoomToBases

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

calcSize, drawBackgroundSelections, drawCrossLines, drawFilteredTrack, drawFilteredTracks, drawForegroundSelections, 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, getMinMagnification, 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, getToolTipText, getZoom, getZoom, hasViewHistoryItems, 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, 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

ipd_nan_marker

protected static final double ipd_nan_marker

See Also:

Constant Field Values

ipd_baseline

protected static final double ipd_baseline

See Also:

Constant Field Values

min_ipdratio_plot

protected static final double min_ipdratio_plot

See Also:

Constant Field Values

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

GenomicViewDetails

public GenomicViewDetails(VioletApp mainApp)

Method Detail

initTransientState

protected void initTransientState()

Overrides:

initTransientState in class GenomicViewEvents

initLocals

protected void initLocals()

Specified by:

initLocals in class GenomicViewHorizontal

getDefaultVisibleRange

protected Interval getDefaultVisibleRange()

Returns:

default genomic range interval, centered on chromosome

resetVisibleGenomicRange

public void resetVisibleGenomicRange(boolean firechangeevent)

Description copied from class: GenomicViewHorizontal

Zoom fully out. Autoscale for the region view.

Overrides:

resetVisibleGenomicRange in class GenomicViewHorizontal

changeTrackSize

public void changeTrackSize(boolean bIncrement)

Overrides:

changeTrackSize in class GenomicViewEvents

changeIPDConsensusHeight

public void changeIPDConsensusHeight(boolean bIncrement)

Overrides:

changeIPDConsensusHeight in class GenomicViewEvents

changeDNAFontSize

public void changeDNAFontSize(boolean bIncrement)

Overrides:

changeDNAFontSize in class GenomicViewEvents

updateSize

public java.awt.Dimension updateSize(boolean repaint)

updateLayout

public java.awt.Dimension updateLayout()

Overrides:

updateLayout in class GenomicViewDraw

getScaledWidth

public int getScaledWidth()

Overrides:

getScaledWidth in class GenomicViewEvents

getMaxGenomicRange

public int getMaxGenomicRange()

Overrides:

getMaxGenomicRange in class GenomicViewBase

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 GenomicViewHorizontal

drawGraphStructures

protected void drawGraphStructures(java.awt.Graphics g)

draws various types of graphs

Parameters:

g -

drawLinkStructures

protected void drawLinkStructures(java.awt.Graphics g)

draws graphic structures created for standard reads

Parameters:

g -

drawLineStructures

protected void drawLineStructures(java.awt.Graphics g)

draws graphic structures created for strobes as lines

Parameters:

g -

drawNodeStructures

protected void drawNodeStructures(java.awt.Graphics g)

draws all graphic structures for strobes as rectangles

Parameters:

g -

drawHeaderFooter

protected void drawHeaderFooter(java.awt.Graphics g)

Overrides:

drawHeaderFooter in class GenomicViewDraw

drawHorizontalTracksHeader

protected void drawHorizontalTracksHeader(java.awt.Graphics g)

Description copied from class: GenomicViewHorizontal

Draws the labels for each track

Overrides:

drawHorizontalTracksHeader in class GenomicViewHorizontal

drawReadsFiltered

protected void drawReadsFiltered(java.awt.Graphics gContext)

getListOfReadsToDraw

protected java.util.List<Marker> getListOfReadsToDraw()

drawReadFiltered

protected void drawReadFiltered(java.awt.Graphics g,
                    java.util.List<Marker> variants,
                    Marker marker,
                    int y_start,
                    boolean bDrawDNABases,
                    boolean bDrawQV)

drawReadsUnfiltered

protected void drawReadsUnfiltered(java.awt.Graphics gContext)

drawReadUnfiltered

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

drawReadsKinetics

protected void drawReadsKinetics(java.awt.Graphics gContext)

drawReadKinetic

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

center

public void center(long pos)

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

Overrides:

center in class GenomicViewEvents

Parameters:

pos -

drawReferenceSequence

protected void drawReferenceSequence(java.awt.Graphics g)

drawIPDConsensusRevRefAndBases

protected void drawIPDConsensusRevRefAndBases(java.awt.Graphics g,
                                  char[] dna_sequence,
                                  int const_x_offset,
                                  int y_location,
                                  int dna_letter_width)

Parameters:

g -

dna_sequence -

const_x_offset -

y_location -

dna_letter_width -

drawReferenceBasesOutline

protected void drawReferenceBasesOutline(java.awt.Graphics g,
                             char[] dna_sequence,
                             int y_location,
                             int const_x_offset,
                             int dna_letter_width,
                             boolean bw)

Parameters:

g -

dna_sequence -

y_location -

const_x_offset -

dna_letter_width -

drawReferenceBases

protected void drawReferenceBases(java.awt.Graphics g,
                      char[] dna_sequence,
                      int y_location,
                      int const_x_offset,
                      int dna_letter_width,
                      boolean bw)

Parameters:

g -

dna_sequence -

y_location -

const_x_offset -

dna_letter_width -

bw -

getMaxIPDToPlot

protected double getMaxIPDToPlot()

Returns:

drawIPDConsensusPlot

protected void drawIPDConsensusPlot(java.awt.Graphics g,
                        int y_location,
                        int const_x_offset,
                        int dna_letter_width)

Parameters:

g -

drawDetailsLegend

protected int drawDetailsLegend(java.awt.Graphics g)

Parameters:

g -

drawKineticsLegendToDeviceContext

protected void drawKineticsLegendToDeviceContext(java.awt.Graphics g,
                                     int ctrl_x,
                                     int ctrl_y,
                                     int ctrl_height,
                                     int ctrl_width,
                                     int mode,
                                     int scaling)

Draw kinetics palette in legend area *****version for dual palette for kinetics

Parameters:

g -

ctrl_x -

ctrl_y -

ctrl_height -

mode -

drawMapQVLegendToDeviceContext

protected void drawMapQVLegendToDeviceContext(java.awt.Graphics g,
                                  int ctrl_x,
                                  int ctrl_y,
                                  int ctrl_height,
                                  int ctrl_width)

Draw mapqv palette in legend area

Parameters:

g -

ctrl_x -

ctrl_y -

ctrl_height -

mode -

drawReadLengthLegendToDeviceContext

protected void drawReadLengthLegendToDeviceContext(java.awt.Graphics g,
                                       int ctrl_x,
                                       int ctrl_y,
                                       int ctrl_height,
                                       int ctrl_width)

Draw read length palette in legend area

Parameters:

g -

ctrl_x -

ctrl_y -

ctrl_height -

drawStructureLegend

protected void drawStructureLegend(java.awt.Graphics g,
                       int header_y,
                       int header_width,
                       int delta,
                       int header_height)

Draw legend for structure graphs

Parameters:

g -

header_y -

header_width -

delta -

drawTruncatedEndsOfLink

protected void drawTruncatedEndsOfLink(java.awt.Graphics g,
                           int x_from,
                           int x_to,
                           int y1,
                           int y2)

drawTruncatedEndsOfRead

protected void drawTruncatedEndsOfRead(java.awt.Graphics g,
                           int x_from,
                           int x_to,
                           int y)

drawMinMaxIPDRatioLabel

protected void drawMinMaxIPDRatioLabel(java.awt.Graphics g,
                           double min,
                           double max,
                           int y_offset,
                           int vertical_height,
                           double delta_extent,
                           java.lang.String metric,
                           boolean format_as_int)

Parameters:

g -

min -

max -

y_offset -

vertical_height -

delta_extent -

metric -

format_as_int -

drawSubReads

protected boolean drawSubReads()

saveLastPosition

protected boolean saveLastPosition(int dna_letter_width)