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

Class GenomicViewHorizontal

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

All Implemented Interfaces:

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

Direct Known Subclasses:

GenomicViewDetailsData, GenomicViewRegion

public abstract class GenomicViewHorizontal
extends GenomicViewEvents

Author:

mmilletti

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 int	default_tracks_height
protected static double	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
GenomicViewHorizontal(VioletApp mainApp)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	calcSize()
boolean	canDrawIPDConsensus()
void	drawBackgroundSelections(java.awt.Graphics g) draw marker lines and selected profile lines
protected void	drawCrossLines(java.awt.Graphics g, boolean cutLeft, boolean cutRight, int x1, int x2, int dy, int y) draw cross line if the ends are cut
protected void	drawFilteredTrack(java.awt.Graphics g, java.util.List<Marker> list, MarkerCollection track, java.util.ArrayList<java.lang.Integer> track_indexes, VariableResolutionDataSet slot)
protected void	drawFilteredTracks(java.awt.Graphics g)
void	drawForegroundSelections(java.awt.Graphics graphics)
protected void	drawGene(java.awt.Graphics g, Marker marker, boolean is_selected, java.awt.Color selected_color) Draws a gene into the graphic context
void	drawGenomicViewToGraphicsContext(java.awt.Graphics g) Paints the ideogram into the given graphical context.
protected void	drawHorizontalTracksHeader(java.awt.Graphics g) Draws the labels for each track
protected void	drawIdeogram(java.awt.Graphics g)
protected void	drawLabelWithoutCollision(java.awt.Graphics g, java.lang.String text, java.awt.Color color, int x1, int x2, int yofs, java.awt.Rectangle rect, boolean is_selected)
protected void	drawMarkerHorizontal(java.awt.Graphics g, Marker marker, java.util.ArrayList<java.lang.Integer> track_indexes, java.awt.Rectangle rect, java.awt.Color color, boolean is_selected, java.awt.Color selected_color) Draws a single marker.
protected void	drawMarkerInterval(java.awt.Graphics g, Marker marker, int track, java.awt.Rectangle rect, boolean is_selected, java.awt.Color selected_color)
protected void	drawMarkers(java.awt.Graphics g)
protected void	drawMarkersLegend(java.awt.Graphics g, VariableResolutionDataSet slot, java.awt.Rectangle rect)
protected void	drawModification(java.awt.Graphics g, Marker marker, java.util.ArrayList<java.lang.Integer> track_indexes, java.awt.Rectangle rect, VariableResolutionDataSetValues min_max_values)
protected void	drawModificationInterval(java.awt.Graphics2D g, Marker marker, int track_index, java.awt.Rectangle rect, VariableResolutionDataSetValues min_max_values)
protected void	drawModificationsLegend(java.awt.Graphics2D g, VariableResolutionDataSet slot, java.awt.Rectangle rect) draw legend for motifs/mods track
protected void	drawModificationSummaryHeatmap(java.awt.Graphics2D g2d, Marker marker, int visible_track_index, int num_metrics, int x1, int x2, VariableResolutionDataSetValues minmaxValues)
protected void	drawModificationSummaryHistogram(java.awt.Graphics2D g2d, Marker marker, int visible_track_index, int num_metrics, int x1, int x2, VariableResolutionDataSetValues minmaxValues)
protected void	drawMotifLegend(java.awt.Graphics2D g, java.lang.String motif, int x, int y, int max_x) draws a single motif string up to max x coordinate
protected void	drawRangeSelection(java.awt.Graphics g)
protected void	drawReferenceSequenceOutline(java.awt.Graphics g)
protected void	drawSummaryLegends(java.awt.Graphics g, VariableResolutionDataSet slot, int summary_index, java.awt.Rectangle rect, int char_height) draws summary legends
protected void	drawSummaryTracks(java.awt.Graphics2D g2d, java.util.List<Marker> markers, java.util.ArrayList<java.lang.Integer> track_indexes, java.awt.Color color, VariableResolutionDataSetValues minmaxValues)
protected void	drawUnFilteredTracks(java.awt.Graphics g)
protected void	drawVariant(java.awt.Graphics g, Marker marker, java.util.ArrayList<java.lang.Integer> track_indexes, java.awt.Rectangle rect, VariableResolutionDataSetValues min_max_values)
protected void	drawVariantInterval(java.awt.Graphics2D g, Marker marker, int track, java.awt.Rectangle rect, VariableResolutionDataSetValues min_max_values)
protected void	drawVariantIntervalOrg(java.awt.Graphics2D g, Marker marker, int track, java.awt.Rectangle rect, VariableResolutionDataSetValues min_max_values)
protected void	drawVariantsLegend(java.awt.Graphics2D g, VariableResolutionDataSet slot, java.awt.Rectangle rect)
protected void	drawVariantsLegendOrg(java.awt.Graphics g, java.awt.Rectangle rect) draw legend for variants track
int	getLegendLabelsWidth()
double	getMaxCoverageInInterval(java.util.List<Marker> markers)
double	getMaxCoverageInInterval(VariableResolutionDataSet slot)
protected double	getMaxMagnification()
protected double	getMinMagnification()
int	getTracksHeight()
protected abstract void	initLocals()
boolean	isIdeogramDBLoaded() Do not draw ideogram in horizontal views
void	resetVisibleGenomicRange(boolean firechangeevent) Zoom fully out.
void	selectPoint(java.awt.Point p) TODO: implement???
void	setTracksHeight(int tracks_height) set height of tracks
protected boolean	showDataLabels()
java.awt.Dimension	updateSize(boolean repaint, boolean revalidate)

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

addGenomicRangeToDetailsViewDataRequestsQueue, addSelectionChangedListener, beginSelection, center, changeDNAFontSize, changeIPDConsensusHeight, changeTrackSize, clearSelections, createToolTip, endSelection, findVariantByPositionAndYCoordinate, fireSelectionChanged, getActiveViewForKeyEvents, getDetailsDataStorage, 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, 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, updateLayout, 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

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

default_tracks_height

protected int default_tracks_height

variations_splitter

protected static final double variations_splitter

See Also:

Constant Field Values

Constructor Detail

GenomicViewHorizontal

public GenomicViewHorizontal(VioletApp mainApp)

Parameters:

mainApp -

Method Detail

updateSize

public java.awt.Dimension updateSize(boolean repaint,
                            boolean revalidate)

Overrides:

updateSize in class GenomicViewDraw

getMaxMagnification

protected double getMaxMagnification()

Overrides:

getMaxMagnification in class GenomicViewDraw

getMinMagnification

protected double getMinMagnification()

Overrides:

getMinMagnification in class GenomicViewDraw

calcSize

protected void calcSize()

initLocals

protected abstract void initLocals()

getTracksHeight

public int getTracksHeight()

Returns:

height of tracks

setTracksHeight

public void setTracksHeight(int tracks_height)

set height of tracks

isIdeogramDBLoaded

public boolean isIdeogramDBLoaded()

Do not draw ideogram in horizontal views

Overrides:

isIdeogramDBLoaded in class GenomicViewBase

drawRangeSelection

protected void drawRangeSelection(java.awt.Graphics g)

Overrides:

drawRangeSelection in class GenomicViewDraw

drawBackgroundSelections

public void drawBackgroundSelections(java.awt.Graphics g)

draw marker lines and selected profile lines

Overrides:

drawBackgroundSelections in class GenomicViewDraw

canDrawIPDConsensus

public boolean canDrawIPDConsensus()

Returns:

drawReferenceSequenceOutline

protected void drawReferenceSequenceOutline(java.awt.Graphics g)

drawForegroundSelections

public void drawForegroundSelections(java.awt.Graphics graphics)

Overrides:

drawForegroundSelections in class GenomicViewDraw

selectPoint

public void selectPoint(java.awt.Point p)

TODO: implement???

Overrides:

selectPoint in class GenomicViewEvents

Parameters:

p - Point in component coordinates.

drawGenomicViewToGraphicsContext

public void drawGenomicViewToGraphicsContext(java.awt.Graphics g)

Paints the ideogram into the given graphical context.

Overrides:

drawGenomicViewToGraphicsContext in class GenomicViewDraw

Parameters:

g -

drawIdeogram

protected void drawIdeogram(java.awt.Graphics g)

Overrides:

drawIdeogram in class GenomicViewDraw

resetVisibleGenomicRange

public void resetVisibleGenomicRange(boolean firechangeevent)

Zoom fully out. Autoscale for the region view.

Overrides:

resetVisibleGenomicRange in class GenomicViewEvents

showDataLabels

protected boolean showDataLabels()

Overrides:

showDataLabels in class GenomicViewDraw

drawGene

protected void drawGene(java.awt.Graphics g,
            Marker marker,
            boolean is_selected,
            java.awt.Color selected_color)

Draws a gene into the graphic context

Overrides:

drawGene in class GenomicViewDraw

Parameters:

g - Graphics context

marker - The gene to be drawn

color - The color of the gene marker.

drawLabelWithoutCollision

protected void drawLabelWithoutCollision(java.awt.Graphics g,
                             java.lang.String text,
                             java.awt.Color color,
                             int x1,
                             int x2,
                             int yofs,
                             java.awt.Rectangle rect,
                             boolean is_selected)

drawMarkers

protected void drawMarkers(java.awt.Graphics g)

Overrides:

drawMarkers in class GenomicViewDraw

Parameters:

g -

drawUnFilteredTracks

protected void drawUnFilteredTracks(java.awt.Graphics g)

Parameters:

g -

drawFilteredTracks

protected void drawFilteredTracks(java.awt.Graphics g)

Parameters:

g -

drawFilteredTrack

protected void drawFilteredTrack(java.awt.Graphics g,
                     java.util.List<Marker> list,
                     MarkerCollection track,
                     java.util.ArrayList<java.lang.Integer> track_indexes,
                     VariableResolutionDataSet slot)

Parameters:

g -

list -

track -

track_indexes -

slot -

drawMarkerHorizontal

protected void drawMarkerHorizontal(java.awt.Graphics g,
                        Marker marker,
                        java.util.ArrayList<java.lang.Integer> track_indexes,
                        java.awt.Rectangle rect,
                        java.awt.Color color,
                        boolean is_selected,
                        java.awt.Color selected_color)

Draws a single marker.

Parameters:

g -

marker -

column - The column index (0..n-1)

width - The (line) width of the marker

color_left - Color of a loss

color_right - Color of a gain

show_band - Shows a band across the ideogram

band_color - Color of the band

drawMarkerInterval

protected void drawMarkerInterval(java.awt.Graphics g,
                      Marker marker,
                      int track,
                      java.awt.Rectangle rect,
                      boolean is_selected,
                      java.awt.Color selected_color)

Overrides:

drawMarkerInterval in class GenomicViewDraw

drawVariant

protected void drawVariant(java.awt.Graphics g,
               Marker marker,
               java.util.ArrayList<java.lang.Integer> track_indexes,
               java.awt.Rectangle rect,
               VariableResolutionDataSetValues min_max_values)

drawVariantIntervalOrg

protected void drawVariantIntervalOrg(java.awt.Graphics2D g,
                          Marker marker,
                          int track,
                          java.awt.Rectangle rect,
                          VariableResolutionDataSetValues min_max_values)

drawVariantInterval

protected void drawVariantInterval(java.awt.Graphics2D g,
                       Marker marker,
                       int track,
                       java.awt.Rectangle rect,
                       VariableResolutionDataSetValues min_max_values)

Overrides:

drawVariantInterval in class GenomicViewDraw

drawModification

protected void drawModification(java.awt.Graphics g,
                    Marker marker,
                    java.util.ArrayList<java.lang.Integer> track_indexes,
                    java.awt.Rectangle rect,
                    VariableResolutionDataSetValues min_max_values)

Parameters:

g -

marker -

track_indexes -

width -

is_selected -

color -

max_variants -

max_ipd -

drawModificationInterval

protected void drawModificationInterval(java.awt.Graphics2D g,
                            Marker marker,
                            int track_index,
                            java.awt.Rectangle rect,
                            VariableResolutionDataSetValues min_max_values)

Overrides:

drawModificationInterval in class GenomicViewDraw

drawCrossLines

protected void drawCrossLines(java.awt.Graphics g,
                  boolean cutLeft,
                  boolean cutRight,
                  int x1,
                  int x2,
                  int dy,
                  int y)

draw cross line if the ends are cut

Parameters:

g -

cutLeft -

cutRight -

x1 -

x2 -

dy -

y -

drawSummaryTracks

protected void drawSummaryTracks(java.awt.Graphics2D g2d,
                     java.util.List<Marker> markers,
                     java.util.ArrayList<java.lang.Integer> track_indexes,
                     java.awt.Color color,
                     VariableResolutionDataSetValues minmaxValues)

drawModificationSummaryHistogram

protected void drawModificationSummaryHistogram(java.awt.Graphics2D g2d,
                                    Marker marker,
                                    int visible_track_index,
                                    int num_metrics,
                                    int x1,
                                    int x2,
                                    VariableResolutionDataSetValues minmaxValues)

drawModificationSummaryHeatmap

protected void drawModificationSummaryHeatmap(java.awt.Graphics2D g2d,
                                  Marker marker,
                                  int visible_track_index,
                                  int num_metrics,
                                  int x1,
                                  int x2,
                                  VariableResolutionDataSetValues minmaxValues)

Parameters:

g2d -

marker -

y_basement -

num_metrics -

x1 -

x2 -

minmaxValues -

drawHorizontalTracksHeader

protected void drawHorizontalTracksHeader(java.awt.Graphics g)

Draws the labels for each track

Overrides:

drawHorizontalTracksHeader in class GenomicViewDraw

Parameters:

g -

drawMarkersLegend

protected void drawMarkersLegend(java.awt.Graphics g,
                     VariableResolutionDataSet slot,
                     java.awt.Rectangle rect)

Parameters:

g -

slot -

rect -

drawVariantsLegend

protected void drawVariantsLegend(java.awt.Graphics2D g,
                      VariableResolutionDataSet slot,
                      java.awt.Rectangle rect)

drawVariantsLegendOrg

protected void drawVariantsLegendOrg(java.awt.Graphics g,
                         java.awt.Rectangle rect)

draw legend for variants track

Parameters:

g -

rect -

drawModificationsLegend

protected void drawModificationsLegend(java.awt.Graphics2D g,
                           VariableResolutionDataSet slot,
                           java.awt.Rectangle rect)

draw legend for motifs/mods track

Parameters:

g -

slot -

current_track_idx -

y_offset -

drawMotifLegend

protected void drawMotifLegend(java.awt.Graphics2D g,
                   java.lang.String motif,
                   int x,
                   int y,
                   int max_x)

draws a single motif string up to max x coordinate

Parameters:

g -

motif -

x -

y -

drawSummaryLegends

protected void drawSummaryLegends(java.awt.Graphics g,
                      VariableResolutionDataSet slot,
                      int summary_index,
                      java.awt.Rectangle rect,
                      int char_height)

draws summary legends

Parameters:

g -

slot -

track_index -

y_offset -

y_basement -

char_height -

getMaxCoverageInInterval

public double getMaxCoverageInInterval(VariableResolutionDataSet slot)

getMaxCoverageInInterval

public double getMaxCoverageInInterval(java.util.List<Marker> markers)

getLegendLabelsWidth

public int getLegendLabelsWidth()