org.utgenome.gwt.utgb.client.canvas
Class ReadDisplayStyle

java.lang.Object
  org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle

public class ReadDisplayStyle
extends Object

Configuration of ReadTrack display

Author:

leo

Field Summary

float	clippedRegionAlpha
static String	CONFIG_COVERAGE_STYLE
static String	CONFIG_DRAW_SHADOW
static String	CONFIG_HIDE_MATCHED_BASE
static String	CONFIG_LAYOUT
static String	CONFIG_MIN_READ_HEIGHT
static String	CONFIG_NUM_READ_MAX
static String	CONFIG_PE_OVERLAP
static String	CONFIG_READ_HEIGHT
static String	CONFIG_READ_MARGIN
static String	CONFIG_REVERSE_READ_HISTOGRAM
static String	CONFIG_REVERSE_READ_TRACK
static String	CONFIG_SHOW_BASE_QUALITY
static String	CONFIG_SHOW_LABELS
static String	CONFIG_SHOW_STRAND
String	coverageStyle
boolean	drawShadow
String	layout
int	minReadHeight
int	numReadsMax
boolean	overlapPairedReads
int	readHeight
int	readMargin
boolean	reverseReadHistogram
boolean	reverseReadTrack
boolean	showBaseQuality
boolean	showLabels
boolean	showStrand
boolean	unmatchHighlight

Constructor Summary

ReadDisplayStyle()

Method Summary

static ReadDisplayStyle	defaultStyle()
com.google.gwt.widgetideas.graphics.client.Color	getClippedReadColor(GenomeRange g)
com.google.gwt.widgetideas.graphics.client.Color	getPaddingColor()
com.google.gwt.widgetideas.graphics.client.Color	getReadColor(GenomeRange g)
com.google.gwt.widgetideas.graphics.client.Color	getReadColor(GenomeRange g, float alpha)
com.google.gwt.widgetideas.graphics.client.Color	getSAMReadColor(SAMReadLight r)
static ReadDisplayStyle	highlightImproperMate()
void	loadConfig(TrackConfig config)
void	setup(TrackConfig config)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

showLabels

public boolean showLabels

drawShadow

public boolean drawShadow

showBaseQuality

public boolean showBaseQuality

overlapPairedReads

public boolean overlapPairedReads

showStrand

public boolean showStrand

reverseReadTrack

public boolean reverseReadTrack

reverseReadHistogram

public boolean reverseReadHistogram

unmatchHighlight

public boolean unmatchHighlight

numReadsMax

public int numReadsMax

clippedRegionAlpha

public float clippedRegionAlpha

readHeight

public int readHeight

minReadHeight

public int minReadHeight

readMargin

public int readMargin

coverageStyle

public String coverageStyle

layout

public String layout

CONFIG_LAYOUT

public static final String CONFIG_LAYOUT

See Also:

Constant Field Values

CONFIG_SHOW_LABELS

public static final String CONFIG_SHOW_LABELS

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Constant Field Values

CONFIG_READ_HEIGHT

public static final String CONFIG_READ_HEIGHT

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Constant Field Values

CONFIG_MIN_READ_HEIGHT

public static final String CONFIG_MIN_READ_HEIGHT

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Constant Field Values

CONFIG_NUM_READ_MAX

public static final String CONFIG_NUM_READ_MAX

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Constant Field Values

CONFIG_READ_MARGIN

public static final String CONFIG_READ_MARGIN

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Constant Field Values

CONFIG_REVERSE_READ_TRACK

public static final String CONFIG_REVERSE_READ_TRACK

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Constant Field Values

CONFIG_REVERSE_READ_HISTOGRAM

public static final String CONFIG_REVERSE_READ_HISTOGRAM

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Constant Field Values

CONFIG_SHOW_BASE_QUALITY

public static final String CONFIG_SHOW_BASE_QUALITY

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Constant Field Values

CONFIG_PE_OVERLAP

public static final String CONFIG_PE_OVERLAP

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Constant Field Values

CONFIG_COVERAGE_STYLE

public static final String CONFIG_COVERAGE_STYLE

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Constant Field Values

CONFIG_DRAW_SHADOW

public static final String CONFIG_DRAW_SHADOW

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Constant Field Values

CONFIG_SHOW_STRAND

public static final String CONFIG_SHOW_STRAND

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Constant Field Values

CONFIG_HIDE_MATCHED_BASE

public static final String CONFIG_HIDE_MATCHED_BASE

See Also:

Constant Field Values

Constructor Detail

ReadDisplayStyle

public ReadDisplayStyle()

Method Detail

setup

public void setup(TrackConfig config)

loadConfig

public void loadConfig(TrackConfig config)

getSAMReadColor

public com.google.gwt.widgetideas.graphics.client.Color getSAMReadColor(SAMReadLight r)

getClippedReadColor

public com.google.gwt.widgetideas.graphics.client.Color getClippedReadColor(GenomeRange g)

getPaddingColor

public com.google.gwt.widgetideas.graphics.client.Color getPaddingColor()

getReadColor

public com.google.gwt.widgetideas.graphics.client.Color getReadColor(GenomeRange g)

getReadColor

public com.google.gwt.widgetideas.graphics.client.Color getReadColor(GenomeRange g,
                                                                     float alpha)

defaultStyle

public static ReadDisplayStyle defaultStyle()

highlightImproperMate

public static ReadDisplayStyle highlightImproperMate()