com.pacbio.secondary.vis.common.utils.constants

Class EpiProPalette

java.lang.Object

com.pacbio.secondary.vis.common.utils.constants.EpiProPalette

All Implemented Interfaces:

java.io.Serializable

public class EpiProPalette
extends java.lang.Object
implements java.io.Serializable

Author:

mmilletti

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	EpiProPalette.ColorInfo
class	EpiProPalette.EpiProContigPalette

Field Summary

Fields

Modifier and Type	Field and Description
static float	EPIPRO_PALETTE_BLACK
static int	EPIPRO_PALETTE_SCALING_MODE
static float	EPIPRO_PALETTE_WHITE
protected static int	EPIPRO_READS_BW_PALETTE_SIZE
protected static int	EPIPRO_READS_PALETTE_SIZE
protected java.util.ArrayList<EpiProPalette.EpiProContigPalette>	EpiProReadsPalettes
protected static float	MAX_RAINBOW_COLOR
protected static float	MIN_RAINBOW_COLOR

Constructor Summary

Constructors

Constructor and Description
EpiProPalette()
EpiProPalette(VioletApp app)

Method Summary

Methods

Modifier and Type	Method and Description
java.awt.Color	getEpiProReadColor(int contig, long genomic_location)
java.awt.Color[]	getPaletteForContig(int contig)
EpiProPalette.EpiProContigPalette	getUnmappedReadsContigPalette(int contig)
void	updateUnMappedReadsPalette(int mode)

Methods inherited from class java.lang.Object

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

Field Detail

EPIPRO_READS_PALETTE_SIZE

protected static final int EPIPRO_READS_PALETTE_SIZE

See Also:

Constant Field Values

EPIPRO_READS_BW_PALETTE_SIZE

protected static final int EPIPRO_READS_BW_PALETTE_SIZE

See Also:

Constant Field Values

EPIPRO_PALETTE_SCALING_MODE

public static final int EPIPRO_PALETTE_SCALING_MODE

See Also:

Constant Field Values

EPIPRO_PALETTE_BLACK

public static final float EPIPRO_PALETTE_BLACK

See Also:

Constant Field Values

EPIPRO_PALETTE_WHITE

public static final float EPIPRO_PALETTE_WHITE

See Also:

Constant Field Values

MAX_RAINBOW_COLOR

protected static final float MAX_RAINBOW_COLOR

See Also:

Constant Field Values

MIN_RAINBOW_COLOR

protected static final float MIN_RAINBOW_COLOR

See Also:

Constant Field Values

EpiProReadsPalettes

protected java.util.ArrayList<EpiProPalette.EpiProContigPalette> EpiProReadsPalettes

Constructor Detail

EpiProPalette

public EpiProPalette(VioletApp app)

Parameters:

app -

EpiProPalette

public EpiProPalette()

Method Detail

getUnmappedReadsContigPalette

public EpiProPalette.EpiProContigPalette getUnmappedReadsContigPalette(int contig)

updateUnMappedReadsPalette

public void updateUnMappedReadsPalette(int mode)

Parameters:

mode -

getPaletteForContig

public java.awt.Color[] getPaletteForContig(int contig)

getEpiProReadColor

public java.awt.Color getEpiProReadColor(int contig,
                                long genomic_location)