org.utgenome.graphics
Class GeneCanvas

java.lang.Object
  org.utgenome.graphics.GeneCanvas

public class GeneCanvas
extends Object

Browser-side graphic canvas for drawing gene objects

Author:

leo

Nested Class Summary

class

GeneCanvas.LocusLayout

Constructor Summary

GeneCanvas()

GeneCanvas(int pixelWidth, int pixelHeight, GenomeWindow genomeWindow)

Method Summary

int	colorOffset(int color, float offset)
void	draw(Gene gene, Exon exon, CDS cds, int yPosition)
void	draw(Gene gene, int yPosition)
void	draw(Gene gene, List<Exon> exonList, CDS cds, int yPosition)
void	draw(GenomeRange locus, int yOffset)
<E extends GenomeRange> void	draw(List<E> geneList)
void	drawGeneRect(long x1, long x2, int y, Color c)
Color	getCDSColor(GenomeRange g)
Color	getExonColor(GenomeRange g)
String	getExonColorText(GenomeRange g)
Color	getGeneColor(GenomeRange g)
Color	getGeneColor(GenomeRange g, float offset)
Color	getIntronColor(GenomeRange g)
Color	hexValue2Color(String hex, float offset)
void	setGapWidth(int gapWidth)
void	setGeneHeight(int height)
void	setPixelHeight(int height)
void	setThresholdGenes(int thresholdGeneNames)
void	toPNG(OutputStream out)
static int	width(int x1, int x2)

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneCanvas

public GeneCanvas()

GeneCanvas

public GeneCanvas(int pixelWidth,
                  int pixelHeight,
                  GenomeWindow genomeWindow)

Method Detail

setGeneHeight

public void setGeneHeight(int height)

setPixelHeight

public void setPixelHeight(int height)

width

public static int width(int x1,
                        int x2)

setThresholdGenes

public void setThresholdGenes(int thresholdGeneNames)

setGapWidth

public void setGapWidth(int gapWidth)

draw

public <E extends GenomeRange> void draw(List<E> geneList)

draw

public void draw(GenomeRange locus,
                 int yOffset)

draw

public void draw(Gene gene,
                 List<Exon> exonList,
                 CDS cds,
                 int yPosition)

draw

public void draw(Gene gene,
                 int yPosition)

draw

public void draw(Gene gene,
                 Exon exon,
                 CDS cds,
                 int yPosition)

drawGeneRect

public void drawGeneRect(long x1,
                         long x2,
                         int y,
                         Color c)

toPNG

public void toPNG(OutputStream out)
           throws IOException

Throws:

IOException

getExonColor

public Color getExonColor(GenomeRange g)

getGeneColor

public Color getGeneColor(GenomeRange g)

getGeneColor

public Color getGeneColor(GenomeRange g,
                          float offset)

getCDSColor

public Color getCDSColor(GenomeRange g)

getIntronColor

public Color getIntronColor(GenomeRange g)

getExonColorText

public String getExonColorText(GenomeRange g)

hexValue2Color

public Color hexValue2Color(String hex,
                            float offset)

colorOffset

public int colorOffset(int color,
                       float offset)