org.utgenome.graphics
Class ReadCanvas

java.lang.Object
  org.utgenome.graphics.ReadCanvas

public class ReadCanvas
extends Object

For generating BufferedImage instance of a read layout

Author:

leo

Nested Class Summary

static class

ReadCanvas.DrawStyle

Constructor Summary

ReadCanvas(int width, int height, GenomeWindow window)

ReadCanvas(int width, int height, GenomeWindow window, ReadCanvas.DrawStyle style)

Method Summary

void	draw(List<OnGenome> dataSet)
void	drawBase(char base, long startIndexOnGenome, int yOffset, Color color)
void	drawBases(int startOnGenome, int y, String seq, String qual)
void	drawGeneRect(int startOnGenome, int endOnGenome, int y, Color c)
void	drawPadding(int startOnGenome, int endOnGenome, int y, Color c)
void	drawRegion(int startOnGenome, int endOnGenome, int y, Color c, boolean drawShadow)
void	drawRegion(OnGenome region, int y)
void	drawSAMRead(SAMReadLight r, int y)
Graphics2D	getGraphics()
int	getPixelWidth()
void	setPixelSize(int width, int height)
void	toPNG(File out)
void	toPNG(OutputStream out)

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadCanvas

public ReadCanvas(int width,
                  int height,
                  GenomeWindow window)

ReadCanvas

public ReadCanvas(int width,
                  int height,
                  GenomeWindow window,
                  ReadCanvas.DrawStyle style)

Method Detail

setPixelSize

public void setPixelSize(int width,
                         int height)

getGraphics

public Graphics2D getGraphics()

toPNG

public void toPNG(OutputStream out)
           throws IOException

Throws:

IOException

toPNG

public void toPNG(File out)
           throws IOException

Throws:

IOException

draw

public void draw(List<OnGenome> dataSet)

drawRegion

public void drawRegion(OnGenome region,
                       int y)

drawRegion

public void drawRegion(int startOnGenome,
                       int endOnGenome,
                       int y,
                       Color c,
                       boolean drawShadow)

drawGeneRect

public void drawGeneRect(int startOnGenome,
                         int endOnGenome,
                         int y,
                         Color c)

drawPadding

public void drawPadding(int startOnGenome,
                        int endOnGenome,
                        int y,
                        Color c)

drawSAMRead

public void drawSAMRead(SAMReadLight r,
                        int y)

drawBases

public void drawBases(int startOnGenome,
                      int y,
                      String seq,
                      String qual)

getPixelWidth

public int getPixelWidth()

drawBase

public void drawBase(char base,
                     long startIndexOnGenome,
                     int yOffset,
                     Color color)