org.utgenome.graphics
Class ReadCanvas

java.lang.Object
  extended by 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<GenomeRange> dataSet)
           
 void drawBase(char base, int startIndexOnGenome, int yOffset, Color color)
           
 void drawBases(int startOnGenome, int y, String seq, String qual)
           
 void drawGene(Gene gene, int y)
           
 void drawGeneRect(int startOnGenome, int endOnGenome, int y, Color c)
           
 void drawLabel(GenomeRange region, int yOffset)
           
 void drawPadding(int startOnGenome, int endOnGenome, int y, Color c)
           
 void drawRegion(GenomeRange region, int y)
           
 void drawRegion(int startOnGenome, int endOnGenome, int y, Color c, boolean drawShadow)
           
 void drawRuler()
           
 void drawSAMRead(SAMReadLight r, int y)
           
 BufferedImage getBufferedImage()
           
 Graphics2D getGraphics()
           
 int getPixelWidth()
           
 ReadCanvas.DrawStyle getStyle()
           
 void setPixelSize(int width, int height)
           
 void setStyle(ReadCanvas.DrawStyle style)
           
 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

getStyle

public ReadCanvas.DrawStyle getStyle()

setStyle

public void setStyle(ReadCanvas.DrawStyle style)

setPixelSize

public void setPixelSize(int width,
                         int height)

getGraphics

public Graphics2D getGraphics()

getBufferedImage

public BufferedImage getBufferedImage()

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<GenomeRange> dataSet)

drawGene

public void drawGene(Gene gene,
                     int y)

drawRegion

public void drawRegion(GenomeRange 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()

drawRuler

public void drawRuler()

drawBase

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

drawLabel

public void drawLabel(GenomeRange region,
                      int yOffset)


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