org.utgenome.graphics
Class ChromosomeMapCanvas

java.lang.Object
  extended by org.utgenome.graphics.ChromosomeMapCanvas

public class ChromosomeMapCanvas
extends Object

drawing chromosome map

Author:
yoshimura

Constructor Summary
ChromosomeMapCanvas(int pixelWidth, int pixelHeight, HashMap<String,ChromosomeWindow> windows)
           
 
Method Summary
 int calcLighterValue(int value)
           
 Color colorLighter(Color color)
           
<E extends CytoBand>
void
draw(List<E> cytoBandList)
           
 void drawChrName(String chrName, Integer rank)
           
 void drawCytoBand(CytoBand c, ChromosomeWindow w)
           
 void drawCytoBandName(CytoBand c, ChromosomeWindow w)
           
 void drawGenomeWindow(String chrom, long startOnChrom, long endOnChrom)
           
 void drawMapping(String[] data)
           
 void drawMapping(String chrom, int startOnChrom, int endOnChrom)
           
 void drawMapping(String chrom, int startOnChrom, int endOnChrom, char strand)
           
 void drawRect(int x1, int x2, int y, Color c)
           
 void drawRect(int x, int y, int width, int height, Color color)
           
 void drawText(String text, int x, int y, Color color)
           
 void drawTriangle(int x1, int x2, int y, Color color)
           
 void fillRect(int x1, int x2, int y, Color c)
           
 void fillRect(int x, int y, int width, int height, Color color)
           
 BufferedImage getBufferedImage()
           
 Color getCytoBandColor(CytoBand c)
           
 Color getCytoBandNameColor(CytoBand c)
           
 Color getFrameColor()
           
 double getLighterRate()
           
 boolean isLighter()
           
 void setCharHeight(int charHeight)
           
 void setChromHeight(int height)
           
 void setChromMargin(int margin)
           
 void setLighter(boolean isLighter)
           
 void setLighterRate(double lighterRate)
           
 void setPixelHeight(int height)
           
 void setPixelSize(int width, int height)
           
 void setPixelWidth(int width)
           
 void setRotate()
           
 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

ChromosomeMapCanvas

public ChromosomeMapCanvas(int pixelWidth,
                           int pixelHeight,
                           HashMap<String,ChromosomeWindow> windows)
Method Detail

setPixelSize

public void setPixelSize(int width,
                         int height)

getBufferedImage

public BufferedImage getBufferedImage()

setChromHeight

public void setChromHeight(int height)

setChromMargin

public void setChromMargin(int margin)

setCharHeight

public void setCharHeight(int charHeight)

setPixelHeight

public void setPixelHeight(int height)

setPixelWidth

public void setPixelWidth(int width)

width

public static int width(int x1,
                        int x2)

isLighter

public boolean isLighter()

setLighter

public void setLighter(boolean isLighter)

getLighterRate

public double getLighterRate()

setLighterRate

public void setLighterRate(double lighterRate)

setRotate

public void setRotate()

draw

public <E extends CytoBand> void draw(List<E> cytoBandList)

drawCytoBand

public void drawCytoBand(CytoBand c,
                         ChromosomeWindow w)

drawMapping

public void drawMapping(String[] data)

drawMapping

public void drawMapping(String chrom,
                        int startOnChrom,
                        int endOnChrom)

drawMapping

public void drawMapping(String chrom,
                        int startOnChrom,
                        int endOnChrom,
                        char strand)

drawGenomeWindow

public void drawGenomeWindow(String chrom,
                             long startOnChrom,
                             long endOnChrom)

drawCytoBandName

public void drawCytoBandName(CytoBand c,
                             ChromosomeWindow w)

drawChrName

public void drawChrName(String chrName,
                        Integer rank)

drawText

public void drawText(String text,
                     int x,
                     int y,
                     Color color)

fillRect

public void fillRect(int x1,
                     int x2,
                     int y,
                     Color c)

fillRect

public void fillRect(int x,
                     int y,
                     int width,
                     int height,
                     Color color)

drawRect

public void drawRect(int x1,
                     int x2,
                     int y,
                     Color c)

drawRect

public void drawRect(int x,
                     int y,
                     int width,
                     int height,
                     Color color)

drawTriangle

public void drawTriangle(int x1,
                         int x2,
                         int y,
                         Color color)

toPNG

public void toPNG(OutputStream out)
           throws IOException
Throws:
IOException

getCytoBandColor

public Color getCytoBandColor(CytoBand c)

getCytoBandNameColor

public Color getCytoBandNameColor(CytoBand c)

getFrameColor

public Color getFrameColor()

colorLighter

public Color colorLighter(Color color)

calcLighterValue

public int calcLighterValue(int value)


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