org.utgenome.graphics
Class ChromosomeMapCanvas

java.lang.Object
  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)