gata.geneGlyphs
Class Annotation

java.lang.Object
  gata.geneGlyphs.Annotation

public class Annotation

extends java.lang.Object

Author:

nix Contains methods and fields to construct annotation glyphs.

Constructor Summary

Annotation(AnnoSpecParams annoParams, GATAParams gataParams)

Method Summary

void	assignGenericFeatureTracks()
void	colorizeTrackedGenericGlyphs(int converter) This method converts scores in generic glyphs to changes in alpha, the opacity number for the glyph color.
void	drawDryRunAnnotation()
void	drawGenericGlyphs() Call each time parameters effecting GenericGlyphs change
void	drawGlyphs() Call each time the scale changes or user alters a glyph viewablility
GlyphPanel	getGlyphPanel()
int	getTrackConverter()
void	initializeTrackLabels()
void	makeGenericGlyphs() This makes a sorted array of GenericGlyphs broken down by track
void	makeGlyphs() Call once to make the glyphs used in rendering the gene annotation.
void	redrawAnnotation()
void	setAnnotationBackground()
void	setDefaultTrackThickness()
void	setInitialTrackColors() Use to initialize all generic glyphs color field
void	setTrackDefaults()

Methods inherited from class java.lang.Object

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

Constructor Detail

Annotation

public Annotation(AnnoSpecParams annoParams,
                  GATAParams gataParams)

Method Detail

redrawAnnotation

public void redrawAnnotation()

drawDryRunAnnotation

public void drawDryRunAnnotation()

setAnnotationBackground

public void setAnnotationBackground()

drawGenericGlyphs

public void drawGenericGlyphs()

Call each time parameters effecting GenericGlyphs change

makeGenericGlyphs

public void makeGenericGlyphs()

This makes a sorted array of GenericGlyphs broken down by track

colorizeTrackedGenericGlyphs

public void colorizeTrackedGenericGlyphs(int converter)

This method converts scores in generic glyphs to changes in alpha, the opacity number for the glyph color. The lower the score the lower the alpha. The trickie business is using different scales since sometimes the scores are in log or lnx units. 70 is the lowest alpha allowed, everything else normalized from 70 to 255

setTrackDefaults

public void setTrackDefaults()

setInitialTrackColors

public void setInitialTrackColors()

Use to initialize all generic glyphs color field

setDefaultTrackThickness

public void setDefaultTrackThickness()

initializeTrackLabels

public void initializeTrackLabels()

assignGenericFeatureTracks

public void assignGenericFeatureTracks()

drawGlyphs

public void drawGlyphs()

Call each time the scale changes or user alters a glyph viewablility

makeGlyphs

public void makeGlyphs()

Call once to make the glyphs used in rendering the gene annotation.

getGlyphPanel

public GlyphPanel getGlyphPanel()

getTrackConverter

public int getTrackConverter()