gata.main
Class AnnoSpecParams

java.lang.Object
  gata.main.AnnoSpecParams

public class AnnoSpecParams

extends java.lang.Object

Author:

Nix Contains fields specific for each annotation panel, either for the Reference Sequence or Comparative Sequence

Constructor Summary

AnnoSpecParams()

Method Summary

void	addLabel(java.util.ArrayList list)
void	addNormalDNALines(java.util.ArrayList al)
void	addProteinLines(java.util.ArrayList thinLinesProt, java.util.ArrayList dottedLinesProt)
void	addRNALines(java.awt.geom.Line2D.Double baseLine, java.util.ArrayList fatLines)
void	addThinDNALines(java.util.ArrayList al)
void	clearLines() Wipes all the Line2D.Double ArrayLists, call before reDrawing the Glyphs when params have been changed.
int	getAnnoPanelHeight()
Annotation	getAnnotation()
boolean	getAnyGenericGlyphs()
int	getBiggestGlyphPanelY()
java.util.ArrayList	getDottedProteinLines()
java.util.ArrayList	getFatRNALines()
GeneRepGlyph[]	getGeneGlyphs()
java.io.File	getGffFile()
GlyphPanel	getGlyphPanel()
java.awt.Graphics2D	getGraphics2DN()
java.util.ArrayList	getLabels()
java.util.ArrayList	getNormalDNALines()
double	getNtAtXZero()
double	getReferenceY()
ScaleBar	getScaleBar()
double	getScaleBarX()
double	getScaleBarY()
java.awt.Color	getScaleLineColor()
double	getScaleRulerY()
int	getSmallestGlyphPanelY()
java.util.ArrayList	getThinDNALines()
java.util.ArrayList	getThinProteinLines()
java.util.ArrayList	getThinRNALines()
GenericGlyph[][]	getTrackedGenericGlyphs()
java.util.ArrayList[]	getTrackLabels()
boolean[]	getTrackLabelVis()
int	getTrackNumber()
java.awt.BasicStroke[]	getTrackStrokes()
float[]	getTrackThickness()
boolean[]	getTrackVis()
boolean	isScaleBarVis()
boolean	isScaleRulerVis()
void	setAnnoPanelHeight(int i)
void	setAnnotation(Annotation annotation)
void	setAnyGenericGlyphs(boolean x)
void	setBiggestGlyphPanelY(int i)
void	setGeneGlyphs(GeneRepGlyph[] glyphs)
void	setGffFile(java.io.File file)
void	setGlyphPanel(GlyphPanel panel)
void	setGraphics2DN(java.awt.Graphics2D g2)
void	setNtAtXZero(double d)
void	setReferenceY(double d)
void	setScaleBar(ScaleBar bar)
void	setScaleBarVis(boolean b)
void	setScaleBarX(double d)
void	setScaleBarY(double d)
void	setScaleLineColor(java.awt.Color color)
void	setScaleRulerVis(boolean b)
void	setScaleRulerY(double d)
void	setSmallestGlyphPanelY(int i)
void	setTrackedGenericGlyphs(GenericGlyph[][] glyphs)
void	setTrackLabels(java.util.ArrayList[] lists)
void	setTrackLabelVis(boolean[] bs)
void	setTrackNumber(int i)
void	setTrackThickness(float[] fs)
void	setTrackVis(boolean[] bs)

Methods inherited from class java.lang.Object

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

Constructor Detail

AnnoSpecParams

public AnnoSpecParams()

Method Detail

addLabel

public void addLabel(java.util.ArrayList list)

addNormalDNALines

public void addNormalDNALines(java.util.ArrayList al)

addProteinLines

public void addProteinLines(java.util.ArrayList thinLinesProt,
                            java.util.ArrayList dottedLinesProt)

addRNALines

public void addRNALines(java.awt.geom.Line2D.Double baseLine,
                        java.util.ArrayList fatLines)

addThinDNALines

public void addThinDNALines(java.util.ArrayList al)

clearLines

public void clearLines()

Wipes all the Line2D.Double ArrayLists, call before reDrawing the Glyphs when params have been changed.

getAnnoPanelHeight

public int getAnnoPanelHeight()

getAnnotation

public Annotation getAnnotation()

getAnyGenericGlyphs

public boolean getAnyGenericGlyphs()

getDottedProteinLines

public java.util.ArrayList getDottedProteinLines()

getFatRNALines

public java.util.ArrayList getFatRNALines()

getGeneGlyphs

public GeneRepGlyph[] getGeneGlyphs()

getGlyphPanel

public GlyphPanel getGlyphPanel()

getGraphics2DN

public java.awt.Graphics2D getGraphics2DN()

getLabels

public java.util.ArrayList getLabels()

getNormalDNALines

public java.util.ArrayList getNormalDNALines()

getReferenceY

public double getReferenceY()

getThinDNALines

public java.util.ArrayList getThinDNALines()

getThinProteinLines

public java.util.ArrayList getThinProteinLines()

getThinRNALines

public java.util.ArrayList getThinRNALines()

getTrackLabelVis

public boolean[] getTrackLabelVis()

getTrackVis

public boolean[] getTrackVis()

getTrackedGenericGlyphs

public GenericGlyph[][] getTrackedGenericGlyphs()

getTrackLabels

public java.util.ArrayList[] getTrackLabels()

getTrackNumber

public int getTrackNumber()

setAnnotation

public void setAnnotation(Annotation annotation)

setAnyGenericGlyphs

public void setAnyGenericGlyphs(boolean x)

setGeneGlyphs

public void setGeneGlyphs(GeneRepGlyph[] glyphs)

setGlyphPanel

public void setGlyphPanel(GlyphPanel panel)

setGraphics2DN

public void setGraphics2DN(java.awt.Graphics2D g2)

setTrackLabelVis

public void setTrackLabelVis(boolean[] bs)

setTrackVis

public void setTrackVis(boolean[] bs)

setTrackedGenericGlyphs

public void setTrackedGenericGlyphs(GenericGlyph[][] glyphs)

setTrackLabels

public void setTrackLabels(java.util.ArrayList[] lists)

setTrackNumber

public void setTrackNumber(int i)

setAnnoPanelHeight

public void setAnnoPanelHeight(int i)

getSmallestGlyphPanelY

public int getSmallestGlyphPanelY()

setSmallestGlyphPanelY

public void setSmallestGlyphPanelY(int i)

getBiggestGlyphPanelY

public int getBiggestGlyphPanelY()

setBiggestGlyphPanelY

public void setBiggestGlyphPanelY(int i)

setReferenceY

public void setReferenceY(double d)

getScaleRulerY

public double getScaleRulerY()

setScaleRulerY

public void setScaleRulerY(double d)

getScaleBar

public ScaleBar getScaleBar()

setScaleBar

public void setScaleBar(ScaleBar bar)

getNtAtXZero

public double getNtAtXZero()

setNtAtXZero

public void setNtAtXZero(double d)

getGffFile

public java.io.File getGffFile()

setGffFile

public void setGffFile(java.io.File file)

getTrackStrokes

public java.awt.BasicStroke[] getTrackStrokes()

setTrackThickness

public void setTrackThickness(float[] fs)

getTrackThickness

public float[] getTrackThickness()

getScaleLineColor

public java.awt.Color getScaleLineColor()

setScaleLineColor

public void setScaleLineColor(java.awt.Color color)

isScaleBarVis

public boolean isScaleBarVis()

isScaleRulerVis

public boolean isScaleRulerVis()

setScaleBarVis

public void setScaleBarVis(boolean b)

setScaleRulerVis

public void setScaleRulerVis(boolean b)

getScaleBarX

public double getScaleBarX()

getScaleBarY

public double getScaleBarY()

setScaleBarX

public void setScaleBarX(double d)

setScaleBarY

public void setScaleBarY(double d)