gata.main
Class GATAParams

java.lang.Object
  gata.main.GATAParams

public class GATAParams

extends java.lang.Object

Author:

Nix Master params file for the GATAPlotter program.

Constructor Summary

GATAParams()

Method Summary

boolean	areGenericLabelsVis()
boolean	areLabelsVis()
double	getA()
AlignPanel	getAAlignPanel()
AlignPanel	getAlignPanel()
AlignParams	getAlignParams()
double	getB()
java.awt.Color	getBackgroundColor()
int	getBiggestAlignPanelY()
double	getC()
AnnoSpecParams	getCompAnnoSpecParams()
Console	getConsole()
double	getD()
java.awt.BasicStroke	getDashStroke()
float	getDefaultTrackThickness()
java.awt.Color	getDNAColor()
double	getE()
double	getF()
double	getFatLineThicknes()
java.awt.BasicStroke	getFatStroke()
java.awt.Font	getFont()
GATAFrame	getGataFrame()
GATAPlotter	getGataPlotter()
int	getHeight()
double	getHeightLabels()
java.awt.Color	getLabelColor()
java.awt.BasicStroke	getNormalStroke()
double	getNtPerPixel()
java.io.File	getObjectsFile()
double	getPixBtwDNATracks()
double	getPixBtwLabelTrack()
double	getPixBtwProtRNA()
double	getPixBtwTracks()
double	getPixBtwTransGrpLabel()
double	getPixBtwTransGrps()
double	getPixBtwTransGrpsGene()
float	getPixFatLineThickness()
double	getPixHeightArrows()
double	getPixNormalLineThickness()
double	getPixPerNt()
float	getPixThinLineThickness()
PlotterPreferences	getPlotterPreferences()
java.awt.Color	getProteinColor()
AnnoSpecParams	getRefAnnoSpecParams()
java.awt.Color	getRNAColor()
int	getSmallestAlignPanelY()
java.awt.BasicStroke	getThinStroke()
ToolsFrame	getToolsFrameRef()
int	getWidth()
int	getZoomedWidth()
boolean	isDNAVis()
boolean	isGenericLabelsVis()
boolean	isGffCompPresent()
boolean	isGffRefPresent()
boolean	isLabelsVis()
boolean	isProteinVis()
boolean	isRNAVis()
void	setA(double d)
void	setAAlignPanel(AlignPanel panel)
void	setAlignPanel(AlignPanel a)
void	setAlignParams(AlignParams ap)
void	setB(double d)
void	setBackgroundColor(java.awt.Color color)
void	setBiggestAlignPanelY(int i)
void	setC(double d)
void	setCompAnnoSpecParams(AnnoSpecParams params)
void	setConsole(Console console)
void	setD(double d)
void	setDefaultTrackThickness(float f)
void	setDNAColor(java.awt.Color color)
void	setDNAVis(boolean b)
void	setE(double d)
void	setF(double d)
void	setGataFrame(GATAFrame frame)
void	setGataPlotter(GATAPlotter gata)
void	setGenericLabelsVis(boolean b)
void	setGffCompPresent(boolean b)
void	setGffRefPresent(boolean b)
void	setHeight(int i)
void	setHeightLabels(double d)
void	setLabelColor(java.awt.Color color)
void	setLabelsVis(boolean b)
void	setNtPerPixel(double d)
void	setObjectsFile(java.io.File file)
void	setPixBtwDNATracks(double d)
void	setPixBtwLabelTrack(double d)
void	setPixBtwProtRNA(double d)
void	setPixBtwTracks(double d)
void	setPixBtwTransGrpLabel(double d)
void	setPixBtwTransGrps(double d)
void	setPixBtwTransGrpsGene(double d)
void	setPixFatLineThickness(float f)
void	setPixHeightArrows(double d)
void	setPixNormalLineThickness(float f)
void	setPixPerNt(double d)
void	setPixThinLineThickness(float f)
void	setPlotterPreferences(PlotterPreferences preferences)
void	setProteinColor(java.awt.Color color)
void	setProteinVis(boolean b)
void	setRefAnnoSpecParams(AnnoSpecParams params)
void	setRNAColor(java.awt.Color color)
void	setRNAVis(boolean b)
void	setSmallestAlignPanelY(int i)
void	setToolsFrameRef(ToolsFrame aTF)
void	setWidth(int i)
void	setZoomedWidth(int i)

Methods inherited from class java.lang.Object

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

Constructor Detail

GATAParams

public GATAParams()

Method Detail

areGenericLabelsVis

public boolean areGenericLabelsVis()

areLabelsVis

public boolean areLabelsVis()

isDNAVis

public boolean isDNAVis()

isGffRefPresent

public boolean isGffRefPresent()

isGffCompPresent

public boolean isGffCompPresent()

isProteinVis

public boolean isProteinVis()

isRNAVis

public boolean isRNAVis()

getA

public double getA()

getAlignPanel

public AlignPanel getAlignPanel()

getAlignParams

public AlignParams getAlignParams()

getB

public double getB()

getBackgroundColor

public java.awt.Color getBackgroundColor()

getC

public double getC()

getConsole

public Console getConsole()

getD

public double getD()

getDashStroke

public java.awt.BasicStroke getDashStroke()

getDefaultTrackThickness

public float getDefaultTrackThickness()

getDNAColor

public java.awt.Color getDNAColor()

getE

public double getE()

getF

public double getF()

getFatLineThicknes

public double getFatLineThicknes()

getFatStroke

public java.awt.BasicStroke getFatStroke()

getFont

public java.awt.Font getFont()

getHeight

public int getHeight()

getHeightLabels

public double getHeightLabels()

getLabelColor

public java.awt.Color getLabelColor()

getNormalStroke

public java.awt.BasicStroke getNormalStroke()

getNtPerPixel

public double getNtPerPixel()

getPixBtwDNATracks

public double getPixBtwDNATracks()

getPixBtwLabelTrack

public double getPixBtwLabelTrack()

getPixBtwProtRNA

public double getPixBtwProtRNA()

getPixBtwTracks

public double getPixBtwTracks()

getPixBtwTransGrpLabel

public double getPixBtwTransGrpLabel()

getPixBtwTransGrps

public double getPixBtwTransGrps()

getPixBtwTransGrpsGene

public double getPixBtwTransGrpsGene()

getPixFatLineThickness

public float getPixFatLineThickness()

getPixHeightArrows

public double getPixHeightArrows()

getPixNormalLineThickness

public double getPixNormalLineThickness()

getPixPerNt

public double getPixPerNt()

getProteinColor

public java.awt.Color getProteinColor()

getRNAColor

public java.awt.Color getRNAColor()

getThinStroke

public java.awt.BasicStroke getThinStroke()

getToolsFrameRef

public ToolsFrame getToolsFrameRef()

getWidth

public int getWidth()

getZoomedWidth

public int getZoomedWidth()

setAlignPanel

public void setAlignPanel(AlignPanel a)

setAlignParams

public void setAlignParams(AlignParams ap)

setConsole

public void setConsole(Console console)

setHeightLabels

public void setHeightLabels(double d)

setNtPerPixel

public void setNtPerPixel(double d)

setPixBtwProtRNA

public void setPixBtwProtRNA(double d)

setPixBtwTransGrps

public void setPixBtwTransGrps(double d)

setPixBtwTransGrpsGene

public void setPixBtwTransGrpsGene(double d)

setPixFatLineThickness

public void setPixFatLineThickness(float f)

setPixHeightArrows

public void setPixHeightArrows(double d)

setPixNormalLineThickness

public void setPixNormalLineThickness(float f)

setPixPerNt

public void setPixPerNt(double d)

setToolsFrameRef

public void setToolsFrameRef(ToolsFrame aTF)

setZoomedWidth

public void setZoomedWidth(int i)

getObjectsFile

public java.io.File getObjectsFile()

setObjectsFile

public void setObjectsFile(java.io.File file)

getGataPlotter

public GATAPlotter getGataPlotter()

setGataPlotter

public void setGataPlotter(GATAPlotter gata)

setGffRefPresent

public void setGffRefPresent(boolean b)

setGffCompPresent

public void setGffCompPresent(boolean b)

getAAlignPanel

public AlignPanel getAAlignPanel()

isLabelsVis

public boolean isLabelsVis()

getPixThinLineThickness

public float getPixThinLineThickness()

setA

public void setA(double d)

setAAlignPanel

public void setAAlignPanel(AlignPanel panel)

setB

public void setB(double d)

setBackgroundColor

public void setBackgroundColor(java.awt.Color color)

setC

public void setC(double d)

setD

public void setD(double d)

setDNAColor

public void setDNAColor(java.awt.Color color)

setDNAVis

public void setDNAVis(boolean b)

setE

public void setE(double d)

setF

public void setF(double d)

setHeight

public void setHeight(int i)

setLabelColor

public void setLabelColor(java.awt.Color color)

setLabelsVis

public void setLabelsVis(boolean b)

setPixBtwDNATracks

public void setPixBtwDNATracks(double d)

setPixBtwLabelTrack

public void setPixBtwLabelTrack(double d)

setPixBtwTracks

public void setPixBtwTracks(double d)

setPixBtwTransGrpLabel

public void setPixBtwTransGrpLabel(double d)

setPixThinLineThickness

public void setPixThinLineThickness(float f)

setProteinColor

public void setProteinColor(java.awt.Color color)

setProteinVis

public void setProteinVis(boolean b)

setRNAColor

public void setRNAColor(java.awt.Color color)

setRNAVis

public void setRNAVis(boolean b)

setWidth

public void setWidth(int i)

getGataFrame

public GATAFrame getGataFrame()

setGataFrame

public void setGataFrame(GATAFrame frame)

getBiggestAlignPanelY

public int getBiggestAlignPanelY()

getSmallestAlignPanelY

public int getSmallestAlignPanelY()

setBiggestAlignPanelY

public void setBiggestAlignPanelY(int i)

setSmallestAlignPanelY

public void setSmallestAlignPanelY(int i)

setDefaultTrackThickness

public void setDefaultTrackThickness(float f)

isGenericLabelsVis

public boolean isGenericLabelsVis()

setGenericLabelsVis

public void setGenericLabelsVis(boolean b)

getPlotterPreferences

public PlotterPreferences getPlotterPreferences()

setPlotterPreferences

public void setPlotterPreferences(PlotterPreferences preferences)

getCompAnnoSpecParams

public AnnoSpecParams getCompAnnoSpecParams()

getRefAnnoSpecParams

public AnnoSpecParams getRefAnnoSpecParams()

setCompAnnoSpecParams

public void setCompAnnoSpecParams(AnnoSpecParams params)

setRefAnnoSpecParams

public void setRefAnnoSpecParams(AnnoSpecParams params)