gata.aligner
Class Alignment

java.lang.Object
  gata.aligner.Alignment

All Implemented Interfaces:

java.lang.Comparable, java.io.Serializable

public class Alignment

extends java.lang.Object

implements java.io.Serializable, java.lang.Comparable

Author:

nix Class to represent a windowed sub alignment, a portion of a BLAST local alignment. A serialize array of these are saved and made availible for the GATAPlotter Program.

See Also:

Serialized Form

Constructor Summary

Alignment(java.lang.String s1, int start1, int stop1, java.lang.String s2, int start2, int stop2, int aScore, int ori, AlignParams ap, LocalAlignment la)

Method Summary

int	compareTo(java.lang.Object otherObject)
void	drawAlignment(java.awt.Graphics2D g2) Called every time the alignPanel is repaint() ed
java.lang.String	getAlignmentString()
double	getBitScore()
int[]	getCoordinates()
int	getOrientation()
java.lang.String	getParentLocAlignString()
int[]	getRelativeCoordinates()
int	getScore()
java.lang.String	getSeq1()
java.lang.String	getSeq2()
java.util.ArrayList	getShapes()
boolean	isCompVisible()
void	makeShapes(double refX, double refY, double compX, double compY, double ntLenBig, double widthC, double heightD)
void	printAlignment()
void	setCompVisible(boolean compVisible)
void	setSeqs(java.lang.String s1, java.lang.String s2)

Methods inherited from class java.lang.Object

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

Constructor Detail

Alignment

public Alignment(java.lang.String s1,
                 int start1,
                 int stop1,
                 java.lang.String s2,
                 int start2,
                 int stop2,
                 int aScore,
                 int ori,
                 AlignParams ap,
                 LocalAlignment la)

Method Detail

getScore

public int getScore()

getBitScore

public double getBitScore()

getOrientation

public int getOrientation()

getCoordinates

public int[] getCoordinates()

getShapes

public java.util.ArrayList getShapes()

getSeq1

public java.lang.String getSeq1()

getSeq2

public java.lang.String getSeq2()

setSeqs

public void setSeqs(java.lang.String s1,
                    java.lang.String s2)

drawAlignment

public void drawAlignment(java.awt.Graphics2D g2)

Called every time the alignPanel is repaint() ed

printAlignment

public void printAlignment()

getAlignmentString

public java.lang.String getAlignmentString()

getParentLocAlignString

public java.lang.String getParentLocAlignString()

makeShapes

public void makeShapes(double refX,
                       double refY,
                       double compX,
                       double compY,
                       double ntLenBig,
                       double widthC,
                       double heightD)

compareTo

public int compareTo(java.lang.Object otherObject)

Specified by:

compareTo in interface java.lang.Comparable

getRelativeCoordinates

public int[] getRelativeCoordinates()

setCompVisible

public void setCompVisible(boolean compVisible)

isCompVisible

public boolean isCompVisible()