gata.aligner
Class LocalAlignment

java.lang.Object
  gata.aligner.LocalAlignment

All Implemented Interfaces:

java.io.Serializable

public class LocalAlignment

extends java.lang.Object

implements java.io.Serializable

Author:

nix Similar to but not exactly like Alignment obj, represents the Local Alignment returned by Blast. It's saved and made availible to GATAPlotter.

See Also:

Serialized Form

Constructor Summary

LocalAlignment(java.lang.String seq_1, int startSeq_1, int stopSeq_1, java.lang.String seq_2, int startSeq_2, int stopSeq_2, int ori_, AlignParams ap_, int score_)

Method Summary

java.util.ArrayList	clearDups(java.util.ArrayList aligns)
AlignParams	getAP()
int	getLAScore()
java.lang.String	getLocalAlignString(int subStart, int subLength)
int	getOri()
java.util.ArrayList	makeAlignmentObjects(java.util.ArrayList alignNums)
int[][]	makeWindowsFromAlign()
java.util.ArrayList	mergeSubAligns(java.util.ArrayList winds)
java.util.ArrayList	optimizeScores(int[][] aligns)
void	printLocalAlignment()
java.util.ArrayList	processLocalAlignment()

Methods inherited from class java.lang.Object

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

Constructor Detail

LocalAlignment

public LocalAlignment(java.lang.String seq_1,
                      int startSeq_1,
                      int stopSeq_1,
                      java.lang.String seq_2,
                      int startSeq_2,
                      int stopSeq_2,
                      int ori_,
                      AlignParams ap_,
                      int score_)

Method Detail

getAP

public AlignParams getAP()

getOri

public int getOri()

getLAScore

public int getLAScore()

printLocalAlignment

public void printLocalAlignment()

getLocalAlignString

public java.lang.String getLocalAlignString(int subStart,
                                            int subLength)

processLocalAlignment

public java.util.ArrayList processLocalAlignment()

makeWindowsFromAlign

public int[][] makeWindowsFromAlign()

optimizeScores

public java.util.ArrayList optimizeScores(int[][] aligns)

mergeSubAligns

public java.util.ArrayList mergeSubAligns(java.util.ArrayList winds)

clearDups

public java.util.ArrayList clearDups(java.util.ArrayList aligns)

makeAlignmentObjects

public java.util.ArrayList makeAlignmentObjects(java.util.ArrayList alignNums)