gata.aligner
Class Blast

java.lang.Object
  gata.aligner.Blast

public class Blast

extends java.lang.Object

Author:

nix Class to fire and fetch the ncbi bl2seq program.

Field Summary

AlignParams

ap

Constructor Summary

Blast(AlignParams AP)

Method Summary

java.lang.String[]	blastIt(java.lang.String compSeqFileName)
java.util.ArrayList	parseBlast(java.lang.String[] data)
static java.util.ArrayList	parseLine(java.lang.String line, java.util.regex.Pattern pat)

Methods inherited from class java.lang.Object

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

Field Detail

ap

public AlignParams ap

Constructor Detail

Blast

public Blast(AlignParams AP)

Method Detail

blastIt

public java.lang.String[] blastIt(java.lang.String compSeqFileName)

parseBlast

public java.util.ArrayList parseBlast(java.lang.String[] data)

parseLine

public static java.util.ArrayList parseLine(java.lang.String line,
                                            java.util.regex.Pattern pat)