util.bio.wrappers
Class SimpleBlast

java.lang.Object
  util.bio.wrappers.SimpleBlast

public class SimpleBlast

extends java.lang.Object

Wrapper for bl2seq blast.

Constructor Summary

SimpleBlast(java.lang.String bl2seq)

Method Summary

java.lang.String[]	blastIt(java.lang.String seq1File, java.lang.String seq2File)
static java.util.ArrayList	parseBlast(java.lang.String[] data)
static BlastResult[]	parseBlastGeneral(java.lang.String[] data) Parses blast output from blastall for dna into BlastResult objects.
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

Constructor Detail

SimpleBlast

public SimpleBlast(java.lang.String bl2seq)

Method Detail

blastIt

public java.lang.String[] blastIt(java.lang.String seq1File,
                                  java.lang.String seq2File)

parseBlast

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

parseLine

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

parseBlastGeneral

public static BlastResult[] parseBlastGeneral(java.lang.String[] data)

Parses blast output from blastall for dna into BlastResult objects.