util.bio.wrappers
Class BL2Seq

java.lang.Object
  util.bio.wrappers.BL2Seq

public class BL2Seq

extends java.lang.Object

This is a bit of a hack from the SimpleBlast, expand as needed.

Constructor Summary

BL2Seq(java.lang.String fullPathToBL2seq)

Method Summary

BL2SeqHit[]	blastFASTAFiles(java.io.File seq1File, java.io.File seq2File) Uses BLAST bl2seq program to align two sequences found in the seq files, won't work on windows?
java.lang.String[]	getCommandArray()
double	getExpectation()
java.lang.String	getFullPathToBL2seq()
BL2SeqHit[]	getHits()
double	getRawScoreCutOff()
java.lang.String[]	getRawUnparsedResults()
int	getW()
BL2SeqHit[]	parseBl2SeqResults(java.lang.String[] data) This takes an array of BLAST bl2seq results and parses the info into an array
static java.util.ArrayList	parseLine(java.lang.String line, java.util.regex.Pattern pat)
void	setExpectation(double e)
void	setFullPathToBL2seq(java.lang.String fullPathToBL2seq)
void	setGapExtensionCost(int e)
void	setRawScoreCutOff(double rawScoreCutOff)
void	setRawUnparsedResults(java.lang.String[] rawUnparsedResults)
void	setW(int w)

Methods inherited from class java.lang.Object

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

Constructor Detail

BL2Seq

public BL2Seq(java.lang.String fullPathToBL2seq)

Method Detail

blastFASTAFiles

public BL2SeqHit[] blastFASTAFiles(java.io.File seq1File,
                                   java.io.File seq2File)

Uses BLAST bl2seq program to align two sequences found in the seq files, won't work on windows?

parseBl2SeqResults

public BL2SeqHit[] parseBl2SeqResults(java.lang.String[] data)

This takes an array of BLAST bl2seq results and parses the info into an array

parseLine

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

getExpectation

public double getExpectation()

setExpectation

public void setExpectation(double e)

getFullPathToBL2seq

public java.lang.String getFullPathToBL2seq()

setFullPathToBL2seq

public void setFullPathToBL2seq(java.lang.String fullPathToBL2seq)

getRawScoreCutOff

public double getRawScoreCutOff()

setRawScoreCutOff

public void setRawScoreCutOff(double rawScoreCutOff)

getRawUnparsedResults

public java.lang.String[] getRawUnparsedResults()

setRawUnparsedResults

public void setRawUnparsedResults(java.lang.String[] rawUnparsedResults)

getW

public int getW()

setW

public void setW(int w)

getCommandArray

public java.lang.String[] getCommandArray()

getHits

public BL2SeqHit[] getHits()

setGapExtensionCost

public void setGapExtensionCost(int e)