selex
Class SeqFiles

java.lang.Object
  selex.SeqFiles

public class SeqFiles

extends java.lang.Object

Continer for raw sequence information, seqFile, qualFile, and the actual reads from each.

Constructor Summary

SeqFiles(java.lang.String aSeqFile, java.lang.String aQualFile, SelexParams SP)

Method Summary

static java.lang.String	changeQuality(java.lang.String qual, int index, int diff) Modifies a quality file, adding or subtracting scores.
int	getNumReads()
java.lang.String	getQualFile()
java.lang.String	getSeqFile()
SeqRead[]	getSeqReads()
static void	modifySequenceEnds(java.lang.String[] seqs, java.lang.String[] quals, java.lang.String leftSideMatch, java.lang.String leftSideReplace, java.lang.String rightSideMatch, java.lang.String rightSideReplace) Modifies the left side and right side of Sequences also adds (100's) or subtracts quanilty scores to match.
void	printSeqFiles()
static java.lang.String	stringArrayListToString(java.util.ArrayList stringAL, java.lang.String separator) Returns a String separated by the separator given an ArrayList of String.
static java.util.ArrayList	stringArrayToArrayList(java.lang.String[] s) Returns an ArrayList of String given a String[]

Methods inherited from class java.lang.Object

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

Constructor Detail

SeqFiles

public SeqFiles(java.lang.String aSeqFile,
                java.lang.String aQualFile,
                SelexParams SP)

Method Detail

getSeqFile

public java.lang.String getSeqFile()

getQualFile

public java.lang.String getQualFile()

getNumReads

public int getNumReads()

getSeqReads

public SeqRead[] getSeqReads()

printSeqFiles

public void printSeqFiles()

modifySequenceEnds

public static void modifySequenceEnds(java.lang.String[] seqs,
                                      java.lang.String[] quals,
                                      java.lang.String leftSideMatch,
                                      java.lang.String leftSideReplace,
                                      java.lang.String rightSideMatch,
                                      java.lang.String rightSideReplace)

Modifies the left side and right side of Sequences also adds (100's) or subtracts quanilty scores to match. Will modify the first occurance on the left, and the last occurance on the right. Usefull for fixing blunted sequence ends for Selex parsing. Case insensitive.

changeQuality

public static java.lang.String changeQuality(java.lang.String qual,
                                             int index,
                                             int diff)

Modifies a quality file, adding or subtracting scores.

stringArrayToArrayList

public static java.util.ArrayList stringArrayToArrayList(java.lang.String[] s)

Returns an ArrayList of String given a String[]

stringArrayListToString

public static java.lang.String stringArrayListToString(java.util.ArrayList stringAL,
                                                       java.lang.String separator)

Returns a String separated by the separator given an ArrayList of String.