selex
Class SelexParams

java.lang.Object
  selex.SelexParams

public class SelexParams

extends java.lang.Object

Hold parameters and results generated by the SelexSeqParser; also generates reports.

Constructor Summary

SelexParams()

Method Summary

void	addExpectedSubSeq(int expects)
void	addObservedSubSeq(int obs)
void	addObsExpRatio(double ratio)
void	appendLength(int x)
void	appendSub(java.lang.String sub)
int	getAveExpSeqLength()
int	getAveNumExpSubSeqs()
int	getAveNumObsSubSeqs()
java.lang.String	getAveObsExpRatio()
int	getExpectedSize()
java.lang.String	getLeftSideMatch()
java.lang.String	getLeftSideReplace()
int	getLenMax()
int	getLenMin()
java.lang.String	getQualFile(int index)
java.lang.String[]	getQualFiles()
java.lang.String	getRestSite()
java.lang.String	getRightSideMatch()
java.lang.String	getRightSideReplace()
java.lang.StringBuffer	getRunning()
int	getScoreCutOff()
java.lang.String	getSeqFile(int index)
java.lang.String[]	getSeqFiles()
void	incNumFiles(int x)
void	incNumSeqReads(int x)
void	incNumSubs(int x, int y, int z)
void	incrementNumBadSeqReads()
void	incrementNumNoInsertSeqReads()
void	incrementNumShortInsertSeqReads()
java.lang.String	makeFinalReport()
boolean	modifyEnds()
java.lang.String	plotHistogram()
void	printSave(java.lang.String newString)
void	processArgs(java.lang.String[] args)
void	writeReport()
void	writeSubSeqFasta()

Methods inherited from class java.lang.Object

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

Constructor Detail

SelexParams

public SelexParams()

Method Detail

getLeftSideMatch

public java.lang.String getLeftSideMatch()

getLeftSideReplace

public java.lang.String getLeftSideReplace()

modifyEnds

public boolean modifyEnds()

getRightSideMatch

public java.lang.String getRightSideMatch()

getRightSideReplace

public java.lang.String getRightSideReplace()

getRestSite

public java.lang.String getRestSite()

getSeqFile

public java.lang.String getSeqFile(int index)

getSeqFiles

public java.lang.String[] getSeqFiles()

getQualFile

public java.lang.String getQualFile(int index)

getQualFiles

public java.lang.String[] getQualFiles()

getScoreCutOff

public int getScoreCutOff()

getLenMin

public int getLenMin()

getLenMax

public int getLenMax()

getExpectedSize

public int getExpectedSize()

getAveNumExpSubSeqs

public int getAveNumExpSubSeqs()

getAveNumObsSubSeqs

public int getAveNumObsSubSeqs()

getAveExpSeqLength

public int getAveExpSeqLength()

getAveObsExpRatio

public java.lang.String getAveObsExpRatio()

getRunning

public java.lang.StringBuffer getRunning()

addObsExpRatio

public void addObsExpRatio(double ratio)

addExpectedSubSeq

public void addExpectedSubSeq(int expects)

addObservedSubSeq

public void addObservedSubSeq(int obs)

incrementNumShortInsertSeqReads

public void incrementNumShortInsertSeqReads()

incrementNumNoInsertSeqReads

public void incrementNumNoInsertSeqReads()

incrementNumBadSeqReads

public void incrementNumBadSeqReads()

processArgs

public void processArgs(java.lang.String[] args)

printSave

public void printSave(java.lang.String newString)

appendSub

public void appendSub(java.lang.String sub)

incNumSubs

public void incNumSubs(int x,
                       int y,
                       int z)

appendLength

public void appendLength(int x)

incNumFiles

public void incNumFiles(int x)

incNumSeqReads

public void incNumSeqReads(int x)

makeFinalReport

public java.lang.String makeFinalReport()

writeSubSeqFasta

public void writeSubSeqFasta()

writeReport

public void writeReport()

plotHistogram

public java.lang.String plotHistogram()