trans.roc
Class Positive

java.lang.Object
  trans.roc.Positive

public class Positive

extends java.lang.Object

Container for a positive BAC used by the Sgr scripts.

Constructor Summary

Positive(java.lang.String chromosome, int start, int stop)

Method Summary

boolean	contains(int position)
static Positive[]	filter(int bpOffSetEnds, Positive[] pos) Adds the bpOffSetEnds to the end of each Positive.
java.lang.String	getChromosome()
java.util.ArrayList	getScores()
int	getStart()
int	getStop()
int	getTotalNumberWindows()
boolean	isSenseStrand()
boolean	matches(Sgr sgr)
void	setScores(java.util.ArrayList scores)
void	setSenseStrand(boolean senseStrand)
void	setTotalNumberWindows(int totalNumberWindows)
java.lang.String	toString()
java.lang.String	toStringSimple()

Methods inherited from class java.lang.Object

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

Constructor Detail

Positive

public Positive(java.lang.String chromosome,
                int start,
                int stop)

Method Detail

matches

public boolean matches(Sgr sgr)

contains

public boolean contains(int position)

getScores

public java.util.ArrayList getScores()

toStringSimple

public java.lang.String toStringSimple()

filter

public static Positive[] filter(int bpOffSetEnds,
                                Positive[] pos)

Adds the bpOffSetEnds to the end of each Positive. If the start < modified end, the Pos is saved.

toString

public java.lang.String toString()

getChromosome

public java.lang.String getChromosome()

getStart

public int getStart()

getStop

public int getStop()

getTotalNumberWindows

public int getTotalNumberWindows()

setTotalNumberWindows

public void setTotalNumberWindows(int totalNumberWindows)

setScores

public void setScores(java.util.ArrayList scores)

isSenseStrand

public boolean isSenseStrand()

setSenseStrand

public void setSenseStrand(boolean senseStrand)