trans.main
Class Oligo

java.lang.Object
  trans.main.Oligo

All Implemented Interfaces:

java.io.Serializable

public class Oligo

extends java.lang.Object

implements java.io.Serializable

Container to hold information about a particular oligo.

See Also:

Serialized Form

Constructor Summary

Oligo(int index, int start, int hits, java.util.ArrayList intensities, java.lang.String sequence)

Method Summary

float[]	getControlIntensities(int numControlInt)
int	getIndex()
java.util.ArrayList	getIntensities()
double	getLeftSlope()
int	getMatches()
double	getRightSlope()
java.lang.String	getSequence()
double	getSmoothedScore()
int	getStart()
float[]	getTreatmentIntensities(int numTreatInt)
boolean	isInPeak()
void	setInPeak(boolean inPeak)
void	setLeftSlope(double leftSlope)
void	setRightSlope(double rightSlope)
void	setSequence(java.lang.String sequence)
void	setSkip(boolean skip)
void	setSmoothedScore(double smoothedScore)
boolean	skip()
java.lang.String	toString()
java.lang.String	toString(int numTreatInt, int numControlInt, java.lang.String divider)

Methods inherited from class java.lang.Object

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

Constructor Detail

Oligo

public Oligo(int index,
             int start,
             int hits,
             java.util.ArrayList intensities,
             java.lang.String sequence)

Method Detail

toString

public java.lang.String toString()

toString

public java.lang.String toString(int numTreatInt,
                                 int numControlInt,
                                 java.lang.String divider)

getTreatmentIntensities

public float[] getTreatmentIntensities(int numTreatInt)

getControlIntensities

public float[] getControlIntensities(int numControlInt)

getStart

public int getStart()

getIntensities

public java.util.ArrayList getIntensities()

getIndex

public int getIndex()

getSequence

public java.lang.String getSequence()

getSmoothedScore

public double getSmoothedScore()

setSmoothedScore

public void setSmoothedScore(double smoothedScore)

isInPeak

public boolean isInPeak()

setInPeak

public void setInPeak(boolean inPeak)

skip

public boolean skip()

setSkip

public void setSkip(boolean skip)

getLeftSlope

public double getLeftSlope()

setLeftSlope

public void setLeftSlope(double leftSlope)

getRightSlope

public double getRightSlope()

setRightSlope

public void setRightSlope(double rightSlope)

getMatches

public int getMatches()

setSequence

public void setSequence(java.lang.String sequence)