trans.main
Class Window

java.lang.Object
  trans.main.Window

All Implemented Interfaces:

java.lang.Comparable, java.io.Serializable

public class Window

extends java.lang.Object

implements java.lang.Comparable, java.io.Serializable

Class to hold information about a window, a defined portion of the genome typically < 1kb.

See Also:

Serialized Form

Constructor Summary

Window(java.lang.String chromosome, int start, int end, int numberOligos, double[] scores)

Method Summary

int	compareTo(java.lang.Object obj)
java.lang.String	getChromosome()
int	getNumberOligos()
double[]	getScores()
double	getSortBy()
int	getStart1stOligo()
int	getStartLastOligo()
boolean	overlap(Window other)
void	setScores(double[] scores)
void	setSortBy(double sortBy)
void	setStart1stOligo(int start)
void	setStartLastOligo(int end)
java.lang.String	stringRep(int sizeOfOligo) Returns chromosome, start first oligo, start last oligo

Methods inherited from class java.lang.Object

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

Constructor Detail

Window

public Window(java.lang.String chromosome,
              int start,
              int end,
              int numberOligos,
              double[] scores)

Method Detail

compareTo

public int compareTo(java.lang.Object obj)

Specified by:

compareTo in interface java.lang.Comparable

overlap

public boolean overlap(Window other)

stringRep

public java.lang.String stringRep(int sizeOfOligo)

Returns chromosome, start first oligo, start last oligo

getChromosome

public java.lang.String getChromosome()

getStartLastOligo

public int getStartLastOligo()

getStart1stOligo

public int getStart1stOligo()

setSortBy

public void setSortBy(double sortBy)

getSortBy

public double getSortBy()

setStartLastOligo

public void setStartLastOligo(int end)

setStart1stOligo

public void setStart1stOligo(int start)

getScores

public double[] getScores()

setScores

public void setScores(double[] scores)

getNumberOligos

public int getNumberOligos()

Returns:

Returns the numberOligo positions covered by a window, not all the treatments and controls.