trans.main
Class PosRegion

java.lang.Object
  trans.main.PosRegion

All Implemented Interfaces:

java.lang.Comparable

public class PosRegion

extends java.lang.Object

implements java.lang.Comparable

For holding information about a genomic interval, what genes are up, down, overlap, or contain this genomic inteval.

Constructor Summary

PosRegion(java.lang.String name, java.lang.String chromosome, int start, int end)

Method Summary

int	compareTo(java.lang.Object obj)
java.lang.String	getChromosome()
Interval	getClosestInterval()
int	getClosestNonOverlappingInterval()
int	getEnd()
java.lang.String	getName()
java.util.ArrayList	getOverlapping()
PosRegion	getRegion()
int	getStart()
void	setChromosome(java.lang.String chromosome)
void	setClosestInterval(Interval closestInterval)
void	setClosestNonOverlappingInterval(int closestOverlap)
void	setEnd(int end)
void	setName(java.lang.String name)
void	setOverlapping(java.util.ArrayList overlapping)
void	setRegion(PosRegion region)
void	setStart(int start)
java.lang.String	summaryLine() Returns tab delimited line: rank, chrom, start, end, dist to closes gene, gene name(s), # neighbors

Methods inherited from class java.lang.Object

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

Constructor Detail

PosRegion

public PosRegion(java.lang.String name,
                 java.lang.String chromosome,
                 int start,
                 int end)

Method Detail

compareTo

public int compareTo(java.lang.Object obj)

Specified by:

compareTo in interface java.lang.Comparable

summaryLine

public java.lang.String summaryLine()

Returns tab delimited line: rank, chrom, start, end, dist to closes gene, gene name(s), # neighbors

getChromosome

public java.lang.String getChromosome()

getStart

public int getStart()

getEnd

public int getEnd()

getClosestNonOverlappingInterval

public int getClosestNonOverlappingInterval()

setClosestNonOverlappingInterval

public void setClosestNonOverlappingInterval(int closestOverlap)

getName

public java.lang.String getName()

setName

public void setName(java.lang.String name)

getOverlapping

public java.util.ArrayList getOverlapping()

setOverlapping

public void setOverlapping(java.util.ArrayList overlapping)

getRegion

public PosRegion getRegion()

setRegion

public void setRegion(PosRegion region)

setChromosome

public void setChromosome(java.lang.String chromosome)

setEnd

public void setEnd(int end)

setStart

public void setStart(int start)

getClosestInterval

public Interval getClosestInterval()

setClosestInterval

public void setClosestInterval(Interval closestInterval)