trans.anno
Class BindingRegion

java.lang.Object
  trans.anno.BindingRegion

All Implemented Interfaces:

java.lang.Comparable

public class BindingRegion

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

BindingRegion(int rank, double score, java.lang.String chromosome, int start, int end, int sizeNeighborhood)

BindingRegion(Interval interval, int rank)

BindingRegion(int rank, java.lang.String chromosome, int start, int end)

Method Summary

int	bpIntersectionSameChromosome(BindingRegion other) Assumes regions are on the same chromosome, and the end base is included, not interbase numbering.
void	compare(GeneGroup geneGrp) Compares a binding region to a gene grp looking for where it is in relation to the binding region, 5', 3', overlap, contained.
int	compareTo(java.lang.Object obj)
static java.lang.String	extractGeneGrps(java.util.ArrayList geneGrps, boolean returnSummaryLine) Returns summary line or name for each GeneGrp in ArrayList
java.lang.String	getChromosome()
BindingRegion	getClosestBindingRegion()
java.util.ArrayList	getContainingGeneGrps()
int	getDistanceTo3PrimeGeneGrp()
int	getDistanceTo5PrimeGeneGrp()
int	getEnd()
double	getGcContent()
GeneGroup	getGeneGrp3Prime()
GeneGroup	getGeneGrp5Prime()
int	getLength() End-Start+1
int	getNeighborhood()
java.util.ArrayList	getNeighboringGeneGrps()
java.util.ArrayList	getOverlap3PrimeGeneGrps()
java.util.ArrayList	getOverlap5PrimeGeneGrps()
int	getRank()
double	getScore()
int	getStart()
int	intersectReturnBP(BindingRegion other) Returns -1 for no overlap or the # bases of intersection.
int	intersectReturnGap(BindingRegion other) Returns -1 if on diff chromosomes, 0 if they overlap, or the # of bases between the two.
boolean	intersects(BindingRegion other)
int	overlap(BindingRegion other) Returns -1 for no overlap, 0 for complete overlap, or a positive int for the # bases of overlap.
void	setChromosome(java.lang.String chromosome)
void	setClosestBindingRegion(BindingRegion closestBindingRegion)
void	setGcContent(double gcContent)
void	setNeighborhood(int neighborhood)
java.lang.String	simpleSummaryLine() Returns a binding region line, tab delimited: chrom, start, end, score
java.lang.String	simpleSummaryLineWithRank() Returns a binding region line, tab delimited: chrom, start, end, score
java.lang.String	summaryLine() Returns tab delimited line: rank, chrom, start, end, dist to closes gene, gene name(s), # neighbors
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

BindingRegion

public BindingRegion(int rank,
                     double score,
                     java.lang.String chromosome,
                     int start,
                     int end,
                     int sizeNeighborhood)

BindingRegion

public BindingRegion(int rank,
                     java.lang.String chromosome,
                     int start,
                     int end)

BindingRegion

public BindingRegion(Interval interval,
                     int rank)

Method Detail

compareTo

public int compareTo(java.lang.Object obj)

Specified by:

compareTo in interface java.lang.Comparable

intersects

public boolean intersects(BindingRegion other)

intersectReturnGap

public int intersectReturnGap(BindingRegion other)

Returns -1 if on diff chromosomes, 0 if they overlap, or the # of bases between the two.

bpIntersectionSameChromosome

public int bpIntersectionSameChromosome(BindingRegion other)

Assumes regions are on the same chromosome, and the end base is included, not interbase numbering. Returns 0 if the regions abut, positive ints for each base in the gap (ie 1= 1bp between an end of 12 and a start of 14), negative ints for each base of intersection (ie -1= 1bp overlap), max negative int is the length of the smaller region (ie end - start +1).

intersectReturnBP

public int intersectReturnBP(BindingRegion other)

Returns -1 for no overlap or the # bases of intersection.

overlap

public int overlap(BindingRegion other)

Returns -1 for no overlap, 0 for complete overlap, or a positive int for the # bases of overlap.

simpleSummaryLine

public java.lang.String simpleSummaryLine()

Returns a binding region line, tab delimited: chrom, start, end, score

simpleSummaryLineWithRank

public java.lang.String simpleSummaryLineWithRank()

Returns a binding region line, tab delimited: chrom, start, end, score

summaryLine

public java.lang.String summaryLine()

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

toString

public java.lang.String toString()

extractGeneGrps

public static java.lang.String extractGeneGrps(java.util.ArrayList geneGrps,
                                               boolean returnSummaryLine)

Returns summary line or name for each GeneGrp in ArrayList

compare

public void compare(GeneGroup geneGrp)

Compares a binding region to a gene grp looking for where it is in relation to the binding region, 5', 3', overlap, contained. Saves all that overlap or are contained as well as the closest 5' and the closest 3'.

getChromosome

public java.lang.String getChromosome()

getContainingGeneGrps

public java.util.ArrayList getContainingGeneGrps()

getDistanceTo3PrimeGeneGrp

public int getDistanceTo3PrimeGeneGrp()

getDistanceTo5PrimeGeneGrp

public int getDistanceTo5PrimeGeneGrp()

getGeneGrp3Prime

public GeneGroup getGeneGrp3Prime()

getGeneGrp5Prime

public GeneGroup getGeneGrp5Prime()

getOverlap3PrimeGeneGrps

public java.util.ArrayList getOverlap3PrimeGeneGrps()

getOverlap5PrimeGeneGrps

public java.util.ArrayList getOverlap5PrimeGeneGrps()

getRank

public int getRank()

getStart

public int getStart()

getEnd

public int getEnd()

getNeighborhood

public int getNeighborhood()

setNeighborhood

public void setNeighborhood(int neighborhood)

getNeighboringGeneGrps

public java.util.ArrayList getNeighboringGeneGrps()

getScore

public double getScore()

getClosestBindingRegion

public BindingRegion getClosestBindingRegion()

setClosestBindingRegion

public void setClosestBindingRegion(BindingRegion closestBindingRegion)

getLength

public int getLength()

End-Start+1

getGcContent

public double getGcContent()

setGcContent

public void setGcContent(double gcContent)

setChromosome

public void setChromosome(java.lang.String chromosome)