umcg.genetica.genomicboundaries

Class GenomicBoundary<V>

java.lang.Object

umcg.genetica.genomicboundaries.GenomicBoundary<V>

All Implemented Interfaces:

Comparable<GenomicBoundary>

public class GenomicBoundary<V>
extends Object
implements Comparable<GenomicBoundary>

Author:

PatrickDeelen

Constructor Summary

Constructors

Constructor and Description
GenomicBoundary(String chromosome, Integer start, int stop)
GenomicBoundary(String chromosome, Integer start, int stop, V annotation)

Method Summary

Modifier and Type	Method and Description
int	compareTo(GenomicBoundary other)
V	getAnnotation()
String	getChromosome()
int	getLength(boolean isInclusive)
Integer	getStart()
int	getStop()
boolean	isInBoundarie(int position) Assumes that chromosome is correct
boolean	isInBoundarie(int position, int margin) Assumes that chromosome is correct
boolean	isOverlaping(GenomicBoundary other)
boolean	isPartOfBoundary(GenomicBoundary other) Is this boundary a sub boundary of the other boundary.

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomicBoundary

public GenomicBoundary(String chromosome,
                       Integer start,
                       int stop)

GenomicBoundary

public GenomicBoundary(String chromosome,
                       Integer start,
                       int stop,
                       V annotation)

Method Detail

getChromosome

public String getChromosome()

getStart

public Integer getStart()

getStop

public int getStop()

compareTo

public int compareTo(GenomicBoundary other)

Specified by:

compareTo in interface Comparable<GenomicBoundary>

isInBoundarie

public boolean isInBoundarie(int position)

Assumes that chromosome is correct

Parameters:

position -

Returns:

isInBoundarie

public boolean isInBoundarie(int position,
                             int margin)

Assumes that chromosome is correct

Parameters:

position -

margin -

Returns:

isPartOfBoundary

public boolean isPartOfBoundary(GenomicBoundary other)

Is this boundary a sub boundary of the other boundary. Assumes that chromosome is correct

Parameters:

other -

Returns:

isOverlaping

public boolean isOverlaping(GenomicBoundary other)

getAnnotation

public V getAnnotation()

getLength

public int getLength(boolean isInclusive)