com.pacbio.secondary.vis.data.locus

Class Locus

java.lang.Object

com.pacbio.secondary.vis.data.locus.Locus

All Implemented Interfaces:

java.lang.Comparable<Locus>

public class Locus
extends java.lang.Object
implements java.lang.Comparable<Locus>

A genomic locus: contig/chromosome and start and stop basepairs.

Field Summary

Fields

Modifier and Type	Field and Description
int	contig
Interval	interval

Constructor Summary

Constructors

Constructor and Description
Locus()
Locus(int contig, long start, long end)
Locus(int contig, long start, long end, int order)
Locus(Locus locus)

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(Locus other)
boolean	contains(Locus locus)
protected long	getPosition()
boolean	intersects(Locus locus)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

contig

public int contig

interval

public Interval interval

Constructor Detail

Locus

public Locus()

Locus

public Locus(Locus locus)

Locus

public Locus(int contig,
     long start,
     long end)

Locus

public Locus(int contig,
     long start,
     long end,
     int order)

Method Detail

compareTo

public int compareTo(Locus other)

Specified by:

compareTo in interface java.lang.Comparable<Locus>

intersects

public boolean intersects(Locus locus)

Parameters:

locus -

Returns:

True if this locus builds a non-empty intersection with the given locus.

contains

public boolean contains(Locus locus)

Parameters:

locus -

Returns:

True if this locus contains the given locus.

getPosition

protected long getPosition()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object