org.nmdp.ngs.feature

Class Locus

java.lang.Object

org.biojava.bio.symbol.AbstractLocation

org.biojava.bio.symbol.AbstractRangeLocation

org.biojava.bio.symbol.RangeLocation

org.nmdp.ngs.feature.Locus

All Implemented Interfaces:

Serializable, Comparable<Locus>, org.biojava.bio.symbol.Location

Direct Known Subclasses:

Allele

public class Locus
extends org.biojava.bio.symbol.RangeLocation
implements Comparable<Locus>

Locus.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Locus.Util

Field Summary

Fields

Modifier and Type	Field and Description
protected String	contig

Fields inherited from interface org.biojava.bio.symbol.Location

empty, full, naturalOrder

Constructor Summary

Constructors

Constructor and Description
Locus(String contig, int start, int end)
Locus(String contig, org.biojava.bio.symbol.RangeLocation range)

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(Locus right)
boolean	equals(Object right)
String	getContig()
int	getEnd()
int	getStart()
int	hashCode()
Locus	intersection(Locus right)
boolean	isEmpty()
boolean	isPointLocation()
int	length()
boolean	overlaps(Locus right)
String	toString()
Locus	union(Locus right)

Methods inherited from class org.biojava.bio.symbol.RangeLocation

getMax, getMin, translate

Methods inherited from class org.biojava.bio.symbol.AbstractRangeLocation

blockIterator, contains, isContiguous, symbols

Methods inherited from class org.biojava.bio.symbol.AbstractLocation

contains, getDecorator, intersection, newInstance, overlaps, union

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

contig

protected String contig

Constructor Detail

Locus

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

Locus

public Locus(String contig,
     org.biojava.bio.symbol.RangeLocation range)

Method Detail

getStart

public final int getStart()

getEnd

public final int getEnd()

isPointLocation

public boolean isPointLocation()

getContig

public String getContig()

intersection

public Locus intersection(Locus right)

union

public Locus union(Locus right)

length

public final int length()

isEmpty

public boolean isEmpty()

overlaps

public boolean overlaps(Locus right)

equals

public boolean equals(Object right)

Specified by:

equals in interface org.biojava.bio.symbol.Location

Overrides:

equals in class org.biojava.bio.symbol.AbstractLocation

compareTo

public int compareTo(Locus right)

Specified by:

compareTo in interface Comparable<Locus>

hashCode

public int hashCode()

Overrides:

hashCode in class org.biojava.bio.symbol.AbstractLocation

toString

public String toString()

Overrides:

toString in class org.biojava.bio.symbol.RangeLocation