Package ubic.gemma.model.genome

Class PhysicalLocation

java.lang.Object

ubic.gemma.model.genome.ChromosomeLocation

ubic.gemma.model.genome.PhysicalLocation

All Implemented Interfaces:

Serializable, Identifiable

public class PhysicalLocation
extends ChromosomeLocation

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PhysicalLocation.Factory

Constructor Summary

Constructors

Constructor	Description
PhysicalLocation()	No-arg constructor added to satisfy javabean contract

Method Summary

Modifier and Type	Method	Description
int	binFromRange(int start, int end)
int	compareTo(Object object)
static int	computeOverlap(long starta, long enda, long startb, long endb)
int	computeOverlap(PhysicalLocation other)
boolean	equals(Object object)	Returns true if the argument is an ChromosomeLocation instance and all identifiers for this entity equal the identifiers of the argument entity.
Integer	getBin()
Long	getNucleotide()
Integer	getNucleotideLength()
String	getStrand()
int	hashCode()	Returns a hash code based on this entity's identifiers.
void	setBin(Integer bin)
void	setNucleotide(Long nucleotide)
void	setNucleotideLength(Integer nucleotideLength)
void	setStrand(String strand)
String	toString()

Methods inherited from class ubic.gemma.model.genome.ChromosomeLocation

getChromosome, getId, setChromosome, setId

Methods inherited from class java.lang.Object

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

Constructor Detail

PhysicalLocation

public PhysicalLocation()

No-arg constructor added to satisfy javabean contract

Method Detail

computeOverlap

public static int computeOverlap(long starta,
                                 long enda,
                                 long startb,
                                 long endb)

binFromRange

public int binFromRange(int start,
                        int end)

Parameters:

start - start

end - end

Returns:

bin that this start-end segment is in

compareTo

public int compareTo(Object object)

Specified by:

compareTo in class ChromosomeLocation

See Also:

Comparable.compareTo(Object)

hashCode

public int hashCode()

Description copied from class: ChromosomeLocation

Returns a hash code based on this entity's identifiers.

Overrides:

hashCode in class ChromosomeLocation

equals

public boolean equals(Object object)

Description copied from class: ChromosomeLocation

Returns true if the argument is an ChromosomeLocation instance and all identifiers for this entity equal the identifiers of the argument entity. Returns false otherwise.

Overrides:

equals in class ChromosomeLocation

computeOverlap

public int computeOverlap(PhysicalLocation other)

toString

public String toString()

Overrides:

toString in class Object

getBin

public Integer getBin()

Returns:

Index to speed up queries

setBin

public void setBin(Integer bin)

getNucleotide

public Long getNucleotide()

setNucleotide

public void setNucleotide(Long nucleotide)

getNucleotideLength

public Integer getNucleotideLength()

setNucleotideLength

public void setNucleotideLength(Integer nucleotideLength)

getStrand

public String getStrand()

setStrand

public void setStrand(String strand)