net.maizegenetics.pangenome.api

Class ReferenceRange

java.lang.Object

net.maizegenetics.pangenome.api.ReferenceRange

All Implemented Interfaces:

Comparable<ReferenceRange>

public class ReferenceRange
extends Object
implements Comparable<ReferenceRange>

Author:

Terry Casstevens Created June 19, 2017, Zack Miller, Karl Kremling, Jacob Washburn

Constructor Summary

Constructors

Constructor and Description
ReferenceRange(String referenceName, net.maizegenetics.dna.map.Chromosome chromosome, int start, int end, int id)
ReferenceRange(String referenceName, net.maizegenetics.dna.map.Chromosome chromosome, int start, int end, int id, boolean isAnchor)

Method Summary

Modifier and Type	Method and Description
net.maizegenetics.dna.map.Chromosome	chromosome() Chromosome in the reference genome from which this ReferenceRange originates
int	compareTo(ReferenceRange o)
int	end() End position of reference range, inclusive
boolean	equals(Object o)
int	hashCode()
int	id() Identifier for a unique reference range
String	intervalString()
boolean	isAnchor() Return whether this range is an anchor.
String	referenceName() Reference genome (B73, CML247, EP1, etc) from which the reference range originates
int	start() Start position of reference range, inclusive
String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

ReferenceRange

public ReferenceRange(String referenceName,
                      net.maizegenetics.dna.map.Chromosome chromosome,
                      int start,
                      int end,
                      int id)

ReferenceRange

public ReferenceRange(String referenceName,
                      net.maizegenetics.dna.map.Chromosome chromosome,
                      int start,
                      int end,
                      int id,
                      boolean isAnchor)

Method Detail

chromosome

public net.maizegenetics.dna.map.Chromosome chromosome()

Chromosome in the reference genome from which this ReferenceRange originates

start

public int start()

Start position of reference range, inclusive

end

public int end()

End position of reference range, inclusive

id

public int id()

Identifier for a unique reference range

isAnchor

public boolean isAnchor()

Return whether this range is an anchor. False if inter-anchor.

Returns:

whether this is an anchor

referenceName

public String referenceName()

Reference genome (B73, CML247, EP1, etc) from which the reference range originates

intervalString

public String intervalString()

toString

public String toString()

Overrides:

toString in class Object

compareTo

public int compareTo(ReferenceRange o)

Specified by:

compareTo in interface Comparable<ReferenceRange>

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object