sample

Class RefHapSeg

java.lang.Object

sample.RefHapSeg

public class RefHapSeg
extends java.lang.Object

Class RefHapSeg represents a chromosome segment of reference haplotypes.

Instances of class RefHapSeg are immutable.

Constructor Summary

Constructors

Constructor and Description
RefHapSeg(SampleHapPairs refHapPairs, int start, int end) Constructs a new RefHapSegs instance from the specified data.

Method Summary

Modifier and Type	Method and Description
int	allele(int marker, int seq) Return the specified reference haplotype allele.
int	end() Returns the ending marker index (exclusive) of this segment.
int	nSeq() Return the number of reference allele sequences in this segment.
SampleHapPairs	refHapPairs() Returns the reference haplotype pairs.
int	seq(int hap) Return the index of the reference allele sequence in this segment for the specified reference haplotype.
int	start() Returns the starting marker index (inclusive) of this segment.

Methods inherited from class java.lang.Object

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

Constructor Detail

RefHapSeg

public RefHapSeg(SampleHapPairs refHapPairs,
                 int start,
                 int end)

Constructs a new RefHapSegs instance from the specified data.

Parameters:

refHapPairs - the reference haplotype pairs

start - the starting marker index (inclusive)

end - the ending marker index (exclusive)

Throws:

java.lang.IllegalArgumentException - if start < 0 || start >= end || end > refHapPairs.nMarkers()

java.lang.NullPointerException - if refHapPairs == null

Method Detail

refHapPairs

public SampleHapPairs refHapPairs()

Returns the reference haplotype pairs.

Returns:

the reference haplotype pairs

nSeq

public int nSeq()

Return the number of reference allele sequences in this segment.

Returns:

the number of reference allele sequences in this segment

seq

public int seq(int hap)

Return the index of the reference allele sequence in this segment for the specified reference haplotype.

Parameters:

hap - a haplotype index

Returns:

the index of the reference allele sequence in this segment for the specified reference haplotype

Throws:

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.refHapPairs().nHaps()

allele

public int allele(int marker,
                  int seq)

Return the specified reference haplotype allele.

Parameters:

marker - index of a marker in this segment

seq - index of a reference allele sequence in this segment

Returns:

the specified reference haplotype allele

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= (this.end() - this.start())

java.lang.IndexOutOfBoundsException - if seq < 0 || seg >= this.nSeq(segment)

start

public int start()

Returns the starting marker index (inclusive) of this segment.

Returns:

the starting marker index (inclusive) of this segment

end

public int end()

Returns the ending marker index (exclusive) of this segment.

Returns:

the ending marker index (exclusive) of this segment