sample

Class RefHapSegs

java.lang.Object

sample.RefHapSegs

public class RefHapSegs
extends java.lang.Object

Class RefHapSegs represents reference haplotypes that span segments determined by non-overlapping clusters of markers.

Instances of class RefHapSegs are immutable.

Constructor Summary

Constructors

Constructor and Description
RefHapSegs(SampleHapPairs refHapPairs, int[] segStart, int[] segEnd) Constructs a new RefHapSegs instance from the specified data.

Method Summary

Modifier and Type	Method and Description
int	allele(int segment, int marker, int seq) Return the specified reference haplotype allele.
int	nMarkers(int segment) Return the number of markers in the specified chromosome segment.
int	nSegs() Returns the number of marker segments..
int	nSeq(int segment) Return the number of distinct reference allele sequences in the specified chromosome segment.
SampleHapPairs	refHapPairs() Returns the reference haplotype pairs.
int	segEnd(int segment) Returns the index of the last marker (exclusive) in the specified marker segment.
int	segStart(int segment) Returns the index of the first marker (inclusive) in the specified marker segment.
int	seq(int segment, int hap) Return the index of the allele sequence in the specified chromosome segment for the specified reference haplotype.

Methods inherited from class java.lang.Object

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

Constructor Detail

RefHapSegs

public RefHapSegs(SampleHapPairs refHapPairs,
                  int[] segStart,
                  int[] segEnd)

Constructs a new RefHapSegs instance from the specified data.

Parameters:

refHapPairs - the reference haplotype pairs

segStart - an array whose j-th element is the starting reference marker index (inclusive) for the j-th segment of markers

segEnd - an array whose j-th element is the ending reference marker index (exclusive) for the j-th segment of markers

Throws:

java.lang.IllegalArgumentException - if segStart.length != segEnd.length

java.lang.IllegalArgumentException - if (segStart[j] < 0 || segStart[j] >= segEnd[j] || segEnd[j] >= refHapPairs.nMarkers()) for some j satisfying 0 <= j && j < segStart.length

java.lang.NullPointerException - if refHapPairs == null || segStart == null || segEnd == null

Method Detail

refHapPairs

public SampleHapPairs refHapPairs()

Returns the reference haplotype pairs.

Returns:

the reference haplotype pairs

nSeq

public int nSeq(int segment)

Return the number of distinct reference allele sequences in the specified chromosome segment.

Parameters:

segment - index of a chromosome segment determined by the marker clusters

Returns:

the number of distinct reference allele sequences in the specified chromosome segment

Throws:

java.lang.IndexOutOfBoundsException - if segment < 0 || segment > this.nClusters()

nMarkers

public int nMarkers(int segment)

Return the number of markers in the specified chromosome segment.

Parameters:

segment - index of a chromosome segment determined by the marker clusters

Returns:

the number of markers in the specified chromosome segment

Throws:

java.lang.IndexOutOfBoundsException - if segment < 0 || segment > this.nClusters()

seq

public int seq(int segment,
               int hap)

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

Parameters:

segment - index of a chromosome segment determined by the marker clusters

hap - a haplotype index

Returns:

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

Throws:

java.lang.IndexOutOfBoundsException - if segment < 0 || segment > this.nClusters()

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

allele

public int allele(int segment,
                  int marker,
                  int seq)

Return the specified reference haplotype allele.

Parameters:

segment - index of a chromosome segment determined by the marker clusters

marker - index of a marker in the specified interval

seq - index of a reference allele sequence in the specified interval

Returns:

the specified reference haplotype allele

Throws:

java.lang.IndexOutOfBoundsException - if segment < 0 || segment > this.nClusters()

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers(interval)

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

nSegs

public int nSegs()

Returns the number of marker segments..

Returns:

the number of marker segments

segStart

public int segStart(int segment)

Returns the index of the first marker (inclusive) in the specified marker segment.

Parameters:

segment - an index of a marker segment

Returns:

the index of the first marker (inclusive) in the specified marker segment

Throws:

java.lang.IndexOutOfBoundsException - if segment < 0 || segment >= this.nSegs()

segEnd

public int segEnd(int segment)

Returns the index of the last marker (exclusive) in the specified marker segment.

Parameters:

segment - an index of a marker segment

Returns:

the index of the last marker (exclusive) in the specified marker segment

Throws:

java.lang.IndexOutOfBoundsException - if segment 0 || segment >= this.nSegs()