Package imp

Class HapToSeq

java.lang.Object

imp.HapToSeq

public class HapToSeq
extends java.lang.Object

Class HapToSeq stores an array mapping haplotype indices to allele sequences indices.

Instances of class HapToSeq are immutable.

Constructor Summary

Constructors

Constructor	Description
HapToSeq(int[] hap2Seq, int nSeq)	Constructs a new HapAlleles instance from the specified data.
HapToSeq(IntArray hap2Seq, int nSeq)	Constructs a new HapAlleles instance from the specified data.

Method Summary

Modifier and Type	Method	Description
IntArray	hap2Seq()	Returns the array mapping haplotype indices to sequence indices.
int	nHaps()	Returns the number of haplotypes.
int	nSeqs()	Returns the number of sequences.

Methods inherited from class java.lang.Object

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

Constructor Detail

HapToSeq

public HapToSeq(int[] hap2Seq,
                int nSeq)

Constructs a new HapAlleles instance from the specified data. The contract for this constructor and class is unspecified if the sequence indices are not a subset of 0, 1, ..., (nSeq - 1).

Parameters:

hap2Seq - an array mapping haplotype index to sequence index

nSeq - the number of distinct sequence indices

Throws:

java.lang.IllegalArgumentException - if nSeq < 1

java.lang.NullPointerException - ifhap2Seq == null

HapToSeq

public HapToSeq(IntArray hap2Seq,
                int nSeq)

Constructs a new HapAlleles instance from the specified data. The contract for this constructor and class is unspecified if the sequence indices are not a subset of 0, 1, ..., (nSeq - 1).

Parameters:

hap2Seq - an array mapping haplotype index to sequence index

nSeq - the number of distinct sequence indices

Throws:

java.lang.NullPointerException - ifhap2Seq == null

Method Detail

nHaps

public int nHaps()

Returns the number of haplotypes.

Returns:

the number of haplotypes

nSeqs

public int nSeqs()

Returns the number of sequences.

Returns:

the number of sequences

hap2Seq

public IntArray hap2Seq()

Returns the array mapping haplotype indices to sequence indices.

Returns:

the array mapping haplotype indices to sequence indices