public class RefHapSeg
extends java.lang.Object
Class RefHapSeg
represents a chromosome segment of
reference haplotypes.
Instances of class RefHapSeg
are immutable.
Constructor and Description |
---|
RefHapSeg(SampleHapPairs refHapPairs,
int start,
int end)
Constructs a new
RefHapSegs instance from the specified data. |
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.
|
public RefHapSeg(SampleHapPairs refHapPairs, int start, int end)
RefHapSegs
instance from the specified data.refHapPairs
- the reference haplotype pairsstart
- the starting marker index (inclusive)end
- the ending marker index (exclusive)java.lang.IllegalArgumentException
- if
start < 0 || start >= end || end > refHapPairs.nMarkers()
java.lang.NullPointerException
- if refHapPairs == null
public SampleHapPairs refHapPairs()
public int nSeq()
public int seq(int hap)
hap
- a haplotype indexjava.lang.IndexOutOfBoundsException
- if
hap < 0 || hap >= this.refHapPairs().nHaps()
public int allele(int marker, int seq)
marker
- index of a marker in this segmentseq
- index of a reference allele sequence in this segmentjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= (this.end() - this.start())
java.lang.IndexOutOfBoundsException
- if
seq < 0 || seg >= this.nSeq(segment)
public int start()
public int end()