public interface SampleHapPairs extends HapPairs
Interface SampleHapPairs
represents a list of samples and a
haplotype pair for each sample. Each haplotype pair is guaranteed
to have two non-missing alleles at each marker.
All instances of SampleHapPairs
are required to be immutable.
Modifier and Type | Method and Description |
---|---|
int |
alleleCount(int marker,
int allele)
Returns the number of haplotypes that carry the specified allele.
|
int |
hapIndex(int marker,
int allele,
int copy)
Returns index of the haplotype that carries the specified copy of the
specified allele.
|
int |
majorAllele(int marker)
Returns the index of the major allele.
|
int |
nAlleles(int marker)
Returns the number of marker alleles.
|
int |
nSamples()
Returns the number of samples.
|
Samples |
samples()
Returns the samples.
|
boolean |
storesNonMajorIndices(int marker)
Returns
true if this object stores the indices of haplotypes
that carry non-major alleles, and returns false otherwise. |
Samples samples()
k
-th sample corresponds to
the k
-th haplotype pair.int nSamples()
int nAlleles(int marker)
marker
- a marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
boolean storesNonMajorIndices(int marker)
true
if this object stores the indices of haplotypes
that carry non-major alleles, and returns false
otherwise.marker
- a marker indextrue
if this object stores the indices of haplotypes
that carry non-major allelesjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
int majorAllele(int marker)
marker
- a marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.UnsupportedOperationException
- if
storesNonMajorIndices(marker) == false
int alleleCount(int marker, int allele)
marker
- a marker indexallele
- an allele indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IllegalArgumentException
- if
allele == this.majorAllele()
java.lang.IndexOutOfBoundsException
- if
allele < 0 || allele >= this.nAlleles()
java.lang.UnsupportedOperationException
- if
storesNonMajorIndices(marker) == false
int hapIndex(int marker, int allele, int copy)
marker
- a marker indexallele
- an allele indexcopy
- a copy index.java.lang.IllegalArgumentException
- if
allele == this.majorAllele()
java.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
allele < 0 || allele >= this.nAlleles()
java.lang.IndexOutOfBoundsException
- if
copy < 0 || copy >= this.alleleCount(allele)
java.lang.UnsupportedOperationException
- if
storesNonMajorIndices(marker) == false