public final class RevSampleHapPairs extends java.lang.Object implements SampleHapPairs
Class RevSampleHapPairs
is a wrapper for a SampleHapPairs
instance. The wrapper reverses the order of markers in the wrapped object.
Instances of class RevSampleHapPairs
are immutable.
Constructor and Description |
---|
RevSampleHapPairs(SampleHapPairs hapPairs)
Creates a new
RevSampleHapPairs instance from the specified data. |
Modifier and Type | Method and Description |
---|---|
int |
allele(int marker,
int haplotype)
Returns the allele for the specified marker and haplotype.
|
int |
allele1(int marker,
int hapPair)
Returns the first allele for the specified marker and haplotype pair.
|
int |
allele2(int marker,
int hapPair)
Returns the second allele for the specified marker and haplotype pair.
|
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.
|
Marker |
marker(int marker)
Returns the specified marker.
|
Markers |
markers()
Returns the markers.
|
int |
nAlleles(int marker)
Returns the number of marker alleles.
|
int |
nHapPairs()
Returns the number of haplotype pairs.
|
int |
nHaps()
Returns the number of haplotypes.
|
int |
nMarkers()
Returns the number of markers.
|
int |
nSamples()
Returns the number of samples.
|
int |
sampleIndex(int hapPair)
Returns the index of the sample associated with the specified
haplotype pair in the list of samples returned by
this.samples() . |
Samples |
samples()
Returns the samples.
|
Samples |
samples(int hapPair)
Returns a list of samples containing the sample associated with
the specified haplotype pair
|
boolean |
storesNonMajorIndices(int marker)
Returns
true if this object stores the indices of haplotypes
that carry non-major alleles, and returns false otherwise. |
public RevSampleHapPairs(SampleHapPairs hapPairs)
RevSampleHapPairs
instance from the specified data.hapPairs
- the sample haplotype pairs that will be wrapped by the
new instancejava.lang.NullPointerException
- if hapPairs == null
public int allele1(int marker, int hapPair)
HapPairs
public int allele2(int marker, int hapPair)
HapPairs
public int allele(int marker, int haplotype)
HapPairs
public int nMarkers()
HapPairs
public Marker marker(int marker)
HapPairs
public int nHaps()
HapPairs
2*this.nHapPairs()
.public int nHapPairs()
HapPairs
this.nHaps()/2
.public int nSamples()
SampleHapPairs
nSamples
in interface SampleHapPairs
public Samples samples()
SampleHapPairs
k
-th sample corresponds to
the k
-th haplotype pair.samples
in interface SampleHapPairs
public Samples samples(int hapPair)
HapPairs
public int sampleIndex(int hapPair)
HapPairs
this.samples()
.sampleIndex
in interface HapPairs
hapPair
- a haplotype pair indexthis.samples()
public int nAlleles(int marker)
SampleHapPairs
nAlleles
in interface SampleHapPairs
marker
- a marker indexpublic boolean storesNonMajorIndices(int marker)
SampleHapPairs
true
if this object stores the indices of haplotypes
that carry non-major alleles, and returns false
otherwise.storesNonMajorIndices
in interface SampleHapPairs
marker
- a marker indextrue
if this object stores the indices of haplotypes
that carry non-major allelespublic int majorAllele(int marker)
SampleHapPairs
majorAllele
in interface SampleHapPairs
marker
- a marker indexpublic int alleleCount(int marker, int allele)
SampleHapPairs
alleleCount
in interface SampleHapPairs
marker
- a marker indexallele
- an allele indexpublic int hapIndex(int marker, int allele, int copy)
SampleHapPairs
hapIndex
in interface SampleHapPairs
marker
- a marker indexallele
- an allele indexcopy
- a copy index.