Package vcf
Class RestrictedGT
- java.lang.Object
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- vcf.RestrictedGT
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Constructor Summary
Constructors Constructor Description RestrictedGT(GT gt, Markers markers, int[] indices)
Constructs a newNoPhaseGTWrapper
instance from the specified data
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
allele(int marker, int hap)
Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing.int
allele1(int marker, int sample)
Returns the first allele for the specified marker and sample or return -1 if the allele is missing.int
allele2(int marker, int sample)
Returns the second allele for the specified marker and sample or return -1 if the allele is missing.boolean
isPhased()
Returnstrue
if the genotype for each marker and sample is a phased, non-missing genotype, and returnsfalse
otherwise.Marker
marker(int marker)
Returns the specified marker.Markers
markers()
Returns the list of markers.int
nHaps()
Returns the number of haplotypes.int
nMarkers()
Returns the number of markers.int
nSamples()
Returns the number of samples.GT
restrict(Markers markers, int[] indices)
Returns aGT
instance restricted to genotype data for the specified markers.Samples
samples()
Returns the list of samples.java.lang.String
toString()
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Constructor Detail
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RestrictedGT
public RestrictedGT(GT gt, Markers markers, int[] indices)
Constructs a newNoPhaseGTWrapper
instance from the specified data- Parameters:
gt
- the genotypes to be wrappedmarkers
- the list of markers in the returned instanceindices
- the mapping of marker indices frommarkers
togt.markers()
- Throws:
java.lang.IndexOutOfBoundsException
- if there existsj
such that(0 <= j && j < indices.length)
such that(indices[j] < 0 || indices[j] >= gt.nMarkers())
java.lang.IllegalArgumentException
- if there existsj
such that(1 <= j && j < indices.length)
such that(indices[j] <= indice[j - 1])
java.lang.IllegalArgumentException
- if there existsj
such that(0 <= j && j < indices.length)
such that(gt.marker(indices[j]).equals(markers.marker(j)) == false)
java.lang.NullPointerException
- if(gt == null || markers == null || include == null)
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Method Detail
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isPhased
public boolean isPhased()
Description copied from interface:GT
Returnstrue
if the genotype for each marker and sample is a phased, non-missing genotype, and returnsfalse
otherwise.
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allele1
public int allele1(int marker, int sample)
Description copied from interface:GT
Returns the first allele for the specified marker and sample or return -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered ifthis.unphased(marker, sample) == false
.
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allele2
public int allele2(int marker, int sample)
Description copied from interface:GT
Returns the second allele for the specified marker and sample or return -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered ifthis.unphased(marker, sample) == false
.
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allele
public int allele(int marker, int hap)
Description copied from interface:GT
Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing. The two alleles for an individual are arbitrarily ordered ifthis.unphased(marker, hap/2) == false
.
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nMarkers
public int nMarkers()
Description copied from interface:GT
Returns the number of markers.
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marker
public Marker marker(int marker)
Description copied from interface:GT
Returns the specified marker.
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nHaps
public int nHaps()
Description copied from interface:GT
Returns the number of haplotypes. The returned value is equal to2*this.nSamples()
.
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nSamples
public int nSamples()
Description copied from interface:GT
Returns the number of samples.
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restrict
public GT restrict(Markers markers, int[] indices)
Description copied from interface:GT
Returns aGT
instance restricted to genotype data for the specified markers.
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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