RefGT
BasicGT
, BasicRefGT
, EstPhase.HapsGT
, HapPairPhasedGT
, SplicedGT
, XBasicGT
public interface GT
Interface GT
represents genotype data
for a list of markers and a list of samples.
All instances of GT
are required to be immutable.
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.
|
default float |
gl(int marker,
int sample,
int allele1,
int allele2) |
Returns the probability of the observed data for the specified marker
and sample if the specified pair of ordered alleles is the true
ordered genotype.
|
default boolean |
isGTData() |
Returns
true if the value returned by this.gl() is
determined by a called or missing genotype, and returns false
otherwise. |
boolean |
isPhased() |
Returns
true if the genotype for each marker and sample
is a phased, non-missing genotype, and returns false otherwise. |
boolean |
isPhased(int sample) |
Returns
true if the genotype for each marker for the
specified sample is a phased, nonmissing genotype, and returns
false otherwise. |
boolean |
isPhased(int marker,
int sample) |
Returns
true if the genotype for the specified marker
and sample is a phased, nonmissing genotype, and returns false
otherwise. |
Marker |
marker(int marker) |
Returns the specified marker.
|
Markers |
markers() |
Returns the list of markers.
|
default int |
nHaps() |
Returns the number of haplotypes.
|
int |
nMarkers() |
Returns the number of markers.
|
int |
nSamples() |
Returns the number of samples.
|
Samples |
samples() |
Returns the list of samples.
|
int nMarkers()
Markers markers()
Marker marker(int marker)
marker
- a marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
default int nHaps()
2*this.nSamples()
.int nSamples()
Samples samples()
int allele1(int marker, int sample)
this.unphased(marker, sample) == false
.marker
- the marker indexsample
- the sample indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= this.nSamples()
int allele2(int marker, int sample)
this.unphased(marker, sample) == false
.marker
- the marker indexsample
- the sample indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= this.nSamples()
int allele(int marker, int hap)
this.unphased(marker, hap/2) == false
.marker
- the marker indexhap
- the haplotype indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
hap < 0 || hap >= this.nHaps()
boolean isPhased(int marker, int sample)
true
if the genotype for the specified marker
and sample is a phased, nonmissing genotype, and returns false
otherwise.marker
- the marker indexsample
- the sample indextrue
if the genotype for the specified marker
and sample is a phased, nonmissing genotypejava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= this.nSamples()
boolean isPhased(int sample)
true
if the genotype for each marker for the
specified sample is a phased, nonmissing genotype, and returns
false
otherwise.sample
- a sample indextrue
if the genotype for each marker for the
specified sample is a phased, nonmissing genotypejava.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= this.nSamples()
boolean isPhased()
true
if the genotype for each marker and sample
is a phased, non-missing genotype, and returns false
otherwise.true
if the genotype for each marker and sample
is a phased, non-missing genotypedefault boolean isGTData()
true
if the value returned by this.gl()
is
determined by a called or missing genotype, and returns false
otherwise.true
if the value returned by this.gl()
is
determined by a called or missing genotypedefault float gl(int marker, int sample, int allele1, int allele2)
marker
- the marker indexsample
- the sample indexallele1
- the first allele indexallele2
- the second allele indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
samples < 0 || samples >= this.nSamples()
java.lang.IndexOutOfBoundsException
- if
allele1 < 0 || allele1 >= this.marker(marker).nAlleles()
java.lang.IndexOutOfBoundsException
- if
allele2 < 0 || allele2 >= this.marker(marker).nAlleles()