Constructor | Description |
---|---|
BasicGT(Samples samples,
GTRec[] vma) |
Constructs a
BasicGT instance. |
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.
|
static int |
genotype(int a1,
int a2) |
Returns the genotype index corresponding to the
specified unordered alleles.
|
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.
|
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 markerIndex) |
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.
|
Samples |
samples() |
Returns the list of samples.
|
java.lang.String |
toString() |
public BasicGT(Samples samples, GTRec[] vma)
BasicGT
instance.samples
- the list of samples with genotype datavma
- genotype emission probabilitiesjava.lang.IllegalArgumentException
- if elements of vma
corresponding to the same chromosome
are not contiguous and sorted in chromosome position orderjava.lang.IllegalArgumentException
- if any
two vma
elements correspond to the same genetic markerjava.lang.IllegalArgumentException
- if
vma[j].samples().equals(samples) == false
for any j
satisfying 0 <= j && j < vma.length
java.lang.NullPointerException
- if samples == null
java.lang.NullPointerException
- if vma == null
java.lang.NullPointerException
- if vma[j] == null
any j
satisfying 0 <= j && j < vma.length
public static int genotype(int a1, int a2)
a1
- the first allele index of an unordered genotypea2
- the second allele index of an unordered genotypejava.lang.IllegalArgumentException
- if a1 < 0 || a2 < 0
public boolean isPhased()
GT
true
if the genotype for each marker and sample
is a phased, non-missing genotype, and returns false
otherwise.public boolean isGTData()
GT
true
if the value returned by this.gl()
is
determined by a called or missing genotype, and returns false
otherwise.public boolean isPhased(int sample)
GT
true
if the genotype for each marker for the
specified sample is a phased, nonmissing genotype, and returns
false
otherwise.public float gl(int marker, int sample, int allele1, int allele2)
GT
gl
in interface GT
marker
- the marker indexsample
- the sample indexallele1
- the first allele indexallele2
- the second allele indexpublic boolean isPhased(int marker, int sample)
GT
true
if the genotype for the specified marker
and sample is a phased, nonmissing genotype, and returns false
otherwise.public int allele1(int marker, int sample)
GT
this.unphased(marker, sample) == false
.public int allele2(int marker, int sample)
GT
this.unphased(marker, sample) == false
.public int allele(int marker, int hap)
GT
this.unphased(marker, hap/2) == false
.public int nMarkers()
GT
public Marker marker(int markerIndex)
GT
public int nHaps()
GT
2*this.nSamples()
.public int nSamples()
GT
public java.lang.String toString()
toString
in class java.lang.Object