public class BasicAlleleProbs extends java.lang.Object implements AlleleProbs
Class BasicAlleleProbs
stores per-haplotype allele probabilities
for a list of samples.
Instances of class BasicAlleleProbs
are immutable.
Constructor and Description |
---|
BasicAlleleProbs(HapAlleleProbs[] alProbs)
Construct a new
BasicAlleleProbs instance from the specified
data. |
Modifier and Type | Method and Description |
---|---|
int |
allele1(int marker,
int sample)
Returns the marker allele with maximum probability for the
first haplotype of the specified sample.
|
int |
allele2(int marker,
int sample)
Returns the marker allele with maximum probability for the
second haplotype of the specified sample.
|
float |
alProb1(int marker,
int sample,
int allele)
Returns the probability that the specified marker allele is
present on the first haplotype of the specified sample.
|
float |
alProb2(int marker,
int sample,
int allele)
Returns the probability that the specified marker allele is
present on the second haplotype of the specified sample.
|
float |
gtProb(int marker,
int sample,
int allele1,
int allele2)
Returns the phased genotype probability, equal to
(this.allele1(marker, sample, allele1)
* this.allele2(marker, sample, allele2)) . |
Marker |
marker(int marker)
Returns the specified marker.
|
Markers |
markers()
Returns the list of markers.
|
int |
nMarkers()
Returns the number of markers.
|
int |
nSamples()
Returns the number of samples.
|
Samples |
samples()
Returns the list of samples.
|
public BasicAlleleProbs(HapAlleleProbs[] alProbs)
BasicAlleleProbs
instance from the specified
data.alProbs
- allele probabilities for each haplotypejava.lang.IllegalArgumentException
- if
alProbs[j].markers().equals(alProbs[k].markers) == false
for any j, k
satisfying
(0 <= j && j < k && k < alProbs.length)
java.lang.IllegalArgumentException
- if
alProbs[j].samples().equals(alProbs[k].samples) == false
for any j, k
satisfying
(0 <= j && j < k && k < alProbs.length)
java.lang.IllegalArgumentException
- if
alProbs.length == 0 || alProbs.length != alProbs[0].nMarkers()
java.lang.NullPointerException
- if
alProbs == null || alProbs[j] == null
for any j
satisfying
(0 <= j && j < alProbs.length)
public float alProb1(int marker, int sample, int allele)
AlleleProbs
alProb1
in interface AlleleProbs
marker
- a marker indexsample
- a sample indexallele
- an allele indexpublic float alProb2(int marker, int sample, int allele)
AlleleProbs
alProb2
in interface AlleleProbs
marker
- a marker indexsample
- a sample indexallele
- an allele indexpublic float gtProb(int marker, int sample, int allele1, int allele2)
AlleleProbs
(this.allele1(marker, sample, allele1)
* this.allele2(marker, sample, allele2))
.gtProb
in interface AlleleProbs
marker
- a marker indexsample
- a sample indexallele1
- allele index of the allele on the first haplotypeallele2
- allele index of the allele on the second haplotype(this.allele1(marker, sample, allele1)
* this.allele2(marker, sample, allele2))
public int allele1(int marker, int sample)
AlleleProbs
allele1
in interface AlleleProbs
marker
- a marker indexsample
- a sample indexpublic int allele2(int marker, int sample)
AlleleProbs
allele2
in interface AlleleProbs
marker
- a marker indexsample
- a sample indexpublic int nMarkers()
AlleleProbs
nMarkers
in interface AlleleProbs
public Markers markers()
AlleleProbs
markers
in interface AlleleProbs
public Marker marker(int marker)
AlleleProbs
marker
in interface AlleleProbs
marker
- a marker indexpublic int nSamples()
AlleleProbs
nSamples
in interface AlleleProbs
public Samples samples()
AlleleProbs
samples
in interface AlleleProbs