public interface AL
Interface AL
(Allele Likelihoods) represents allele
likelihoods for a set of haplotypes.
AL
are required to be immutable.Modifier and Type | Method and Description |
---|---|
float |
al(int marker,
int haplotype,
int allele)
Returns the probability of the observed data if the specified allele
is the true allele for the specified marker and haplotype.
|
int |
allele(int marker,
int haplotype)
Returns the allele on the specified haplotype if the allele
emission probabilities are determined by a called allele, and
returns -1 otherwise.
|
float |
errProb()
Returns the allelic error probability.
|
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.
|
Samples |
samples()
Returns the list of samples.
|
java.lang.String |
toString()
Returns a string representation of
this . |
float al(int marker, int haplotype, int allele)
marker
- a marker indexhaplotype
- a haplotype indexallele
- a allele indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
haplotype < 0 || haplotype >= this.nHaps()
java.lang.IndexOutOfBoundsException
- if
allele < 0 || allele >= this.marker(marker).nAlleles()
int allele(int marker, int haplotype)
marker
- a marker indexhaplotype
- a haplotype indexjava.lang.IndexOutOfBoundsException
- if
hap < 0 || hap >= this.nHaps()
int nMarkers()
Marker marker(int marker)
marker
- the marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
Markers markers()
int nSamples()
Samples samples()
int nHaps()
float errProb()
java.lang.String toString()
this
. The exact
details of the representation are unspecified and subject to change.toString
in class java.lang.Object
this