Modifier and Type | Method and Description |
---|---|
int |
allele(int marker,
int hap)
Returns the allele on the specified haplotype for the specified marker
if the observed data include a non-missing allele, and returns
-1 otherwise.
|
int |
allele1(int marker,
int sample)
Returns the first allele for the specified marker and sample
if the observed data include a non-missing allele, and returns -1
otherwise.
|
int |
allele2(int marker,
int sample)
Returns the second allele for the specified marker and sample
if the observed data include a non-missing allele, and
returns -1 otherwise.
|
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 |
isPhased(int marker,
int sample)
Returns
true if the observed data for the specified
marker and sample includes a phased genotype, and returns false
otherwise. |
boolean |
isRefData()
Returns
true if the observed data for each marker and sample
includes a phased genotype that has no missing alleles,
and returns false 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.
|
Samples |
samples()
Returns the list of samples.
|
java.lang.String |
toString()
Returns a string representation of
this . |
boolean isRefData()
true
if the observed data for each marker and sample
includes a phased genotype that has no missing alleles,
and returns false
otherwise.true
if the observed data for each marker and sample
includes a phased genotype that has no missing alleles,
and false
otherwisefloat 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()
boolean isPhased(int marker, int sample)
true
if the observed data for the specified
marker and sample includes a phased genotype, and returns false
otherwise.marker
- the marker indexsample
- the sample indextrue
if the observed data for the specified
marker and sample includes a phased genotype, and false
otherwisejava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
sample < 0 || samples >= this.nSamples()
int allele1(int marker, int sample)
marker
- the marker indexsample
- the sample indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
sample < 0 || samples >= this.nSamples()
int allele2(int marker, int sample)
marker
- the marker indexsample
- the sample indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- if
sample < 0 || samples >= this.nSamples()
int allele(int marker, int hap)
marker
- the marker indexhap
- the haplotype indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
java.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 nHaps()
int nSamples()
Samples samples()
java.lang.String toString()
this
. The exact
details of the representation are unspecified and subject to change.toString
in class java.lang.Object
this