XBasicGT1
public interface XGT1
Interface XGT1
(Genotype Likelihoods) represents genotype
likelihoods for one sample.
Instances of XGT1
are required to be immutable.
Modifier and Type | Method | Description |
---|---|---|
int |
allele1(int marker) |
Returns the first allele for the specified marker if the observed data
include a non-missing allele, and returns -1 otherwise.
|
int |
allele2(int marker) |
Returns the second allele for the specified marker if the observed data
include a non-missing allele, and returns -1 otherwise.
|
float |
gl(int marker,
int allele1,
int allele2) |
Returns the probability of the observed data for the specified marker
if the specified pair of ordered alleles is the true ordered genotype.
|
int |
idIndex() |
Returns the sample identifier index.
|
boolean |
isPhased(int marker) |
Returns
true if the observed data for the specified
marker includes a phased genotype, and returns false otherwise. |
boolean |
isRefSample() |
Returns
true if the observed data for each marker
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 |
nMarkers() |
Returns the number of markers.
|
java.lang.String |
toString() |
Returns a string representation of
this . |
boolean isRefSample()
true
if the observed data for each marker
includes a phased genotype that has no missing alleles,
and returns false
otherwise.true
if the observed data for each marker
includes a phased genotype that has no missing alleles,
and false
otherwisefloat gl(int marker, int allele1, int allele2)
marker
- the marker indexallele1
- the first allele indexallele2
- the second allele indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
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)
true
if the observed data for the specified
marker includes a phased genotype, and returns false
otherwise.marker
- the marker indextrue
if the observed data for the specified
marker includes a phased genotype, and false
otherwisejava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
int allele1(int marker)
marker
- the marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
int allele2(int marker)
marker
- the marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
int nMarkers()
Marker marker(int marker)
marker
- the marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
Markers markers()
int idIndex()
java.lang.String toString()
this
. The exact
details of the representation are unspecified and subject to change.toString
in class java.lang.Object
this