Constructor | Description |
---|---|
XBasicGT1(GT gl,
int sample) |
Constructs a
XBasicGL1 instance from the specified data. |
XBasicGT1(GT gt,
int sample,
int father,
int mother) |
Constructs a
XBasicGL1 instance from the specified data. |
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 a1,
int a2) |
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 markerIndex) |
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 . |
public XBasicGT1(GT gl, int sample)
XBasicGL1
instance from the specified data.gl
- the genotype likelihoodssample
- the sample indexjava.lang.IndexOutOfBoundsException
- if
samples < 0 || sample >= gl.nSamples()
java.lang.NullPointerException
- if gl == null
public XBasicGT1(GT gt, int sample, int father, int mother)
XBasicGL1
instance from the specified data.gt
- the genotype datasample
- the sample indexfather
- the sample index of the sample's father, or -1 if the
father is not genotypedmother
- the sample index of the sample's mother, or -1 if the
mother is not genotypedjava.lang.IndexOutOfBoundsException
- if
samples < 0 || sample >= gl.nSamples()
java.lang.NullPointerException
- if gl == null
public boolean isRefSample()
XGT1
true
if the observed data for each marker
includes a phased genotype that has no missing alleles,
and returns false
otherwise.isRefSample
in interface XGT1
true
if the observed data for each marker
includes a phased genotype that has no missing alleles,
and false
otherwisepublic float gl(int marker, int a1, int a2)
XGT1
public boolean isPhased(int marker)
XGT1
true
if the observed data for the specified
marker includes a phased genotype, and returns false
otherwise.public int allele1(int marker)
XGT1
public int allele2(int marker)
XGT1
public int nMarkers()
XGT1
public Marker marker(int markerIndex)
XGT1
public Markers markers()
XGT1
public int idIndex()
XGT1
public java.lang.String toString()
XGT1
this
. The exact
details of the representation are unspecified and subject to change.