public final class MaskedEndsGL extends java.lang.Object implements GL
Class MaskedEndsGL
is a wrapper for a GL
instance that masks the genotype emission probabilities for a
user-specified number of starting and ending markers. The gl()
,
allele1()
, and allele2()
methods return
1.0f
, -1
, and -1
respectively if a genotype
emission probability for a marker is masked.
Instances of class MaskedEndsGL
are immutable.
Constructor and Description |
---|
MaskedEndsGL(GL gl,
int start,
int end)
Constructs a new
MaskedEndsGL instance. |
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 . |
public MaskedEndsGL(GL gl, int start, int end)
MaskedEndsGL
instance.gl
- genotype emission probabilities for all markersstart
- the starting marker index (inclusive) of the markers
whose genotype emission probabilities are not maskedend
- the ending marker index (exclusive) of the markers
whose genotype emission probabilities are not maskedjava.lang.IllegalArgumentException
- if
start < 0 || start > end || end > gl.nMarkers()
java.lang.NullPointerException
- if gl == null
public boolean isRefData()
GL
true
if the observed data for each marker and sample
includes a phased genotype that has no missing alleles,
and returns false
otherwise.public float gl(int marker, int sample, int allele1, int allele2)
GL
gl
in interface GL
marker
- the marker indexsample
- the sample indexallele1
- the first allele indexallele2
- the second allele indexpublic boolean isPhased(int marker, int sample)
GL
true
if the observed data for the specified
marker and sample includes a phased genotype, and returns false
otherwise.public int allele1(int marker, int sample)
GL
public int allele2(int marker, int sample)
GL
public int allele(int marker, int hap)
GL
public Marker marker(int marker)
GL
public int nMarkers()
GL
public int nHaps()
GL
public int nSamples()
GL
public java.lang.String toString()
GL
this
. The exact
details of the representation are unspecified and subject to change.