BasicGT

java.lang.Object
- vcf.BasicGT

All Implemented Interfaces:

GT
```
public final class BasicGT
extends java.lang.Object
implements GT
```
Class BasicGT represents genotype emission probabilities for a set of samples.
Instances of class BasicGT are immutable.

Constructor Summary

Constructors
Constructor Description

BasicGT(Samples samples, GTRec[] vma)
Constructs a BasicGT instance.

Constructors
Constructor	Description
`BasicGT(Samples samples, GTRec[] vma)`	Constructs a `BasicGT` instance.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`allele(int marker, int hap)`	Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing.
`int`	`allele1(int marker, int sample)`	Returns the first allele for the specified marker and sample or return -1 if the allele is missing.
`int`	`allele2(int marker, int sample)`	Returns the second allele for the specified marker and sample or return -1 if the allele is missing.
`static int`	`genotype(int a1, int a2)`	Returns the genotype index corresponding to the specified unordered alleles.
`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`	`isGTData()`	Returns `true` if the value returned by `this.gl()` is determined by a called or missing genotype, and returns `false` otherwise.
`boolean`	`isPhased()`	Returns `true` if the genotype for each marker and sample is a phased, non-missing genotype, and returns `false` otherwise.
`boolean`	`isPhased(int sample)`	Returns `true` if the genotype for each marker for the specified sample is a phased, nonmissing genotype, and returns `false` otherwise.
`boolean`	`isPhased(int marker, int sample)`	Returns `true` if the genotype for the specified marker and sample is a phased, nonmissing genotype, and returns `false` otherwise.
`Marker`	`marker(int markerIndex)`	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()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - BasicGT
```
public BasicGT(Samples samples,
               GTRec[] vma)
```
    Constructs a BasicGT instance.
    
    Parameters:
    
    samples - the list of samples with genotype data
    
    vma - genotype emission probabilities
    
    Throws:
    
    java.lang.IllegalArgumentException - if elements of vma corresponding to the same chromosome are not contiguous and sorted in chromosome position order
    
    java.lang.IllegalArgumentException - if any two vma elements correspond to the same genetic marker
    
    java.lang.IllegalArgumentException - if vma[j].samples().equals(samples) == false for any j satisfying 0 <= j && j < vma.length
    
    java.lang.NullPointerException - if samples == null
    
    java.lang.NullPointerException - if vma == null
    
    java.lang.NullPointerException - if vma[j] == null any j satisfying 0 <= j && j < vma.length
- Method Detail
  - genotype
```
public static int genotype(int a1,
                           int a2)
```
    Returns the genotype index corresponding to the specified unordered alleles.
    
    Parameters:
    
    a1 - the first allele index of an unordered genotype
    
    a2 - the second allele index of an unordered genotype
    
    Returns:
    
    the genotype index corresponding to the specified unordered alleles
    
    Throws:
    
    java.lang.IllegalArgumentException - if a1 < 0 || a2 < 0
  - isPhased
```
public boolean isPhased()
```
    Description copied from interface: GT
    
    Returns true if the genotype for each marker and sample is a phased, non-missing genotype, and returns false otherwise.
    
    Specified by:
    
    isPhased in interface GT
    
    Returns:
    
    true if the genotype for each marker and sample is a phased, non-missing genotype
  - isGTData
```
public boolean isGTData()
```
    Description copied from interface: GT
    
    Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.
    
    Specified by:
    
    isGTData in interface GT
    
    Returns:
    
    true if the value returned by this.gl() is determined by a called or missing genotype
  - isPhased
```
public boolean isPhased(int sample)
```
    Description copied from interface: GT
    
    Returns true if the genotype for each marker for the specified sample is a phased, nonmissing genotype, and returns false otherwise.
    
    Specified by:
    
    isPhased in interface GT
    
    Parameters:
    
    sample - a sample index
    
    Returns:
    
    true if the genotype for each marker for the specified sample is a phased, nonmissing genotype
  - gl
```
public float gl(int marker,
                int sample,
                int allele1,
                int allele2)
```
    Description copied from interface: GT
    
    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.
    
    Specified by:
    
    gl in interface GT
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    allele1 - the first allele index
    
    allele2 - the second allele index
    
    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
  - isPhased
```
public boolean isPhased(int marker,
                        int sample)
```
    Description copied from interface: GT
    
    Returns true if the genotype for the specified marker and sample is a phased, nonmissing genotype, and returns false otherwise.
    
    Specified by:
    
    isPhased in interface GT
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    Returns:
    
    true if the genotype for the specified marker and sample is a phased, nonmissing genotype
  - allele1
```
public int allele1(int marker,
                   int sample)
```
    Description copied from interface: GT
    
    Returns the first allele for the specified marker and sample or return -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.
    
    Specified by:
    
    allele1 in interface GT
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    Returns:
    
    the first allele for the specified marker and sample
  - allele2
```
public int allele2(int marker,
                   int sample)
```
    Description copied from interface: GT
    
    Returns the second allele for the specified marker and sample or return -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.
    
    Specified by:
    
    allele2 in interface GT
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    Returns:
    
    the allele for the specified marker and sample
  - allele
```
public int allele(int marker,
                  int hap)
```
    Description copied from interface: GT
    
    Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing. The two alleles for an individual are arbitrarily ordered if this.unphased(marker, hap/2) == false.
    
    Specified by:
    
    allele in interface GT
    
    Parameters:
    
    marker - the marker index
    
    hap - the haplotype index
    
    Returns:
    
    the allele on the specified haplotype for the specified marker
  - nMarkers
```
public int nMarkers()
```
    Description copied from interface: GT
    
    Returns the number of markers.
    
    Specified by:
    
    nMarkers in interface GT
    
    Returns:
    
    the number of markers
  - marker
```
public Marker marker(int markerIndex)
```
    Description copied from interface: GT
    
    Returns the specified marker.
    
    Specified by:
    
    marker in interface GT
    
    Parameters:
    
    markerIndex - a marker index
    
    Returns:
    
    the specified marker
  - markers
```
public Markers markers()
```
    Description copied from interface: GT
    
    Returns the list of markers.
    
    Specified by:
    
    markers in interface GT
    
    Returns:
    
    the list of markers
  - nHaps
```
public int nHaps()
```
    Description copied from interface: GT
    
    Returns the number of haplotypes. The returned value is equal to 2*this.nSamples().
    
    Specified by:
    
    nHaps in interface GT
    
    Returns:
    
    the number of haplotypes
  - nSamples
```
public int nSamples()
```
    Description copied from interface: GT
    
    Returns the number of samples.
    
    Specified by:
    
    nSamples in interface GT
    
    Returns:
    
    the number of samples
  - samples
```
public Samples samples()
```
    Description copied from interface: GT
    
    Returns the list of samples.
    
    Specified by:
    
    samples in interface GT
    
    Returns:
    
    the list of samples
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object

Class BasicGT

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BasicGT

Method Detail

genotype

isPhased

isGTData

isPhased

gl

isPhased

allele1

allele2

allele

nMarkers

marker

markers

nHaps

nSamples

samples

toString