All Known Subinterfaces:

RefGT

All Known Implementing Classes:

BasicGT, BasicRefGT, EstPhase.HapsGT, HapPairPhasedGT, SplicedGT, XBasicGT
```
public interface GT
```
Interface GT represents genotype data for a list of markers and a list of samples.

All instances of GT are required to be immutable.

Method Summary

All Methods Instance Methods Abstract Methods Default 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.
`default 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.
`default 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 marker)`	Returns the specified marker.
`Markers`	`markers()`	Returns the list of markers.
`default 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.

- Method Detail
  - nMarkers
```
int nMarkers()
```
    Returns the number of markers.
    
    Returns:
    
    the number of markers
  - markers
```
Markers markers()
```
    Returns the list of markers.
    
    Returns:
    
    the list of markers
  - marker
```
Marker marker(int marker)
```
    Returns the specified marker.
    
    Parameters:
    
    marker - a marker index
    
    Returns:
    
    the specified marker
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
  - nHaps
```
default int nHaps()
```
    Returns the number of haplotypes. The returned value is equal to 2*this.nSamples().
    
    Returns:
    
    the number of haplotypes
  - nSamples
```
int nSamples()
```
    Returns the number of samples.
    
    Returns:
    
    the number of samples
  - samples
```
Samples samples()
```
    Returns the list of samples.
    
    Returns:
    
    the list of samples
  - allele1
```
int allele1(int marker,
            int sample)
```
    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.
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    Returns:
    
    the first allele for the specified marker and sample
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - allele2
```
int allele2(int marker,
            int sample)
```
    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.
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    Returns:
    
    the allele for the specified marker and sample
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - allele
```
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. The two alleles for an individual are arbitrarily ordered if this.unphased(marker, hap/2) == false.
    
    Parameters:
    
    marker - the marker index
    
    hap - the haplotype index
    
    Returns:
    
    the allele on the specified haplotype for the specified marker
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
    
    java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.nHaps()
  - isPhased
```
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.
    
    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
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - isPhased
```
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.
    
    Parameters:
    
    sample - a sample index
    
    Returns:
    
    true if the genotype for each marker for the specified sample is a phased, nonmissing genotype
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - isPhased
```
boolean isPhased()
```
    Returns true if the genotype for each marker and sample is a phased, non-missing genotype, and returns false otherwise.
    
    Returns:
    
    true if the genotype for each marker and sample is a phased, non-missing genotype
  - isGTData
```
default boolean isGTData()
```
    Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.
    
    Returns:
    
    true if the value returned by this.gl() is determined by a called or missing genotype
  - gl
```
default 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.
    
    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
    
    Throws:
    
    java.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()

Interface GT

Method Summary

Method Detail

nMarkers

markers

marker

nHaps

nSamples

samples

allele1

allele2

allele

isPhased

isPhased

isPhased

isGTData

gl