All Known Implementing Classes:

BasicGT, RefGT, RestrictedGT, SplicedGT, XRefGT
```
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 Static Methods Instance Methods Abstract 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 float`	`gl(GT gt, 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 unordered alleles is the true genotype.
`boolean`	`isPhased()`	Returns `true` if the genotype for each marker and sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns `false` otherwise.
`boolean`	`isReversed()`	Returns `true` if the markers are ordered by decreasing chromosome base position, and returns `false` otherwise.
`Marker`	`marker(int marker)`	Returns the specified marker.
`Markers`	`markers()`	Returns the list of markers in order of increasing chromosome position.
`int`	`nHaps()`	Returns the number of haplotypes.
`int`	`nMarkers()`	Returns the number of markers.
`int`	`nSamples()`	Returns the number of samples.
`GT`	`restrict(int start, int end)`	Returns a new `GT` instance restricted to genotype data for the specified markers.
`GT`	`restrict(Markers markers, int[] indices)`	Returns a `GT` instance restricted to genotype data for the specified markers.
`Samples`	`samples()`	Returns the list of samples.

- Method Detail
  - isReversed
```
boolean isReversed()
```
    Returns true if the markers are ordered by decreasing chromosome base position, and returns false otherwise.
    
    Returns:
    
    true if the markers are ordered by decreasing chromosome base position
  - nMarkers
```
int nMarkers()
```
    Returns the number of markers.
    
    Returns:
    
    the number 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()
  - markers
```
Markers markers()
```
    Returns the list of markers in order of increasing chromosome position. If (this.isReversed() == false) then (this.markers().marker(j).equals(this.marker(j)) == true) for all (0 <= j && j < this.nMarkers()). If (this.isReversed() == true) then (this.markers().marker(this.nMarkers() - 1 - j).equals(this.marker(j)) == true) for all (0 <= j && j < this.nMarkers())
    
    Returns:
    
    the list of markers in order of increasing chromosome position
  - nHaps
```
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
  - isPhased
```
boolean isPhased()
```
    Returns true if the genotype for each marker and sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns false otherwise.
    
    Returns:
    
    true if the genotype for each marker and sample is a phased, non-missing genotype
  - 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 order of the two alleles is unspecified if this.isPhased() == 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 order of the two alleles is unspecified if this.isPhased() == 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 order of the two alleles is unspecified if this.isPhased() == 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()
  - restrict
```
GT restrict(Markers markers,
            int[] indices)
```
    Returns a GT instance restricted to genotype data for the specified markers.
    
    Parameters:
    
    markers - the list of markers in the returned instance
    
    indices - a list of distinct marker indices (from this.markers()) in increasing order
    
    Returns:
    
    a GT instance restricted to genotype data for the specified markers
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if there exists j such that (0 <= j && j < indices.length) such that (indices[j] < 0 || indices[j] >= this.nMarkers())
    
    java.lang.IllegalArgumentException - if there exists j such that (1 <= j && j < indices.length) such that (indices[j] <= indice[j - 1])
    
    java.lang.IllegalArgumentException - if there exists j such that (0 <= j && j < indices.length) such that (this.marker(indices[j]).equals(markers.marker(j)) == false)
    
    java.lang.NullPointerException - if indices == null
    
    java.lang.UnsupportedOperationException - if this.isReversed() == true
  - restrict
```
GT restrict(int start,
            int end)
```
    Returns a new GT instance restricted to genotype data for the specified markers.
    
    Parameters:
    
    start - the start marker (inclusive)
    
    end - the end marker (exclusive)
    
    Returns:
    
    a GT instance restricted to genotype data for the specified markers
    
    Throws:
    
    java.lang.IllegalArgumentException - if start >= end
    
    java.lang.IndexOutOfBoundsException - if start < 0 || end > this.markers()
  - gl
```
static float gl(GT gt,
                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 unordered alleles is the true genotype. Returns 1.0f if the corresponding genotype determined by the isPhased(), allele1(), and allele2() methods is consistent with the specified ordered genotype, and returns 0.0f otherwise.
    
    Parameters:
    
    gt - the genotype data
    
    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

isReversed

nMarkers

marker

markers

nHaps

nSamples

samples

isPhased

allele1

allele2

allele

restrict

restrict

gl