java.lang.Object
- vcf.BasicGT

All Implemented Interfaces:

GT
```
public final class BasicGT
extends java.lang.Object
implements GT
```
Class BasicGT represents genotypes for a list of markers and samples.

Instances of class BasicGT are immutable

Constructor Summary

Constructors
Constructor	Description
`BasicGT(GTRec[] recs)`	Constructs a `BasicGT` instance from the specified data
`BasicGT(Markers markers, Samples samples, GTRec[] recs)`	Constructs a `BasicGT` instance from the specified data.
`BasicGT(Samples samples, GTRec[] recs)`	Constructs a `BasicGT` instance from the specified data

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.
`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 markerIndex)`	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.
`BasicGT`	`restrict(int start, int end)`	Returns a new `GT` instance restricted to genotype data for the specified markers.
`static BasicGT`	`restrict(BasicGT gt, int[] indices)`	Returns a `BasicGT` instance restricted to genotype data for the specified markers.
`BasicGT`	`restrict(Markers restrictedMarkers, int[] indices)`	Returns a `GT` instance restricted to genotype data for the specified markers.
`Samples`	`samples()`	Returns the list of samples.
`java.lang.String`	`toString()`	Returns a string representation of `this`.

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

- Constructor Detail
  - BasicGT
```
public BasicGT(GTRec[] recs)
```
    Constructs a BasicGT instance from the specified data
    
    Parameters:
    
    recs - genotype records for a list of markers
    
    Throws:
    
    java.lang.IllegalArgumentException - if elements of recs corresponding to the same chromosome are not contiguous and sorted in chromosome position order
    
    java.lang.IllegalArgumentException - if recs.length == 0
    
    java.lang.IllegalArgumentException - if any two elements of recs correspond to the same genetic marker
    
    java.lang.IllegalArgumentException - if (recs[j].samples().equals(recs[k].samples()) == false) for any j, k satisfying (0 <= j && j < k && j < recs.length)
    
    java.lang.NullPointerException - if recs == null
    
    java.lang.NullPointerException - if (recs[j] == null) any j satisfying (0 <= j && j < recs.length)
  - BasicGT
```
public BasicGT(Samples samples,
               GTRec[] recs)
```
    Constructs a BasicGT instance from the specified data
    
    Parameters:
    
    samples - the list of samples with genotype data
    
    recs - genotype records for a list of markers
    
    Throws:
    
    java.lang.IllegalArgumentException - if elements of recs corresponding to the same chromosome are not contiguous and sorted in chromosome position order
    
    java.lang.IllegalArgumentException - if any two elements of recs correspond to the same genetic marker
    
    java.lang.IllegalArgumentException - if (recs[j].samples().equals(samples) == false) for any j satisfying (0 <= j && j < recs.length)
    
    java.lang.NullPointerException - if samples == null || recs == null
    
    java.lang.NullPointerException - if (recs[j] == null) any j satisfying (0 <= j && j < recs.length)
  - BasicGT
```
public BasicGT(Markers markers,
               Samples samples,
               GTRec[] recs)
```
    Constructs a BasicGT instance from the specified data.
    
    Parameters:
    
    markers - the list of markers with genotype data
    
    samples - the list of samples with genotype data
    
    recs - the genotype data for each marker
    
    Throws:
    
    java.lang.IllegalArgumentException - if (recs[j].marker().equals(markers.marker(j)) == false) for any j satisfying (0 <= j && j < recs.length)
    
    java.lang.IllegalArgumentException - if (recs[j].samples().equals(samples) == false) for any j satisfying (0 <= j && j < recs.length)
    
    java.lang.NullPointerException - if (markers == null || samples == null || recs == null)
    
    java.lang.NullPointerException - if (recs[j] == null) any j satisfying (0 <= j && j < recs.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
  - isReversed
```
public boolean isReversed()
```
    Description copied from interface: GT
    
    Returns true if the markers are ordered by decreasing chromosome base position, and returns false otherwise.
    
    Specified by:
    
    isReversed in interface GT
    
    Returns:
    
    true if the markers are ordered by decreasing chromosome base position
  - 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 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())
    
    Specified by:
    
    markers in interface GT
    
    Returns:
    
    the list of markers in order of increasing chromosome position
  - 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
  - isPhased
```
public boolean isPhased()
```
    Description copied from interface: GT
    
    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.
    
    Specified by:
    
    isPhased in interface GT
    
    Returns:
    
    true if the genotype for each marker and sample is a phased, non-missing 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 order of the two alleles is unspecified if this.isPhased() == 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 order of the two alleles is unspecified if this.isPhased() == 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 order of the two alleles is unspecified if this.isPhased() == 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
  - restrict
```
public static BasicGT restrict(BasicGT gt,
                               int[] indices)
```
    Returns a BasicGT instance restricted to genotype data for the specified markers.
    
    Parameters:
    
    gt - the BasicGT instance to be restricted
    
    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] >= gt.nMarkers())
    
    java.lang.IllegalArgumentException - if there exists j such that (1 <= j && j < indices.length) such that (indices[j] <= indice[j - 1])
    
    java.lang.NullPointerException - if gt == null || indices == null
  - restrict
```
public BasicGT restrict(Markers restrictedMarkers,
                        int[] indices)
```
    Description copied from interface: GT
    
    Returns a GT instance restricted to genotype data for the specified markers.
    
    Specified by:
    
    restrict in interface GT
    
    Parameters:
    
    restrictedMarkers - 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
  - restrict
```
public BasicGT restrict(int start,
                        int end)
```
    Description copied from interface: GT
    
    Returns a new GT instance restricted to genotype data for the specified markers.
    
    Specified by:
    
    restrict in interface GT
    
    Parameters:
    
    start - the start marker (inclusive)
    
    end - the end marker (exclusive)
    
    Returns:
    
    a GT instance restricted to genotype data for the specified markers
  - toString
```
public java.lang.String toString()
```
    Returns a string representation of this. The exact details of the representation are unspecified and subject to change.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    a string representation of this

Class BasicGT

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BasicGT

BasicGT

BasicGT

Method Detail

genotype

isReversed

nMarkers

marker

markers

nHaps

nSamples

samples

isPhased

allele1

allele2

allele

restrict

restrict

restrict

toString