java.lang.Object
- vcf.XRefGT

All Implemented Interfaces:

GT
```
public final class XRefGT
extends java.lang.Object
implements GT
```
Class XRefGT represents phased, non-missing genotypes for a list of samples that are stored in column-major (i.e. haplotype-major) order.

Instances of class XRefGT are immutable.

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 XRefGT`	`combine(XRefGT first, XRefGT second)`	Returns a new `XRefGT` instance from the specified data.
`void`	`copyTo(int hap, int start, int end, BitArray bitList)`	Copies the specified bit sequence to the specified `bitList`
`static XRefGT`	`from(Markers markers, Samples samples, BitArray[] haps)`	Returns a new `XRefGT` instance from the specified data.
`static XRefGT`	`from(Samples samples, java.util.concurrent.atomic.AtomicReferenceArray<SamplePhase> phase)`	Returns a new `XRefGT` instance from the specified data.
`static XRefGT`	`fromPhasedGT(GT gt, int nThreads)`	Returns a new `XRefGT` instance from the specified data.
`int`	`hash(int hap, int start, int end)`	Returns a hash code for the specified 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.
`XRefGT`	`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.
`BitArray[]`	`toBitLists(int nThreads)`	Returns the phased, non-missing genotypes as a `BitArray[]`.
`java.lang.String`	`toString()`

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

- Method Detail
  - combine
```
public static XRefGT combine(XRefGT first,
                             XRefGT second)
```
    Returns a new XRefGT instance from the specified data. The order of samples and haplotypes is preserved. Samples in the first XRefGT parameter are placed before samples in the second XRefGT parameter in the returned XRefGT instance.
    
    Parameters:
    
    first - phased genotype data for a list of samples
    
    second - phased genotype data for a list of samples
    
    Returns:
    
    a new XRefGT instance
    
    Throws:
    
    java.lang.NullPointerException - if first == null || second == null
    
    java.lang.IllegalArgumentException - if the lists of samples in the two specified XRefGT parameters are not disjoint
    
    java.lang.IllegalArgumentException - if first.markers().equals(second.markers()) == false
  - from
```
public static XRefGT from(Markers markers,
                          Samples samples,
                          BitArray[] haps)
```
    Returns a new XRefGT instance from the specified data. The specified haplotypes will be copied, and the returned XRefGT instance will not contain a reference to the specified haplotypes.
    
    Parameters:
    
    markers - the list of markers
    
    samples - the list of samples
    
    haps - the list of haplotypes corresponding to the list of samples
    
    Returns:
    
    a newXRefGT instance
    
    Throws:
    
    java.lang.IllegalArgumentException - if there exists (0 <= j && j < haps.length) such that (haps[j].size() != markers.sumHaplotypeBits())
    
    java.lang.IllegalArgumentException - if 2*samples.size() != haps.length
    
    java.lang.NullPointerException - if markers == null || samples == null || haps == null
  - from
```
public static XRefGT from(Samples samples,
                          java.util.concurrent.atomic.AtomicReferenceArray<SamplePhase> phase)
```
    Returns a new XRefGT instance from the specified data.
    
    Parameters:
    
    samples - the list of samples
    
    phase - the phased genotypes
    
    Returns:
    
    a new XRefGT instance
    
    Throws:
    
    java.lang.IllegalArgumentException - if phase.length()==0 || samples.size() != phase.length()
    
    java.lang.IllegalArgumentException - if if there exists j such that (0 <= j && j < phase.length() && phase.get(j).markers().equals(phase.get(j).markers())==false
    
    java.lang.NullPointerException - if samples == null || phase == null
    
    java.lang.NullPointerException - if there exists j such that (0 <= j && j < phase.length() && phase.get(j) == null)
  - toBitLists
```
public BitArray[] toBitLists(int nThreads)
```
    Returns the phased, non-missing genotypes as a BitArray[].
    
    Parameters:
    
    nThreads - the maximum number of computational threads for object construction
    
    Returns:
    
    the phased, non-missing genotypes as a BitArray[]
    
    Throws:
    
    java.lang.IllegalArgumentException - if nThreads < 1
  - fromPhasedGT
```
public static XRefGT fromPhasedGT(GT gt,
                                  int nThreads)
```
    Returns a new XRefGT instance from the specified data. The returned XRefGT instance will represent the same genotypes, the same list of markers, and same list of samples as the specified genotype data,
    
    Parameters:
    
    gt - phased, nonmissing genotype data
    
    nThreads - the maximum number of computational threads for object construction
    
    Returns:
    
    an XRefGT instance
    
    Throws:
    
    java.lang.IllegalArgumentException - if gt.isPhased() == false
    
    java.lang.IllegalArgumentException - if nThreads < 1
    
    java.lang.NullPointerException - if refGT == null
  - hash
```
public int hash(int hap,
                int start,
                int end)
```
    Returns a hash code for the specified alleles.
    
    Parameters:
    
    hap - a haplotype
    
    start - the first marker (inclusive)
    
    end - the last marker (exclusive)
    
    Returns:
    
    a hash code for the specified alleles
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.nHaps()
    
    java.lang.IndexOutOfBoundsException - if start < 0 || start > to || end >= this.nMarkers()
  - 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 GT restrict(Markers markers,
                   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:
    
    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
  - restrict
```
public XRefGT 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
  - copyTo
```
public void copyTo(int hap,
                   int start,
                   int end,
                   BitArray bitList)
```
    Copies the specified bit sequence to the specified bitList
    
    Parameters:
    
    hap - the haplotype index
    
    start - the start marker
    
    end - the end marker
    
    bitList - the destination bitList
    
    Throws:
    
    java.lang.IllegalArgumentException - if start > end
    
    java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.nHaps()
    
    java.lang.IndexOutOfBoundsException - if start < 0 || end > this.markers()
    
    java.lang.IndexOutOfBoundsException - if end <= this.markers() && bitList.size() < this.markers().sumHaplotypeBits(end)
    
    java.lang.NullPointerException - if bitList == null
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object

Class XRefGT

Method Summary

Methods inherited from class java.lang.Object

Method Detail

combine

from

from

toBitLists

fromPhasedGT

hash

isReversed

nMarkers

marker

markers

nHaps

nSamples

samples

isPhased

allele1

allele2

allele

restrict

restrict

copyTo

toString