java.lang.Object
- phase.EstPhase

```
public final class EstPhase
extends java.lang.Object
```
Class EstPhase stores haplotype pairs, missing genotypes, and unphased, nonmissing heteroygote genotypes for a list of samples.

Instances of class EstPhase are thread-safe.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

class EstPhase.HapsGT

Constructor Summary

Constructors
Constructor Description

EstPhase(GT gt, java.util.List<LongArray> haps)
Constructs a new EstPhase instance from the specified data.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`IntArray`	`getMissing(int sample)`	Returns a list of marker indices in increasing order for which the specified sample has a missing genotype.
`void`	`getMissing(int sample, boolean[] isMissing)`	Sets the `k`-th entry of the specified `isMissing` array to `true` if the specified sample's genotype at the `k`-th marker is missing, and to `false` otherwise.
`IntArray`	`getUnphasedHets(int sample)`	Returns a list of marker indices in increasing order for which the specified sample has an unphased, non-missing heterozygote genotype.
`void`	`getUnphasedHets(int sample, boolean[] isUnphased)`	Sets the `k`-th entry of the specified `isUnphased` array to `true` if the specified sample's genotype at the `k`-th marker is an unphased, nonmissing heterozygote, and to `false` otherwise.
`EstPhase.HapsGT`	`hapsGT()`
`boolean`	`hasMissingGT(int sample)`	Returns `true` if the specified sample has a missing genotype, and returns `false` otherwise.
`boolean`	`hasUnphasedHets(int sample)`	Returns `true` if the specified sample has an unphased heterozygote genotype, and returns `false` otherwise.
`Markers`	`markers()`	Returns the list of markers.
`int`	`nMarkers()`	Returns the number of markers.
`int`	`nSamples()`	Returns the number of samples.
`int`	`nUnphasedHets(int sample)`	Returns the number of unphased, non-missing heterozygote genotypes.
`Samples`	`samples()`	Returns the list of target samples.
`void`	`setHapPair(int sample, int[] hap1, int[] hap2)`	Sets the haplotype pair for the specified sample to the specified haplotypes.
`void`	`setHapsWithMaskedMissingAlleles(int sample, int[] hap1, int[] hap2)`	Sets the `k`-th element of the specified `hap1` and `hap2` arrays to the specified sample's phased genotype at the `k`-th marker if the genotype is nonmissing, and sets the `k`-th element of `hap1` and `hap2` to `-1` otherwise.
`void`	`setUnphasedHets(int sample, IntArray newUnphased)`	Sets the array with marker indices of unphased, nonmissing heterozygote genotypes to the specified array.

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

- Constructor Detail
  - EstPhase
```
public EstPhase(GT gt,
                java.util.List<LongArray> haps)
```
    Constructs a new EstPhase instance from the specified data. The haplotypes for the k-th sample must be stored in entries haps.get(2*k} and haps.get(2*k + 1)
    
    Parameters:
    
    gt - the observed genotype data
    
    haps - the initial haplotypes for each sample
    
    Throws:
    
    java.lang.IllegalArgumentException - if gt.nSamples() != hapPairs.nSamples()
    
    java.lang.IllegalArgumentException - if (hapPairs.get(s).idIndex!= this.gt().samples().idIndex(s)) for any s satisfying (0 <= s && s < gt.nSamples())
    
    java.lang.NullPointerException - if gt == null || hapPairs == null
    
    java.lang.NullPointerException - if (hapPairs.get(j) == null) for any j satisfying (0 <= j && j < hapPairs.size())
- Method Detail
  - nSamples
```
public int nSamples()
```
    Returns the number of samples.
    
    Returns:
    
    the number of samples
  - samples
```
public Samples samples()
```
    Returns the list of target samples.
    
    Returns:
    
    the list of target samples
  - nMarkers
```
public int nMarkers()
```
    Returns the number of markers.
    
    Returns:
    
    the number of markers
  - markers
```
public Markers markers()
```
    Returns the list of markers.
    
    Returns:
    
    the list of markers
  - hasUnphasedHets
```
public boolean hasUnphasedHets(int sample)
```
    Returns true if the specified sample has an unphased heterozygote genotype, and returns false otherwise.
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    true if the specified sample has an unphased heterozygote genotype
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - nUnphasedHets
```
public int nUnphasedHets(int sample)
```
    Returns the number of unphased, non-missing heterozygote genotypes.
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    the number of unphased, non-missing heterozygote genotypes
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - getUnphasedHets
```
public IntArray getUnphasedHets(int sample)
```
    Returns a list of marker indices in increasing order for which the specified sample has an unphased, non-missing heterozygote genotype.
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    a list of marker indices in increasing order for which the specified sample has an unphased heterozygote genotype
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - setUnphasedHets
```
public void setUnphasedHets(int sample,
                            IntArray newUnphased)
```
    Sets the array with marker indices of unphased, nonmissing heterozygote genotypes to the specified array.
    
    Parameters:
    
    sample - the sample index
    
    newUnphased - the marker indices of unphased heterozygote genotypes
    
    Throws:
    
    java.lang.IllegalArgumentException - if the specified newUnphased list is not sorted in increasing order, contains a duplicate elements, or is not a subset of this.getUnphased(sample).
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
    
    java.lang.NullPointerException - if newUnphased == null
  - setHapPair
```
public void setHapPair(int sample,
                       int[] hap1,
                       int[] hap2)
```
    Sets the haplotype pair for the specified sample to the specified haplotypes.
    
    Parameters:
    
    sample - the sample index
    
    hap1 - an array whose k-th entry is the estimated allele carried by the sample's first haplotype.
    
    hap2 - an array whose k-th entry is the estimated allele carried by the sample's second haplotype.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
    
    java.lang.IllegalArgumentException - if hap1.length != this.nMarkers() || hap2.length != this.nMarkers()
    
    java.lang.IllegalArgumentException - if (hap1[k] < 0 || hap1[k] >= this.markers().marker(k).nAlleles()) for any k satisfying (0 <= k && k < this.nMarkers())
    
    java.lang.IllegalArgumentException - if (hap2[k] < 0 || hap2[k] >= this.markers().marker(k).nAlleles()) for any k satisfying (0 <= k && k < this.nMarkers())
    
    java.lang.NullPointerException - if hap1 == null || hap2 == null
  - getUnphasedHets
```
public void getUnphasedHets(int sample,
                            boolean[] isUnphased)
```
    Sets the k-th entry of the specified isUnphased array to true if the specified sample's genotype at the k-th marker is an unphased, nonmissing heterozygote, and to false otherwise.
    
    Parameters:
    
    sample - the sample index
    
    isUnphased - an array whose k-th entry will be set to true if the specified sample's genotype at the k-th marker is an unphased, nonmissing heterozygote, and to false otherwise.
    
    Throws:
    
    java.lang.IllegalArgumentException - if isUnphased.length != this.nMarkers()
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
    
    java.lang.NullPointerException - if isUnphased == null
  - hasMissingGT
```
public boolean hasMissingGT(int sample)
```
    Returns true if the specified sample has a missing genotype, and returns false otherwise.
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    true if the specified sample has a missing genotype
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - getMissing
```
public IntArray getMissing(int sample)
```
    Returns a list of marker indices in increasing order for which the specified sample has a missing genotype.
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    a list of marker indices in increasing order for which the specified sample has a missing genotype
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - getMissing
```
public void getMissing(int sample,
                       boolean[] isMissing)
```
    Sets the k-th entry of the specified isMissing array to true if the specified sample's genotype at the k-th marker is missing, and to false otherwise.
    
    Parameters:
    
    sample - the sample index
    
    isMissing - an array whose k-th entry will be set to true if the specified sample's genotype at the k-th marker is missing and to false otherwise
    
    Throws:
    
    java.lang.IllegalArgumentException - if isMissing.length != this.nMarkers()
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
    
    java.lang.NullPointerException - if isMissing == null
  - setHapsWithMaskedMissingAlleles
```
public void setHapsWithMaskedMissingAlleles(int sample,
                                            int[] hap1,
                                            int[] hap2)
```
    Sets the k-th element of the specified hap1 and hap2 arrays to the specified sample's phased genotype at the k-th marker if the genotype is nonmissing, and sets the k-th element of hap1 and hap2 to -1 otherwise.
    
    Parameters:
    
    sample - the sample index
    
    hap1 - an array whose k-th entry will be set to the current estimated allele carried by the sample's first haplotype if the observed genotype is non-missing and to -1 otherwise.
    
    hap2 - an array whose k-th entry will be set to the current estimated allele carried by the sample's second haplotype if the observed genotype is non-missing and to -1 otherwise.
    
    Throws:
    
    java.lang.IllegalArgumentException - if hap1.length != this.nMarkers()
    
    java.lang.IllegalArgumentException - if hap2.length != this.nMarkers()
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
    
    java.lang.NullPointerException - if hap1 == null || hap2 == null
  - hapsGT
```
public EstPhase.HapsGT hapsGT()
```

Class EstPhase

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

EstPhase

Method Detail

nSamples

samples

nMarkers

markers

hasUnphasedHets

nUnphasedHets

getUnphasedHets

setUnphasedHets

setHapPair

getUnphasedHets

hasMissingGT

getMissing

getMissing

setHapsWithMaskedMissingAlleles

hapsGT