java.lang.Object
- picard.fingerprint.HaplotypeProbabilities
- - picard.fingerprint.HaplotypeProbabilitiesFromGenotype

```
public class HaplotypeProbabilitiesFromGenotype
extends HaplotypeProbabilities
```
Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.

Nested Class Summary
- Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities
  HaplotypeProbabilities.Genotype

Constructor Summary

Constructors
Constructor	Description
`HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype other)`
`HaplotypeProbabilitiesFromGenotype(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`HaplotypeProbabilitiesFromGenotype`	`deepCopy()`
`double[]`	`getLikelihoods()`	Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence
`Snp`	`getRepresentativeSnp()`	Returns the SNP who's genotype was used to construct the likelihoods.
`HaplotypeProbabilitiesFromGenotype`	`merge(HaplotypeProbabilities other)`	Merges in the likelihood information from the supplied haplotype probabilities object.

Methods inherited from class picard.fingerprint.HaplotypeProbabilities
getHaplotype, getLodMostProbableGenotype, getLogLikelihoods, getMostLikelyGenotype, getMostLikelyHaplotype, getObsAllele1, getObsAllele2, getPosteriorLikelihoods, getPosteriorProbabilities, getPriorProbablities, getTotalObs, hasEvidence, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies

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

- Constructor Detail
  - HaplotypeProbabilitiesFromGenotype
```
public HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype other)
```
  - HaplotypeProbabilitiesFromGenotype
```
public HaplotypeProbabilitiesFromGenotype(Snp snp,
                                          HaplotypeBlock haplotypeBlock,
                                          double AA,
                                          double Aa,
                                          double aa)
```
- Method Detail
  - deepCopy
```
public HaplotypeProbabilitiesFromGenotype deepCopy()
```
    Specified by:
    
    deepCopy in class HaplotypeProbabilities
  - getRepresentativeSnp
```
public Snp getRepresentativeSnp()
```
    Returns the SNP who's genotype was used to construct the likelihoods.
    
    Specified by:
    
    getRepresentativeSnp in class HaplotypeProbabilities
  - getLikelihoods
```
public double[] getLikelihoods()
```
    Description copied from class: HaplotypeProbabilities
    
    Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence
    Mathematically this is P(evidence | haplotype) where haplotype={AA,Aa,aa}. Will be normalized.
    
    Specified by:
    
    getLikelihoods in class HaplotypeProbabilities
  - merge
```
public HaplotypeProbabilitiesFromGenotype merge(HaplotypeProbabilities other)
```
    Description copied from class: HaplotypeProbabilities
    
    Merges in the likelihood information from the supplied haplotype probabilities object.
    
    Specified by:
    
    merge in class HaplotypeProbabilities

Class HaplotypeProbabilitiesFromGenotype

Nested Class Summary

Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities

Constructor Summary

Method Summary

Methods inherited from class picard.fingerprint.HaplotypeProbabilities

Methods inherited from class java.lang.Object

Constructor Detail

HaplotypeProbabilitiesFromGenotype

HaplotypeProbabilitiesFromGenotype

Method Detail

deepCopy

getRepresentativeSnp

getLikelihoods

merge