PhaseBaum1

java.lang.Object
- phase.PhaseBaum1

```
public class PhaseBaum1
extends java.lang.Object
```
Class PhaseBaum1 implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model. It evaluates probabilities of diplotypes in a window defined by two heterozygote genotypes.

Instances of class PhaseBaum1 are not thread-safe.

Constructor Summary

Constructors
Constructor Description

PhaseBaum1(PhaseData phaseData, PhaseIbs phaseIbs)
Creates a PhaseLSBaum instance from the specified data.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`phase(EstPhase estPhase, int sample, Regress recombRegress)`	Estimates and returns phased haploytpes for the specified sample

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

- Constructor Detail
  - PhaseBaum1
```
public PhaseBaum1(PhaseData phaseData,
                  PhaseIbs phaseIbs)
```
    Creates a PhaseLSBaum instance from the specified data. The contract for this class is unspecified if any element of the unphased AtomicReferenceArray is null.
    
    Parameters:
    
    phaseData - the input data for an iteration of genotype phasing
    
    phaseIbs - the IBS haplotype segments
    
    Throws:
    
    java.lang.IllegalArgumentException - if nItsRemaining < 1
    
    java.lang.NullPointerException - if any input parameter is null
- Method Detail
  - phase
```
public void phase(EstPhase estPhase,
                  int sample,
                  Regress recombRegress)
```
    Estimates and returns phased haploytpes for the specified sample
    
    Parameters:
    
    estPhase - the estimated sample phase
    
    sample - a sample index
    
    recombRegress - object for storing data points for regression of state-switch probability on inter-marker genetic distance or null if no regression is to be performed
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= samplePhase.gl().nSamples()