sample

Class SamplerData

java.lang.Object

sample.SamplerData

public class SamplerData
extends java.lang.Object

Class SamplerData contains immutable input data for the current marker window.

Instances of class SamplerData are immutable.

Constructor Summary

Constructors

Constructor and Description
SamplerData(Par par, CurrentData cd, java.util.List<HapPair> hapPairs, boolean revMarkers, RunStats runStats) Constructs a new SamplerData instance from the specified data.

Method Summary

Modifier and Type	Method and Description
float	err() Returns the allele error rate
GL	gl() Returns the genotype likelihoods for the target samples at the target data markers.
Markers	markers() returns the list of markers.
boolean	markersAreReversed() Returns true if the order of markers is reversed, and false otherwise
int	nHaps() Returns the number of haplotypes.
int	nMarkers() Returns the number of markers.
int	nSamples() Returns the number of samples.
Par	par() Returns the analysis parameters.
float	pRecomb(int marker) Returns the probability of recombination between (marker - 1) and marker.
RestrictedDag	rdag() Returns the DAG model.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SamplerData

public SamplerData(Par par,
                   CurrentData cd,
                   java.util.List<HapPair> hapPairs,
                   boolean revMarkers,
                   RunStats runStats)

Constructs a new SamplerData instance from the specified data. The contract for this method is undefined if the specified hapPairs is inconsistent with the input data contained in the cd parameter.

Parameters:

par - the analysis parameters

cd - the input data for the current marker window

hapPairs - the target haplotype pairs used to build the haplotype frequency model

revMarkers - true if the order of markers should be reversed when building the haplotype frequency model, and false otherwise

runStats - the object to which run-time statistics will be written

Throws:

java.lang.IllegalArgumentException - if haps.isEmpty() == true

java.lang.NullPointerException - if any parameter is null

Method Detail

markersAreReversed

public boolean markersAreReversed()

Returns true if the order of markers is reversed, and false otherwise

Returns:

true if the order of markers is reversed, and false otherwise

nMarkers

public int nMarkers()

Returns the number of markers.

Returns:

the number of markers

nSamples

public int nSamples()

Returns the number of samples.

Returns:

the number of samples

nHaps

public int nHaps()

Returns the number of haplotypes.

Returns:

the number of haplotypes

markers

public Markers markers()

returns the list of markers.

Returns:

the list of markers

par

public Par par()

Returns the analysis parameters.

Returns:

the analysis parameters

rdag

public RestrictedDag rdag()

Returns the DAG model.

Returns:

the DAG model

gl

public GL gl()

Returns the genotype likelihoods for the target samples at the target data markers.

Returns:

the genotype likelihoods for the target samples at the target data markers.

err

public float err()

Returns the allele error rate

Returns:

the allele error rate

pRecomb

public float pRecomb(int marker)

Returns the probability of recombination between (marker - 1) and marker.

Parameters:

marker - a marker index

Returns:

the probability of recombination between (marker - 1) and marker

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()