haplotype

Class Weights

java.lang.Object

haplotype.Weights

public class Weights
extends java.lang.Object

Class Weights represents per-haplotype weights.

Instances of class Weights are immutable.

Constructor Summary

Constructors

Constructor and Description
Weights(NuclearFamilies fam) Constructs a new Weights instance with a weight of 1.0f for all samples.
Weights(NuclearFamilies fam, float nonRefWt) Constructs a new Weights instance with a weight of 1.0f for reference samples, and a weight of nonRefWt for non-reference samples.

Method Summary

Modifier and Type	Method and Description
NuclearFamilies	families() Returns the parent-offspring relationships.
float[]	get(HapPairs haps) Returns an array of length haps.nHaps() with per-haplotype weights.
float	nonRefWt() Returns the non-reference sample weight.

Methods inherited from class java.lang.Object

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

Constructor Detail

Weights

public Weights(NuclearFamilies fam)

Constructs a new Weights instance with a weight of 1.0f for all samples.

Parameters:

fam - the parent-offspring relationships

Throws:

java.lang.NullPointerException - if fam == null

Weights

public Weights(NuclearFamilies fam,
               float nonRefWt)

Constructs a new Weights instance with a weight of 1.0f for reference samples, and a weight of nonRefWt for non-reference samples. Non-reference samples are samples which are not present in fam.samples().

Parameters:

fam - the parent-offspring data

nonRefWt - the non-reference sample weight

Throws:

java.lang.IllegalArgumentException - if nonRefWt < 0.0f || nonRefWt > 1.0f || Float.isNaN(nonRefWt)

java.lang.NullPointerException - if fam == null

Method Detail

get

public float[] get(HapPairs haps)

Returns an array of length haps.nHaps() with per-haplotype weights. Array elements 2*j and 2*j + 1 are the weights for the first and second haplotype in the j-th haplotype pair. Reference haplotypes are assigned a weight of 1.0f. Non-reference haplotypes are assigned a weight of this.nonRefWt() if the haplotype is not inherited from a parent in the sample, and a weight of 0.01f if the haplotype is inherited from a parent in the sample. The first haplotype in the offspring is required to be the transmitted transmitted haplotype for a parent-offspring duo.

Parameters:

haps - an array of haplotype pairs

Returns:

an array of per-haplotype weights

Throws:

java.lang.NullPointerException - if hapPairs == null

families

public NuclearFamilies families()

Returns the parent-offspring relationships.

Returns:

the parent-offspring relationships

nonRefWt

public float nonRefWt()

Returns the non-reference sample weight.

Returns:

the non-reference sample weight