sample

Class RestrictedDag

java.lang.Object

sample.RestrictedDag

public class RestrictedDag
extends java.lang.Object

Class RestrictedDag is a wrapper for a Dag object that stores segments of identity by descent.

Instances of class RestrictedDag are immutable.

Constructor Summary

Constructors

Constructor and Description
RestrictedDag(SampleHapPairs haps, float[] weights, int nInitLevels, float scale, double ibdLength, double ibdExtend) Constructs a RestrictedDag instance.

Method Summary

Modifier and Type	Method and Description
Dag	dag() Returns the DAG.
SampleHapPairs	sampleHaps() Returns the haplotypes used to construct this.
DiploidStates	singleStates(int sample) Returns the permitted states for the specified sample.

Methods inherited from class java.lang.Object

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

Constructor Detail

RestrictedDag

public RestrictedDag(SampleHapPairs haps,
                     float[] weights,
                     int nInitLevels,
                     float scale,
                     double ibdLength,
                     double ibdExtend)

Constructs a RestrictedDag instance.

Parameters:

haps - the sample haplotypes

weights - an array of length hapPairs.nHaps() whose j-th element is the weight for the j-th haplotype

nInitLevels - the number of initial levels to read

scale - a parameter that multiplicatively scales the node similarity threshold

ibdLength - the minimum length of an IBD segment

ibdExtend - the length by which an IBD segment will be extended

Throws:

java.lang.IllegalArgumentException - if hapPairs.nMarkers() == 0

java.lang.IllegalArgumentException - if weights.length != 2*haps.nSamples()

java.lang.IllegalArgumentException - if (weights[j] <= 0 || Float.isFinite(weights[j]) == false) for any j satisfying (0 <= j && j < weights.length)

java.lang.IllegalArgumentException - if nInitLevels < 1

java.lang.IllegalArgumentException - if Double.isFinite(scale) == false || scale <= 0

java.lang.IllegalArgumentException - if ibdLength < 0 || ibdExtend < 0

java.lang.NullPointerException - if hapPairs == null || weights == null

Method Detail

sampleHaps

public SampleHapPairs sampleHaps()

Returns the haplotypes used to construct this.

Returns:

the haplotypes used to construct this

dag

public Dag dag()

Returns the DAG.

Returns:

the DAG

singleStates

public DiploidStates singleStates(int sample)

Returns the permitted states for the specified sample.

Parameters:

sample - the sample index

Returns:

the permitted states for the specified sample

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= haps.nSamples()