sample

Class ConsumeSingleSamples

java.lang.Object

sample.ConsumeSingleSamples

All Implemented Interfaces:

java.lang.Runnable

public class ConsumeSingleSamples
extends java.lang.Object
implements java.lang.Runnable

Class ConsumeSingleSamples samples haplotype pairs conditional on the observed genotype data and a haplotype frequency model. Class ConsumeSingleSamples is designed for use as a consumer in a producer-consumer design pattern.

Instances of class ConsumeSingleSamples are thread-safe if the synchronization requirements for the constructor are satisfied.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.Integer	POISON A sentinel Integer.

Constructor Summary

Constructors

Constructor and Description
ConsumeSingleSamples(boolean markersAreReversed, SingleBaumInterface baum, java.util.concurrent.BlockingQueue<java.lang.Integer> qIn, java.util.List<HapPair> hapList) Constructs a new ConsumeSingleSample instance.
ConsumeSingleSamples(boolean markersAreReversed, SingleBaumInterface baum, java.util.concurrent.BlockingQueue<java.lang.Integer> qIn, java.util.List<HapPair> hapList, GenotypeValues gv) Constructs a new ConsumeSingleSample instance.

Method Summary

Modifier and Type	Method and Description
void	run() Takes sample indices from the thread-safe work-queue specified at time of construction and samples haplotype pairs for each sample.

Methods inherited from class java.lang.Object

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

Field Detail

POISON

public static final java.lang.Integer POISON

A sentinel Integer.

Constructor Detail

ConsumeSingleSamples

public ConsumeSingleSamples(boolean markersAreReversed,
                            SingleBaumInterface baum,
                            java.util.concurrent.BlockingQueue<java.lang.Integer> qIn,
                            java.util.List<HapPair> hapList)

Constructs a new ConsumeSingleSample instance.

Parameters:

markersAreReversed - true if the baum parameter randomSample() method produces sampled haplotype pairs that have their marker order reversed and false otherwise

baum - a thread-confined instance of class sample.SingleBaumInterface

qIn - a thread-safe input work queue

hapList - a thread-safe list for storing sampled haplotype pairs

Throws:

java.lang.NullPointerException - if any parameter is null

ConsumeSingleSamples

public ConsumeSingleSamples(boolean markersAreReversed,
                            SingleBaumInterface baum,
                            java.util.concurrent.BlockingQueue<java.lang.Integer> qIn,
                            java.util.List<HapPair> hapList,
                            GenotypeValues gv)

Constructs a new ConsumeSingleSample instance.

Parameters:

markersAreReversed - true if the baum parameter randomSample() method produces sampled haplotype pairs that have their marker order reversed and false otherwise

baum - a thread-confined instance of class sample.SingleBaumInterface

qIn - a thread-safe input work queue

hapList - a thread-safe list for storing sampled haplotype pairs

gv - a thread-safe object which stores scaled posterior genotype probabilities

Throws:

java.lang.NullPointerException - if any parameter is null

Method Detail

run

public void run()

Takes sample indices from the thread-safe work-queue specified at time of construction and samples haplotype pairs for each sample. The method exits when ConsumeSingleSamples.POISON is taken from the work queue.

Specified by:

run in interface java.lang.Runnable