net.maizegenetics.pangenome.api

Class ReferenceRangeEmissionProbability

java.lang.Object

net.maizegenetics.analysis.imputation.EmissionProbability

net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability

public class ReferenceRangeEmissionProbability
extends net.maizegenetics.analysis.imputation.EmissionProbability

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ReferenceRangeEmissionProbability.Builder
static class	ReferenceRangeEmissionProbability.METHOD

Method Summary

Modifier and Type	Method and Description
double	allCounts_oops(int state, int anchor)
double	allCounts(int state, int anchor)
double	allCountsWeighted(int state, int anchor)
static ReferenceRangeEmissionProbability	getInstanceFromHapidCountMap(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes, Map<Integer,Integer> hapidCountMap, double probCorrect)
static ReferenceRangeEmissionProbability	getInstanceFromHapidCounts(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes, com.google.common.collect.Multiset<Integer> hapidCounts, double probCorrect)
static ReferenceRangeEmissionProbability	getInstanceFromNodeCounts(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes, com.google.common.collect.Multiset<HaplotypeNode> nodeCounts, double probCorrect)
double	getProbObsGivenState(int state, int anchor)
double	getProbObsGivenState(int state, int obs, int node)
String	toString()
double	weightedMax(int state, int anchor)
double	weightedSum(int state, int anchor)

Methods inherited from class net.maizegenetics.analysis.imputation.EmissionProbability

getLnProbObsGivenState, getLnProbObsGivenState, setEmissionProbability

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Method Detail

getInstanceFromHapidCounts

public static ReferenceRangeEmissionProbability getInstanceFromHapidCounts(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes,
                                                                           com.google.common.collect.Multiset<Integer> hapidCounts,
                                                                           double probCorrect)

getInstanceFromNodeCounts

public static ReferenceRangeEmissionProbability getInstanceFromNodeCounts(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes,
                                                                          com.google.common.collect.Multiset<HaplotypeNode> nodeCounts,
                                                                          double probCorrect)

getInstanceFromHapidCountMap

public static ReferenceRangeEmissionProbability getInstanceFromHapidCountMap(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes,
                                                                             Map<Integer,Integer> hapidCountMap,
                                                                             double probCorrect)

getProbObsGivenState

public double getProbObsGivenState(int state,
                                   int anchor)

Overrides:

getProbObsGivenState in class net.maizegenetics.analysis.imputation.EmissionProbability

getProbObsGivenState

public double getProbObsGivenState(int state,
                                   int obs,
                                   int node)

Overrides:

getProbObsGivenState in class net.maizegenetics.analysis.imputation.EmissionProbability

allCounts_oops

public double allCounts_oops(int state,
                             int anchor)

allCounts

public double allCounts(int state,
                        int anchor)

allCountsWeighted

public double allCountsWeighted(int state,
                                int anchor)

weightedSum

public double weightedSum(int state,
                          int anchor)

weightedMax

public double weightedMax(int state,
                          int anchor)

toString

public String toString()

Overrides:

toString in class Object