Uses of Class
net.maizegenetics.analysis.clustering.Haplotype

Packages that use Haplotype

Package	Description
net.maizegenetics.analysis.clustering	The clustering package provides classes to cluster genotype sequence for the purpose of identifying common haplotypes.
net.maizegenetics.analysis.imputation	Methods for genotypic imputation including Viterbi HMM, FSFHap, and FILLIN

Uses of Haplotype in net.maizegenetics.analysis.clustering

Methods in net.maizegenetics.analysis.clustering that return Haplotype

Modifier and Type	Method and Description
Haplotype	HaplotypeCluster.get(int index)
Haplotype	Haplotype.subHaplotype(int size, boolean fromStart)

Methods in net.maizegenetics.analysis.clustering that return types with arguments of type Haplotype

Modifier and Type	Method and Description
ArrayList<Haplotype>	HaplotypeCluster.getHaplotypeList()
Iterator<Haplotype>	HaplotypeCluster.getIterator()

Methods in net.maizegenetics.analysis.clustering with parameters of type Haplotype

Modifier and Type	Method and Description
void	HaplotypeCluster.add(Haplotype hap)
int	Haplotype.compareTo(Haplotype arg0)
boolean	HaplotypeCluster.contains(Haplotype hap)
int	Haplotype.distanceFrom(Haplotype h0) Distance is defined as the sum of the distances between each pair of sites.
static int	Haplotype.getDistance(Haplotype hap0, Haplotype hap1)
int	HaplotypeCluster.getMaximumDistance(Haplotype hap)
void	HaplotypeCluster.remove(Haplotype hap)

Constructors in net.maizegenetics.analysis.clustering with parameters of type Haplotype

Constructor and Description
HaplotypeCluster(Haplotype hap)
HaplotypeCluster(Haplotype hap, double initialScore)

Constructor parameters in net.maizegenetics.analysis.clustering with type arguments of type Haplotype

Constructor and Description
HaplotypeCluster(ArrayList<Haplotype> hapList)
HaplotypeCluster(ArrayList<Haplotype> hapList, double initialScore)
HaplotypeClusterer(ArrayList<Haplotype> haplotypes)

Uses of Haplotype in net.maizegenetics.analysis.imputation

Methods in net.maizegenetics.analysis.imputation that return types with arguments of type Haplotype

Modifier and Type	Method and Description
static ArrayList<ArrayList<Haplotype>>	BiparentalHaplotypeFinder.getParentHaplotypes(ArrayList<ArrayList<Haplotype>> previousParents, ArrayList<Haplotype> candidates, int overlap, boolean forward)
static ArrayList<ArrayList<Haplotype>>	BiparentalHaplotypeFinder.getParentHaplotypesV1(ArrayList<ArrayList<Haplotype>> previousParents, ArrayList<Haplotype> candidates, int overlap, boolean forward)
ArrayList<Haplotype>	BiparentalHaplotypeFinder.mergeMajorHaplotypes(HaplotypeClusterer clusterMaker, int minClusterSize)

Methods in net.maizegenetics.analysis.imputation with parameters of type Haplotype

Modifier and Type	Method and Description
static boolean	BiparentalHaplotypeFinder.doesOverlapMatch(Haplotype h0, Haplotype h1, int overlap, boolean forward)

Method parameters in net.maizegenetics.analysis.imputation with type arguments of type Haplotype

Modifier and Type	Method and Description
static ArrayList<ArrayList<Haplotype>>	BiparentalHaplotypeFinder.getParentHaplotypes(ArrayList<ArrayList<Haplotype>> previousParents, ArrayList<Haplotype> candidates, int overlap, boolean forward)
static ArrayList<ArrayList<Haplotype>>	BiparentalHaplotypeFinder.getParentHaplotypes(ArrayList<ArrayList<Haplotype>> previousParents, ArrayList<Haplotype> candidates, int overlap, boolean forward)
static ArrayList<ArrayList<Haplotype>>	BiparentalHaplotypeFinder.getParentHaplotypesV1(ArrayList<ArrayList<Haplotype>> previousParents, ArrayList<Haplotype> candidates, int overlap, boolean forward)
static ArrayList<ArrayList<Haplotype>>	BiparentalHaplotypeFinder.getParentHaplotypesV1(ArrayList<ArrayList<Haplotype>> previousParents, ArrayList<Haplotype> candidates, int overlap, boolean forward)
void	BiparentalHaplotypeFinder.updatePopulationDataAlleles(ArrayList<ArrayList<Haplotype>> parentHaplotypes, ArrayList<Position> positions, int start, int length)