net.maizegenetics.analysis.clustering

Class HaplotypeCluster

net.maizegenetics.analysis.clustering.HaplotypeCluster

public class HaplotypeCluster

A HaplotypeCluster is a List of Haplotypes that are all similar. Size and score are alternate methods of measuring cluster importance. For score, Haplotypes are weighted by the number of clusters to which they belong since a Haplotype can belong to more than one cluster. The natural order for clusters is determined by score then by size, both in descending order.

Field Detail

ReturnHaplotype

public static net.maizegenetics.analysis.clustering.HaplotypeCluster.TYPE ReturnHaplotype

The TYPE used to represent all HaplotypeClusters

Constructor Detail

HaplotypeCluster

public HaplotypeCluster(java.util.ArrayList<net.maizegenetics.analysis.clustering.Haplotype> hapList)

Parameters:

hapList - an ArrayList of Haplotypes

HaplotypeCluster

public HaplotypeCluster(Haplotype hap)

Parameters:

hap - a single Haplotype used to seed the cluster

HaplotypeCluster

public HaplotypeCluster(Haplotype hap,
                        double initialScore)

Parameters:

hap - a Haplotype

initialScore - the initial cluster score, usually set to 1

HaplotypeCluster

public HaplotypeCluster(java.util.ArrayList<net.maizegenetics.analysis.clustering.Haplotype> hapList,
                        double initialScore)

Parameters:

hapList - an ArrayList of Haplotype objects

initialScore - the initial score assigned to this cluster

Method Detail

getSize

public int getSize()

Returns:

org.jetbrains.dokka.NodeRenderContent@2b546a12: the number of Haplotypes in this cluster

getHaplotypeList

public java.util.ArrayList<net.maizegenetics.analysis.clustering.Haplotype> getHaplotypeList()

Returns:

org.jetbrains.dokka.NodeRenderContent@542319f6: the Haplotypes in the cluster

getScore

public double getScore()

Returns:

org.jetbrains.dokka.NodeRenderContent@4d1dbc03: the cluster score. Typically this represents the importance of a cluster but be used for anything by the calling program. A typical use is as the sum of the individual Haplotype scores where a score equals the 1 divided by the number of clusters containing a Haplotype.

setScore

public void setScore(double newScore)

Sets the score of this haplotype to the new score.

Parameters:

newScore - the new score

incrementScore

public void incrementScore(double val)

Parameters:

val - the value to be added to the cluster score

get

public Haplotype get(int index)

Parameters:

index - the index of a Haplotype in this cluster

Returns:

org.jetbrains.dokka.NodeRenderContent@153c32bd: the Haplotype indexed by index

add

public void add(Haplotype hap)

Parameters:

hap - a Haplotype

remove

public void remove(Haplotype hap)

Parameters:

hap - a Haplotype to be removed from the cluster

removeAll

public void removeAll(HaplotypeCluster cluster)

All haplotypes in cluster that are also in this cluster will be removed from this cluster

Parameters:

cluster - another cluster

addAll

public void addAll(HaplotypeCluster cluster)

This function does not prevent Haplotypes from being duplicated. To avoid duplicates use addAllUnique.

Parameters:

cluster - Adds all Haplotypes in cluster to this cluster.

getIterator

public java.util.Iterator<net.maizegenetics.analysis.clustering.Haplotype> getIterator()

Returns:

org.jetbrains.dokka.NodeRenderContent@1db0def2: an Iterator for the Haplotypes in this cluster

addAllUnique

public void addAllUnique(HaplotypeCluster cluster)

Adds Haplotypes from cluster that are not already contained in this cluster

Parameters:

cluster - another cluster

getCountOfHaplotypesNotInThisCluster

public int getCountOfHaplotypesNotInThisCluster(HaplotypeCluster cluster)

Counts the number of Haplotypes in cluster that are not also in this cluster

Parameters:

cluster - another cluster

Returns:

org.jetbrains.dokka.NodeRenderContent@5110981b: the count of Haplotypes unique to cluster

getMaximumDistance

public int getMaximumDistance(Haplotype hap)

Parameters:

hap - a Haplotype

Returns:

org.jetbrains.dokka.NodeRenderContent@71cdcb9e: the maximum distance of this Haplotype from each Haplotype in this cluster

getAllelesAtSite

public kotlin.Array[] getAllelesAtSite(int site)

Parameters:

site -

Returns:

org.jetbrains.dokka.NodeRenderContent@510b6c0: the alleles at this site with respective count, sorted by count, high to low The first dimension is the allele number. For the second dimension, the zero element is the byte value of the allele and the second element is the number of individuals carrying that allele.

countAllelesAtAllSites

public void countAllelesAtAllSites()

copy

public HaplotypeCluster copy()

This function returns a copy of the component Haplotypes not references to them.

Returns:

org.jetbrains.dokka.NodeRenderContent@1eccbfde: a deep copy of this cluster.

compareTo

public int compareTo(HaplotypeCluster cluster)

getHaplotype

public kotlin.Array[] getHaplotype()

The common haplotype of this cluster. The type is determined by the field ReturnHaplotype.

Returns:

org.jetbrains.dokka.NodeRenderContent@4bc93c5c: a byte array representing the haplotype of this cluster

getHaplotypeAsString

public java.lang.String getHaplotypeAsString()

The common haplotype of this cluster. The type is determined by the field ReturnHaplotype.

Returns:

org.jetbrains.dokka.NodeRenderContent@54479f80: a String representing the haplotype of this cluster

getMajorityHaplotype

public kotlin.Array[] getMajorityHaplotype()

The majority haplotype of this cluster where each site is assigned value of the major allele within the cluster.

Returns:

org.jetbrains.dokka.NodeRenderContent@5461857e: a byte array representing the haplotype of this cluster

getCensoredMajorityHaplotype

public kotlin.Array[] getCensoredMajorityHaplotype(double maxMinorFreq,
                                                   int maxMinorCount)

This returns the majority haplotype for sites with either minor allele frequency below maxMinorFreq or minor allele count less than or equal to maxMinorCount. Missing is returned at sites not meeting the stated criteria.

Parameters:

maxMinorFreq - the maximum proportion of offtypes (alternate alleles) allowed before site is set to missing

maxMinorCount - the maximum minor allele count allowed before site is set to missing

Returns:

org.jetbrains.dokka.NodeRenderContent@2fa8e263: a byte array representing the haplotype of this cluster

getUnanimousHaplotype

public kotlin.Array[] getUnanimousHaplotype()

The unanimous haplotype of this cluster. Only monomorphic sites are reported. Others will be unknown.

Returns:

org.jetbrains.dokka.NodeRenderContent@2d811016: a byte array representing the haplotype of this cluster

byteHaplotypeAsString

public java.lang.String byteHaplotypeAsString(kotlin.Array[] hap)

Converts a byte sequence to a String

Parameters:

hap - an array of byte genotype or haplotype values

Returns:

org.jetbrains.dokka.NodeRenderContent@455231b9: the String representation

getNumberOfSites

public int getNumberOfSites()

listTaxaInCluster

public kotlin.Array[] listTaxaInCluster()

countTaxaSharedWith

public int countTaxaSharedWith(HaplotypeCluster hapCluster)

contains

public boolean contains(Haplotype hap)

countHeterozygousSites

public int countHeterozygousSites()

toString

public java.lang.String toString()