net.maizegenetics.taxa.tree

Class CladeSystem

net.maizegenetics.taxa.tree.CladeSystem

public class CladeSystem

data structure for a set of splits

Constructor Detail

CladeSystem

public CladeSystem(TaxaList idGroup,
                   int size)

Parameters:

idGroup - sequence labels

size - number of clades

Method Detail

getCladeCount

public int getCladeCount()

get number of clades

getLabelCount

public int getLabelCount()

get number of labels

getCladeArray

public kotlin.Array[] getCladeArray()

get clade array

getClade

public kotlin.Array[] getClade(int i)

get clade

getIdGroup

public TaxaList getIdGroup()

get idGroup

hasClade

public boolean hasClade(kotlin.Array[] clade)

+ test whether a clade is contained in this clade system (assuming the same leaf order)

Parameters:

clade - clade

toString

public java.lang.String toString()

print clade system

getCladeSystems

public static CladeSystem[] getCladeSystems(Tree[] trees)

Returns:

org.jetbrains.dokka.NodeRenderContent@694f69c1: all clade systems for a group of trees.

calculateCladeProbabilities

public static void calculateCladeProbabilities(Tree tree,
                                               CladeSystem[] cladeSystems)

getClades

public static CladeSystem getClades(TaxaList idGroup,
                                    Tree tree)

creates a clade system from a tree (using a pre-specified order of sequences)

Parameters:

idGroup - sequence order for the matrix

tree -

getClades

public static CladeSystem getClades(Tree tree)

creates a clade system from a tree (using tree-induced order of sequences)

Parameters:

tree -

getClade

public static void getClade(TaxaList idGroup,
                            Node internalNode,
                            kotlin.Array[] clade)

get clade for internal node

Parameters:

idGroup - order of labels

internalNode - Node

clade -

isSame

public static boolean isSame(kotlin.Array[] s1,
                             kotlin.Array[] s2)

checks whether two clades are identical (assuming they are of the same length and use the same leaf order)

Parameters:

s1 - clade 1

s2 - clade 2