public class CladeSystem
data structure for a set of splits
public CladeSystem(TaxaList idGroup, int size)
idGroup - sequence labelssize - number of cladespublic int getCladeCount()
get number of clades
public int getLabelCount()
get number of labels
public kotlin.Array[] getCladeArray()
get clade array
public kotlin.Array[] getClade(int i)
get clade
public TaxaList getIdGroup()
get idGroup
public boolean hasClade(kotlin.Array[] clade)
+ test whether a clade is contained in this clade system (assuming the same leaf order)
clade - cladepublic java.lang.String toString()
print clade system
public static CladeSystem[] getCladeSystems(Tree[] trees)
public static void calculateCladeProbabilities(Tree tree, CladeSystem[] cladeSystems)
public static CladeSystem getClades(TaxaList idGroup, Tree tree)
creates a clade system from a tree (using a pre-specified order of sequences)
idGroup - sequence order for the matrixtree - public static CladeSystem getClades(Tree tree)
creates a clade system from a tree (using tree-induced order of sequences)
tree - public static void getClade(TaxaList idGroup, Node internalNode, kotlin.Array[] clade)
get clade for internal node
idGroup - order of labelsinternalNode - Nodeclade - 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)
s1 - clade 1s2 - clade 2