CladeSystem

Constructors
Constructor	Description
`CladeSystem(IdGroup idGroup, int size)`

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static void`	`calculateCladeProbabilities(Tree tree, CladeSystem[] cladeSystems)`
`boolean[]`	`getClade(int i)`	get clade
`static void`	`getClade(IdGroup idGroup, Node internalNode, boolean[] clade)`	get clade for internal node
`boolean[][]`	`getCladeArray()`	get clade array
`int`	`getCladeCount()`	get number of clades
`static CladeSystem`	`getClades(IdGroup idGroup, Tree tree)`	creates a clade system from a tree (using a pre-specified order of sequences)
`static CladeSystem`	`getClades(Tree tree)`	creates a clade system from a tree (using tree-induced order of sequences)
`static CladeSystem[]`	`getCladeSystems(Tree[] trees)`
`IdGroup`	`getIdGroup()`	get idGroup
`int`	`getLabelCount()`	get number of labels
`boolean`	`hasClade(boolean[] clade)`	+ test whether a clade is contained in this clade system (assuming the same leaf order)
`static boolean`	`isSame(boolean[] s1, boolean[] s2)`	checks whether two clades are identical (assuming they are of the same length and use the same leaf order)
`java.lang.String`	`toString()`	print clade system

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

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

public static CladeSystem getClades(IdGroup idGroup,
                                    Tree tree)

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

public static void getClade(IdGroup idGroup,
                            Node internalNode,
                            boolean[] clade)

get clade for internal node

Parameters:: idGroup - order of labels; internalNode - Node; boolean - [] clade

Class CladeSystem