public class CladeSystem
extends java.lang.Object
Constructor | Description |
---|---|
CladeSystem(IdGroup idGroup,
int size) |
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
|
public CladeSystem(IdGroup idGroup, int size)
idGroup
- sequence labelssize
- number of cladespublic int getCladeCount()
public int getLabelCount()
public boolean[][] getCladeArray()
public boolean[] getClade(int i)
public IdGroup getIdGroup()
public boolean hasClade(boolean[] clade)
clade
- cladepublic java.lang.String toString()
toString
in class java.lang.Object
public static CladeSystem[] getCladeSystems(Tree[] trees)
public static void calculateCladeProbabilities(Tree tree, CladeSystem[] cladeSystems)
public static CladeSystem getClades(IdGroup idGroup, Tree tree)
idGroup
- sequence order for the matrixtree
- public static CladeSystem getClades(Tree tree)
tree
- public static void getClade(IdGroup idGroup, Node internalNode, boolean[] clade)
idGroup
- order of labelsinternalNode
- Nodeboolean
- [] cladepublic static boolean isSame(boolean[] s1, boolean[] s2)
s1
- clade 1s2
- clade 2