public class CladeSystem
extends java.lang.Object
Constructor and Description |
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CladeSystem(IdGroup idGroup,
int size) |
Modifier and Type | Method and Description |
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static void |
calculateCladeProbabilities(Tree tree,
CladeSystem[] cladeSystems) |
static void |
getClade(IdGroup idGroup,
Node internalNode,
boolean[] clade)
get clade for internal node
|
boolean[] |
getClade(int i)
get clade
|
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