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java.lang.Objectpal.tree.CladeSystem
public class CladeSystem
data structure for a set of splits
Constructor Summary | |
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CladeSystem(IdGroup idGroup,
int size)
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Method Summary | |
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static void |
calculateCladeProbabilities(Tree tree,
CladeSystem[] cladeSystems)
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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)
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public CladeSystem(IdGroup idGroup, int size)
idGroup
- sequence labelssize
- number of cladesMethod Detail |
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public 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
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