Package pal.tree
Class CladeSystem
- java.lang.Object
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- pal.tree.CladeSystem
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public class CladeSystem extends java.lang.Object
data structure for a set of splits- Version:
- $Id: CladeSystem.java,v 1.1 2002/06/03 09:17:52 alexi Exp $
- Author:
- Alexei Drummond
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Constructor Summary
Constructors Constructor Description CladeSystem(IdGroup idGroup, int size)
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Method Summary
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 cladestatic void
getClade(IdGroup idGroup, Node internalNode, boolean[] clade)
get clade for internal nodeboolean[][]
getCladeArray()
get clade arrayint
getCladeCount()
get number of cladesstatic 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 idGroupint
getLabelCount()
get number of labelsboolean
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
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Constructor Detail
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CladeSystem
public CladeSystem(IdGroup idGroup, int size)
- Parameters:
idGroup
- sequence labelssize
- number of clades
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Method Detail
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getCladeCount
public int getCladeCount()
get number of clades
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getLabelCount
public int getLabelCount()
get number of labels
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getCladeArray
public boolean[][] getCladeArray()
get clade array
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getClade
public boolean[] getClade(int i)
get clade
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getIdGroup
public IdGroup getIdGroup()
get idGroup
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hasClade
public boolean hasClade(boolean[] clade)
+ test whether a clade is contained in this clade system (assuming the same leaf order)- Parameters:
clade
- clade
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toString
public java.lang.String toString()
print clade system- Overrides:
toString
in classjava.lang.Object
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getCladeSystems
public static CladeSystem[] getCladeSystems(Tree[] trees)
- Returns:
- all clade systems for a group of trees.
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calculateCladeProbabilities
public static void calculateCladeProbabilities(Tree tree, CladeSystem[] cladeSystems)
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getClades
public static CladeSystem getClades(IdGroup idGroup, Tree tree)
creates a clade system from a tree (using a pre-specified order of sequences)- Parameters:
idGroup
- sequence order for the matrixtree
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getClades
public static CladeSystem getClades(Tree tree)
creates a clade system from a tree (using tree-induced order of sequences)- Parameters:
tree
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getClade
public static void getClade(IdGroup idGroup, Node internalNode, boolean[] clade)
get clade for internal node- Parameters:
idGroup
- order of labelsinternalNode
- Nodeboolean
- [] clade
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isSame
public 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)- Parameters:
s1
- clade 1s2
- clade 2
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