Package pal.tree
Class CladeSystem
java.lang.Object
pal.tree.CladeSystem
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 -
Method Summary
Modifier and TypeMethodDescriptionstatic void
calculateCladeProbabilities
(Tree tree, CladeSystem[] cladeSystems) boolean[]
getClade
(int i) get cladestatic void
get clade for internal nodeboolean[][]
get clade arrayint
get number of cladesstatic CladeSystem
creates a clade system from a tree (using a pre-specified order of sequences)static CladeSystem
creates a clade system from a tree (using tree-induced order of sequences)static CladeSystem[]
getCladeSystems
(Tree[] trees) get idGroupint
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)toString()
print clade system
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Constructor Details
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CladeSystem
- Parameters:
idGroup
- sequence labelssize
- number of clades
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Method Details
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getCladeCount
public int getCladeCount()get number of clades -
getLabelCount
public int getLabelCount()get number of labels -
getCladeArray
public boolean[][] getCladeArray()get clade array -
getClade
public boolean[] getClade(int i) get clade -
getIdGroup
get idGroup -
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
print clade system -
getCladeSystems
- Returns:
- all clade systems for a group of trees.
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calculateCladeProbabilities
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getClades
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
creates a clade system from a tree (using tree-induced order of sequences)- Parameters:
tree
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getClade
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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