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java.lang.Objectde.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloTree
public class PhyloTree
This class implements a simple (phylogenetic) tree.
A PhyloTree contains the root node of type PhyloNode
Constructor Summary | |
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PhyloTree(StringBuffer xml)
The standard constructor for the interface Storable . |
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PhyloTree(String name,
PhyloNode root)
Construct an instance of the class PhyloTree |
Method Summary | |
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PhyloTree |
clone()
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ArrayList<PhyloNode> |
getAllLeafs()
This method returns a list of PhyloNode s that represent the leafs of the tree |
String |
getName()
This method returns the name of the PhyloTree |
int |
getNumberOfNodes()
This method returns the total number of nodes in the tree |
PhyloNode |
getRoot()
This method returns the root node of the tree |
StringBuffer |
toXML()
This method returns an XML representation as StringBuffer of an
instance of the implementing class. |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PhyloTree(String name, PhyloNode root)
name
- the name of the PhyloTreeroot
- the root nodepublic PhyloTree(StringBuffer xml) throws NonParsableException
Storable
.
Constructs a PhyloTree
out of an XML representation.
xml
- the XML representation as StringBuffer
NonParsableException
- if the PhyloTree
could not be reconstructed out of
the StringBuffer
xml
Method Detail |
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public PhyloTree clone() throws CloneNotSupportedException
clone
in class Object
CloneNotSupportedException
public String getName()
public PhyloNode getRoot()
public int getNumberOfNodes()
public ArrayList<PhyloNode> getAllLeafs()
PhyloNode
s that represent the leafs of the tree
public StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.
toXML
in interface Storable
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