Package pal.tree
Interface Tree
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- All Superinterfaces:
IdGroup
,java.io.Serializable
,Units
,UnitsProvider
- All Known Subinterfaces:
ParameterizedTree
- All Known Implementing Classes:
ClockTree
,ClusterTree
,DemographicClockTree
,LogParameterizedTree
,MutationRateModelTree
,NeighborJoiningTree
,ParameterizedTree.ParameterizedTreeBase
,ReadTree
,SimpleTree
,SUPGMATree
,Tree.TreeBase
,UnconstrainedTree
,UPGMATree
public interface Tree extends IdGroup, Units, java.io.Serializable, UnitsProvider
Interface for a phylogenetic or genealogical tree.- Version:
- $Id: Tree.java,v 1.22 2002/10/03 06:06:55 matt Exp $
- Author:
- Alexei Drummond
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
Tree.TreeBase
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
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Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
createNodeList()
This method is called to ensure that the calls to other methods in this interface are valid.java.lang.Object
getAttribute(Node node, java.lang.String name)
Tree
getCopy()
Node
getExternalNode(int i)
int
getExternalNodeCount()
Node
getInternalNode(int i)
int
getInternalNodeCount()
Node
getRoot()
int
getUnits()
Gets the units that this tree's branch lengths and node heights are expressed in.void
setAttribute(Node node, java.lang.String name, java.lang.Object value)
Sets an named attribute for a given node.void
setRoot(Node root)
This method constructs a tree from the given root node.-
Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Method Detail
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getRoot
Node getRoot()
- Returns:
- the root node of this tree.
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setRoot
void setRoot(Node root)
This method constructs a tree from the given root node.- Parameters:
root
- the root node of the tree to construct.
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getExternalNodeCount
int getExternalNodeCount()
- Returns:
- a count of the number of external nodes (tips) in this tree.
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getInternalNodeCount
int getInternalNodeCount()
- Returns:
- a count of the number of internal nodes (and hence clades) in this tree.
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getExternalNode
Node getExternalNode(int i)
- Returns:
- the ith external node in the tree.
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getInternalNode
Node getInternalNode(int i)
- Returns:
- the ith internal node in the tree.
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createNodeList
void createNodeList()
This method is called to ensure that the calls to other methods in this interface are valid.
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getUnits
int getUnits()
Gets the units that this tree's branch lengths and node heights are expressed in.- Specified by:
getUnits
in interfaceUnitsProvider
- Returns:
- the units relating to this object.
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setAttribute
void setAttribute(Node node, java.lang.String name, java.lang.Object value)
Sets an named attribute for a given node.- Parameters:
node
- the node whose attribute is being set.name
- the name of the attribute.value
- the new value of the attribute.
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getAttribute
java.lang.Object getAttribute(Node node, java.lang.String name)
- Parameters:
node
- the node being interrogated.name
- the name of the attribute of interest.- Returns:
- an object representing the named attributed for the numbered node.
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getCopy
Tree getCopy()
- Returns:
- a clone of this tree
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