Package jebl.evolution.trees
Interface Tree
- All Superinterfaces:
Attributable
,Graph
- All Known Subinterfaces:
RootedTree
- All Known Implementing Classes:
CompactRootedTree
,FilteredRootedTree
,MutableRootedTree
,ReRootedTree
,RootedFromUnrooted
,RootedSubtree
,SimpleRootedTree
,SimpleTree
,SortedRootedTree
,TransformedRootedTree
A rooted or unrooted tree. This interface is the common base class for all trees,
and contains only operations for unrooted trees. The subinterface RootedTree
contains additional methods that make sense only on rooted trees.
Both interfaces contain no mutator methods. As of 2006-12-08, the only way
to mutate a tree after it has been built is to use its concrete class
instead of the Tree or RootedTree interface.
- Version:
- $Id: Tree.java 627 2007-01-15 03:50:40Z pepster $
- Author:
- rambaut, Alexei Drummond
-
Nested Class Summary
Nested classes/interfaces inherited from interface jebl.evolution.graphs.Graph
Graph.NoEdgeException, Graph.Utils
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Method Summary
Modifier and TypeMethodDescriptiongetTaxa()
boolean
isExternal
(Node node) void
renameTaxa
(Taxon from, Taxon to) Methods inherited from interface jebl.util.Attributable
getAttribute, getAttributeMap, getAttributeNames, removeAttribute, setAttribute
Methods inherited from interface jebl.evolution.graphs.Graph
getAdjacencies, getEdge, getEdgeLength, getEdges, getEdges, getNodes, getNodes, getNodes
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Method Details
-
getExternalNodes
- Returns:
- a set of all nodes that have degree 1. These nodes are often refered to as 'tips'.
-
getInternalNodes
- Returns:
- a set of all nodes that have degree 2 or more. These nodes are often refered to as internal nodes.
-
getExternalEdges
- Returns:
- a set of all edges that have a degree 1 node.
-
getInternalEdges
- Returns:
- a set of all edges for which both nodes have degree 2 or more.
-
getTaxa
- Returns:
- the set of taxa associated with the external nodes of this tree. The size of this set should be the same as the size of the external nodes set.
-
getTaxon
- Parameters:
node
- the node whose associated taxon is being requested.- Returns:
- the taxon object associated with the given node, or null if the node is an internal node.
-
isExternal
- Parameters:
node
- the node- Returns:
- true if the node is of degree 1.
-
getNode
- Parameters:
taxon
- the taxon- Returns:
- the external node associated with the given taxon, or null if the taxon is not a member of the taxa set associated with this tree.
-
renameTaxa
-