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java.lang.Object jebl.evolution.trees.FilteredRootedTree
public abstract class FilteredRootedTree
Nested Class Summary |
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Nested classes/interfaces inherited from interface jebl.evolution.graphs.Graph |
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Graph.NoEdgeException, Graph.Utils |
Field Summary | |
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protected RootedTree |
source
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Constructor Summary | |
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FilteredRootedTree(RootedTree source)
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Method Summary | |
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boolean |
conceptuallyUnrooted()
Due to current implementation limitations, trees store "branch" information in nodes. |
List<Node> |
getAdjacencies(Node node)
Returns a list of nodes connected to this node by an edge |
Object |
getAttribute(String name)
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Map<String,Object> |
getAttributeMap()
Gets the entire attribute map. |
Set<String> |
getAttributeNames()
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List<Node> |
getChildren(Node node)
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Edge |
getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes |
double |
getEdgeLength(Node node1,
Node node2)
Returns the length of the edge that connects these two nodes |
Set<Edge> |
getEdges()
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List<Edge> |
getEdges(Node node)
Returns a list of edges connected to this node |
Set<Edge> |
getExternalEdges()
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Set<Node> |
getExternalNodes()
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double |
getHeight(Node node)
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Set<Edge> |
getInternalEdges()
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Set<Node> |
getInternalNodes()
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double |
getLength(Node node)
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Node |
getNode(Taxon taxon)
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Set<Node> |
getNodes()
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Node[] |
getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge. |
Set<Node> |
getNodes(int degree)
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Node |
getParent(Node node)
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Node |
getRootNode()
The root of the tree has the largest node height of all nodes in the tree. |
RootedTree |
getSource()
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Set<Taxon> |
getTaxa()
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Taxon |
getTaxon(Node node)
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boolean |
hasHeights()
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boolean |
hasLengths()
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boolean |
isExternal(Node node)
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boolean |
isRoot(Node node)
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void |
removeAttribute(String name)
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void |
setAttribute(String name,
Object value)
Sets an named attribute for this object. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected final RootedTree source
Constructor Detail |
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public FilteredRootedTree(RootedTree source)
Method Detail |
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public RootedTree getSource()
public boolean conceptuallyUnrooted()
RootedTree
conceptuallyUnrooted
in interface RootedTree
public List<Node> getChildren(Node node)
getChildren
in interface RootedTree
node
- the node whose children are being requested.
public boolean hasHeights()
hasHeights
in interface RootedTree
public double getHeight(Node node)
getHeight
in interface RootedTree
node
- the node whose height is being requested.
public boolean hasLengths()
hasLengths
in interface RootedTree
public double getLength(Node node)
getLength
in interface RootedTree
node
- the node whose branch length (to its parent) is being requested.
public Node getParent(Node node)
getParent
in interface RootedTree
node
- the node whose parent is requested
public Node getRootNode()
RootedTree
getRootNode
in interface RootedTree
public Set<Node> getExternalNodes()
getExternalNodes
in interface Tree
public Set<Node> getInternalNodes()
getInternalNodes
in interface Tree
public Set<Edge> getExternalEdges()
getExternalEdges
in interface Tree
public Set<Edge> getInternalEdges()
getInternalEdges
in interface Tree
public Node getNode(Taxon taxon)
getNode
in interface Tree
taxon
- the taxon
public Set<Taxon> getTaxa()
getTaxa
in interface Tree
public Taxon getTaxon(Node node)
getTaxon
in interface Tree
node
- the node whose associated taxon is being requested.
public boolean isExternal(Node node)
isExternal
in interface Tree
node
- the node
public List<Node> getAdjacencies(Node node)
Graph
getAdjacencies
in interface Graph
public List<Edge> getEdges(Node node)
Graph
getEdges
in interface Graph
public Set<Edge> getEdges()
getEdges
in interface Graph
public Node[] getNodes(Edge edge)
Graph
getNodes
in interface Graph
public Edge getEdge(Node node1, Node node2) throws Graph.NoEdgeException
Graph
getEdge
in interface Graph
Graph.NoEdgeException
- if the nodes are not directly connected by an edge.public double getEdgeLength(Node node1, Node node2) throws Graph.NoEdgeException
Graph
getEdgeLength
in interface Graph
Graph.NoEdgeException
- if the nodes are not directly connected by an edge.public Set<Node> getNodes()
getNodes
in interface Graph
public Set<Node> getNodes(int degree)
getNodes
in interface Graph
degree
- the number of edges connected to a node
public boolean isRoot(Node node)
isRoot
in interface RootedTree
node
- the node
public void setAttribute(String name, Object value)
Attributable
setAttribute
in interface Attributable
name
- the name of the attribute.value
- the new value of the attribute.public Object getAttribute(String name)
getAttribute
in interface Attributable
name
- the name of the attribute of interest.
public void removeAttribute(String name)
removeAttribute
in interface Attributable
name
- name of attribute to removepublic Set<String> getAttributeNames()
getAttributeNames
in interface Attributable
public Map<String,Object> getAttributeMap()
Attributable
getAttributeMap
in interface Attributable
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