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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
Interface for a phylogenetic or genealogical tree.
Fields inherited from interface pal.misc.Units |
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, YEARS |
Method Summary | |
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)
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Node |
getExternalNode(int i)
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int |
getExternalNodeCount()
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Node |
getInternalNode(int i)
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int |
getInternalNodeCount()
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Node |
getRoot()
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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. |
void |
setUnits(int units)
Sets the units that this tree's branch lengths and node heights are expressed in. |
Method Detail |
public Node getRoot()
public void setRoot(Node root)
root
- the root node of the tree to construct.public int getExternalNodeCount()
public int getInternalNodeCount()
public Node getExternalNode(int i)
public Node getInternalNode(int i)
public void createNodeList()
public int getUnits()
public void setUnits(int units)
public void setAttribute(Node node, java.lang.String name, java.lang.Object value)
node
- the node whose attribute is being set.name
- the name of the attribute.value
- the new value of the attribute.public java.lang.Object getAttribute(Node node, java.lang.String name)
node
- the node being interrogated.name
- the name of the attribute of interest.
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