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java.lang.Objectpal.tree.ParameterizedTree.ParameterizedTreeBase
public abstract static class ParameterizedTree.ParameterizedTreeBase
For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Nested classes/interfaces inherited from interface pal.tree.Tree |
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Tree.TreeBase |
Field Summary |
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Fields inherited from interface pal.misc.Units |
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DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS |
Constructor Summary | |
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ParameterizedTree.ParameterizedTreeBase()
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protected |
ParameterizedTree.ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)
Cloning constructor |
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ParameterizedTree.ParameterizedTreeBase(Tree baseTree)
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Method Summary | |
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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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protected Tree |
getBaseTree()
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Tree |
getCopy()
The cheapy copy that just creates a SimpleTree |
Node |
getExternalNode(int i)
returns the ith external node in the tree. |
int |
getExternalNodeCount()
returns a count of the number of external nodes (tips) in this tree. |
int |
getIdCount()
Returns the number of identifiers in this group |
Identifier |
getIdentifier(int i)
Returns the ith identifier. |
Node |
getInternalNode(int i)
returns the ith internal node in the tree. |
int |
getInternalNodeCount()
returns a count of the number of internal nodes (and hence clades) in this tree. |
int |
getNodeCount()
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OrthogonalHints |
getOrthogonalHints()
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Node |
getRoot()
Returns the root node of this tree. |
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. |
protected void |
setBaseTree(Tree baseTree)
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void |
setIdentifier(int i,
Identifier id)
Sets the ith identifier. |
void |
setRoot(Node root)
This method constructs a tree from the given root node. |
java.lang.String |
toString()
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int |
whichIdNumber(java.lang.String s)
returns the index of the identifier with the given name. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface pal.misc.Parameterized |
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getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE |
Constructor Detail |
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protected ParameterizedTree.ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)
public ParameterizedTree.ParameterizedTreeBase()
public ParameterizedTree.ParameterizedTreeBase(Tree baseTree)
Method Detail |
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protected void setBaseTree(Tree baseTree)
protected Tree getBaseTree()
public final Node getRoot()
getRoot
in interface Tree
public final void setRoot(Node root)
Tree
setRoot
in interface Tree
root
- the root node of the tree to construct.public final Identifier getIdentifier(int i)
IdGroup
getIdentifier
in interface IdGroup
public final void setIdentifier(int i, Identifier id)
IdGroup
setIdentifier
in interface IdGroup
public final int getIdCount()
IdGroup
getIdCount
in interface IdGroup
public final int whichIdNumber(java.lang.String s)
IdGroup
whichIdNumber
in interface IdGroup
public final int getExternalNodeCount()
getExternalNodeCount
in interface Tree
public final int getInternalNodeCount()
getInternalNodeCount
in interface Tree
public final int getNodeCount()
public final Node getExternalNode(int i)
getExternalNode
in interface Tree
public final Node getInternalNode(int i)
getInternalNode
in interface Tree
public final void createNodeList()
createNodeList
in interface Tree
public final int getUnits()
Tree
getUnits
in interface UnitsProvider
getUnits
in interface Tree
public final void setAttribute(Node node, java.lang.String name, java.lang.Object value)
Tree
setAttribute
in interface Tree
node
- the node whose attribute is being set.name
- the name of the attribute.value
- the new value of the attribute.public final java.lang.Object getAttribute(Node node, java.lang.String name)
getAttribute
in interface Tree
node
- the node being interrogated.name
- the name of the attribute of interest.
public java.lang.String toString()
toString
in class java.lang.Object
public Tree getCopy()
getCopy
in interface Tree
public OrthogonalHints getOrthogonalHints()
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