Package pal.tree
Class ParameterizedTree.ParameterizedTreeBase
- java.lang.Object
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- pal.tree.ParameterizedTree.ParameterizedTreeBase
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- All Implemented Interfaces:
java.io.Serializable
,IdGroup
,Parameterized
,Units
,UnitsProvider
,Tree
- Direct Known Subclasses:
ClockTree
,LogParameterizedTree
,MutationRateModelTree
,UnconstrainedTree
- Enclosing interface:
- ParameterizedTree
public abstract static class ParameterizedTree.ParameterizedTreeBase extends java.lang.Object implements Parameterized, Tree
For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
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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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Constructor Summary
Constructors Modifier Constructor Description ParameterizedTreeBase()
protected
ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)
Cloning constructorParameterizedTreeBase(Tree baseTree)
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Method Summary
All Methods Instance Methods Concrete 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)
protected Tree
getBaseTree()
Tree
getCopy()
The cheapy copy that just creates a SimpleTreeNode
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 groupIdentifier
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()
OrthogonalHints
getOrthogonalHints()
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)
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()
int
whichIdNumber(java.lang.String s)
returns the index of the identifier with the given name.-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
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Constructor Detail
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ParameterizedTreeBase
protected ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)
Cloning constructor
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ParameterizedTreeBase
public ParameterizedTreeBase()
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ParameterizedTreeBase
public ParameterizedTreeBase(Tree baseTree)
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Method Detail
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setBaseTree
protected void setBaseTree(Tree baseTree)
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getBaseTree
protected Tree getBaseTree()
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getRoot
public final Node getRoot()
Returns the root node of this tree.
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setRoot
public final void setRoot(Node root)
Description copied from interface:Tree
This method constructs a tree from the given root node.
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getIdentifier
public final Identifier getIdentifier(int i)
Description copied from interface:IdGroup
Returns the ith identifier.- Specified by:
getIdentifier
in interfaceIdGroup
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setIdentifier
public final void setIdentifier(int i, Identifier id)
Description copied from interface:IdGroup
Sets the ith identifier.- Specified by:
setIdentifier
in interfaceIdGroup
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getIdCount
public final int getIdCount()
Description copied from interface:IdGroup
Returns the number of identifiers in this group- Specified by:
getIdCount
in interfaceIdGroup
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whichIdNumber
public final int whichIdNumber(java.lang.String s)
Description copied from interface:IdGroup
returns the index of the identifier with the given name.- Specified by:
whichIdNumber
in interfaceIdGroup
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getExternalNodeCount
public final int getExternalNodeCount()
returns a count of the number of external nodes (tips) in this tree.- Specified by:
getExternalNodeCount
in interfaceTree
- Returns:
- a count of the number of external nodes (tips) in this tree.
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getInternalNodeCount
public final int getInternalNodeCount()
returns a count of the number of internal nodes (and hence clades) in this tree.- Specified by:
getInternalNodeCount
in interfaceTree
- Returns:
- a count of the number of internal nodes (and hence clades) in this tree.
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getNodeCount
public final int getNodeCount()
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getExternalNode
public final Node getExternalNode(int i)
returns the ith external node in the tree.- Specified by:
getExternalNode
in interfaceTree
- Returns:
- the ith external node in the tree.
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getInternalNode
public final Node getInternalNode(int i)
returns the ith internal node in the tree.- Specified by:
getInternalNode
in interfaceTree
- Returns:
- the ith internal node in the tree.
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createNodeList
public final void createNodeList()
This method is called to ensure that the calls to other methods in this interface are valid.- Specified by:
createNodeList
in interfaceTree
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getUnits
public final int getUnits()
Description copied from interface:Tree
Gets the units that this tree's branch lengths and node heights are expressed in.- Specified by:
getUnits
in interfaceTree
- Specified by:
getUnits
in interfaceUnitsProvider
- Returns:
- the units relating to this object.
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setAttribute
public final void setAttribute(Node node, java.lang.String name, java.lang.Object value)
Description copied from interface:Tree
Sets an named attribute for a given node.- Specified by:
setAttribute
in interfaceTree
- 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
public final java.lang.Object getAttribute(Node node, java.lang.String name)
- Specified by:
getAttribute
in interfaceTree
- 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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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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getCopy
public Tree getCopy()
The cheapy copy that just creates a SimpleTree
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getOrthogonalHints
public OrthogonalHints getOrthogonalHints()
- Returns:
- null by default (implying not hint information)
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