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