ParameterizedTree.ParameterizedTreeBase

java.lang.Object
- pal.tree.ParameterizedTree.ParameterizedTreeBase

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

Nested Class Summary
- 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

Field Summary
- Fields inherited from interface pal.misc.Units
  DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

Constructors
Modifier	Constructor and Description
	`ParameterizedTreeBase()`
`protected`	`ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)` Cloning constructor
	`ParameterizedTreeBase(Tree baseTree)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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 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()`
`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

Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE

- Constructor Detail
  - ParameterizedTreeBase
```
protected ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)
```
    Cloning constructor
  - ParameterizedTreeBase
```
public ParameterizedTreeBase()
```
  - ParameterizedTreeBase
```
public ParameterizedTreeBase(Tree baseTree)
```
- Method Detail
  - setBaseTree
```
protected void setBaseTree(Tree baseTree)
```
  - getBaseTree
```
protected Tree getBaseTree()
```
  - getRoot
```
public final Node getRoot()
```
    Returns the root node of this tree.
    
    Specified by:
    
    getRoot in interface Tree
    
    Returns:
    
    the root node of this tree.
  - setRoot
```
public final void setRoot(Node root)
```
    Description copied from interface: Tree
    
    This method constructs a tree from the given root node.
    
    Specified by:
    
    setRoot in interface Tree
    
    Parameters:
    
    root - the root node of the tree to construct.
  - getIdentifier
```
public final Identifier getIdentifier(int i)
```
    Description copied from interface: IdGroup
    
    Returns the ith identifier.
    
    Specified by:
    
    getIdentifier in interface IdGroup
  - setIdentifier
```
public final void setIdentifier(int i,
                                Identifier id)
```
    Description copied from interface: IdGroup
    
    Sets the ith identifier.
    
    Specified by:
    
    setIdentifier in interface IdGroup
  - getIdCount
```
public final int getIdCount()
```
    Description copied from interface: IdGroup
    
    Returns the number of identifiers in this group
    
    Specified by:
    
    getIdCount in interface IdGroup
  - 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 interface IdGroup
  - getExternalNodeCount
```
public final int getExternalNodeCount()
```
    returns a count of the number of external nodes (tips) in this tree.
    
    Specified by:
    
    getExternalNodeCount in interface Tree
    
    Returns:
    
    a count of the number of external nodes (tips) in this tree.
  - getInternalNodeCount
```
public final int getInternalNodeCount()
```
    returns a count of the number of internal nodes (and hence clades) in this tree.
    
    Specified by:
    
    getInternalNodeCount in interface Tree
    
    Returns:
    
    a count of the number of internal nodes (and hence clades) in this tree.
  - getNodeCount
```
public final int getNodeCount()
```
  - getExternalNode
```
public final Node getExternalNode(int i)
```
    returns the ith external node in the tree.
    
    Specified by:
    
    getExternalNode in interface Tree
    
    Returns:
    
    the ith external node in the tree.
  - getInternalNode
```
public final Node getInternalNode(int i)
```
    returns the ith internal node in the tree.
    
    Specified by:
    
    getInternalNode in interface Tree
    
    Returns:
    
    the ith internal node in the tree.
  - 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 interface Tree
  - 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 interface UnitsProvider
    
    Specified by:
    
    getUnits in interface Tree
    
    Returns:
    
    the units relating to this object.
  - 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 interface Tree
    
    Parameters:
    
    node - the node whose attribute is being set.
    
    name - the name of the attribute.
    
    value - the new value of the attribute.
  - getAttribute
```
public final java.lang.Object getAttribute(Node node,
                                           java.lang.String name)
```
    Specified by:
    
    getAttribute in interface Tree
    
    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.
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - getCopy
```
public Tree getCopy()
```
    The cheapy copy that just creates a SimpleTree
    
    Specified by:
    
    getCopy in interface Tree
    
    Returns:
    
    a clone of this tree
  - getOrthogonalHints
```
public OrthogonalHints getOrthogonalHints()
```
    Returns:
    
    null by default (implying not hint information)

Class ParameterizedTree.ParameterizedTreeBase

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Nested classes/interfaces inherited from interface pal.tree.Tree

Field Summary

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface pal.misc.Parameterized

Constructor Detail

ParameterizedTreeBase

ParameterizedTreeBase

ParameterizedTreeBase

Method Detail

setBaseTree

getBaseTree

getRoot

setRoot

getIdentifier

setIdentifier

getIdCount

whichIdNumber

getExternalNodeCount

getInternalNodeCount

getNodeCount

getExternalNode

getInternalNode

createNodeList

getUnits

setAttribute

getAttribute

toString

getCopy

getOrthogonalHints