pal.tree
Class UnconstrainedTree
java.lang.Object
|
+--pal.tree.ParameterizedTree
|
+--pal.tree.UnconstrainedTree
- All Implemented Interfaces:
- Parameterized, java.io.Serializable, Tree, Units
- public class UnconstrainedTree
- extends ParameterizedTree
provides parameter interface to an unconstrained tree
(parameters are all available branch lengths)
- See Also:
- Serialized Form
Constructor Summary |
UnconstrainedTree(Tree t)
take any tree and afford it with an interface
suitable for an unconstrained tree (parameters
are all available branch lengths) |
Methods inherited from class pal.tree.ParameterizedTree |
createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setBaseTree, setRoot, setUnits, toString |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
UnconstrainedTree
public UnconstrainedTree(Tree t)
- take any tree and afford it with an interface
suitable for an unconstrained tree (parameters
are all available branch lengths)
getNumParameters
public int getNumParameters()
- Description copied from interface:
Parameterized
- get number of parameters
- Following copied from interface:
pal.misc.Parameterized
- Returns:
- number of parameters
setParameter
public void setParameter(double param,
int n)
- Description copied from interface:
Parameterized
- set model parameter
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
param
- parameter valuen
- parameter number
getParameter
public double getParameter(int n)
- Description copied from interface:
Parameterized
- get model parameter
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
n
- parameter number- Returns:
- parameter value
setParameterSE
public void setParameterSE(double paramSE,
int n)
- Description copied from interface:
Parameterized
- set standard errors for model parameter
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
paramSE
- standard error of parameter valuen
- parameter number
getLowerLimit
public double getLowerLimit(int n)
- Description copied from interface:
Parameterized
- get lower parameter limit
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
getUpperLimit
public double getUpperLimit(int n)
- Description copied from interface:
Parameterized
- get upper parameter limit
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
getDefaultValue
public double getDefaultValue(int n)
- Description copied from interface:
Parameterized
- get default value of parameter
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
n
- parameter number- Returns:
- default value