public class UnconstrainedTree extends ParameterizedTree.ParameterizedTreeBase implements ParameterizedTree
ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Tree.TreeBase
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Modifier | Constructor and Description |
---|---|
|
UnconstrainedTree(Tree t)
take any tree and afford it with an interface
suitable for an unconstrained tree (parameters
are all available branch lengths)
|
protected |
UnconstrainedTree(UnconstrainedTree toCopy) |
Modifier and Type | Method and Description |
---|---|
Tree |
getCopy()
The cheapy copy that just creates a SimpleTree
|
double |
getDefaultValue(int n)
get default value of parameter
|
double |
getLowerLimit(int n)
get lower parameter limit
|
int |
getNumParameters()
get number of parameters
|
double |
getParameter(int n)
get model parameter
|
java.lang.String |
getParameterizationInfo() |
static ParameterizedTree.Factory |
getParameterizedTreeFactory()
Obtain a ParameterizedTree.Factory for generating Unconstrained trees
|
double |
getUpperLimit(int n)
get upper parameter limit
|
void |
setParameter(double param,
int n)
set model parameter
|
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter
|
createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getOrthogonalHints, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumber
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
getOrthogonalHints
createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot
getIdCount, getIdentifier, setIdentifier, whichIdNumber
public UnconstrainedTree(Tree t)
protected UnconstrainedTree(UnconstrainedTree toCopy)
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public void setParameter(double param, int n)
Parameterized
setParameter
in interface Parameterized
param
- parameter valuen
- parameter numberpublic java.lang.String getParameterizationInfo()
getParameterizationInfo
in interface ParameterizedTree
public double getParameter(int n)
Parameterized
getParameter
in interface Parameterized
n
- parameter numberpublic void setParameterSE(double paramSE, int n)
Parameterized
setParameterSE
in interface Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
getLowerLimit
in interface Parameterized
n
- parameter numberpublic double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter numberpublic Tree getCopy()
ParameterizedTree.ParameterizedTreeBase
getCopy
in interface Tree
getCopy
in class ParameterizedTree.ParameterizedTreeBase
public static final ParameterizedTree.Factory getParameterizedTreeFactory()