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java.lang.Objectpal.tree.ParameterizedTree.ParameterizedTreeBase
pal.tree.UnconstrainedTree
public class UnconstrainedTree
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree |
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ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase |
Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Nested classes/interfaces inherited from interface pal.tree.Tree |
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Tree.TreeBase |
Field Summary |
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Fields inherited from interface pal.misc.Units |
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DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS |
Constructor Summary | |
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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)
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Method Summary | |
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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()
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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 |
Methods inherited from class pal.tree.ParameterizedTree.ParameterizedTreeBase |
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createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getOrthogonalHints, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface pal.tree.ParameterizedTree |
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getOrthogonalHints |
Methods inherited from interface pal.tree.Tree |
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createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot |
Methods inherited from interface pal.misc.IdGroup |
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getIdCount, getIdentifier, setIdentifier, whichIdNumber |
Constructor Detail |
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public UnconstrainedTree(Tree t)
protected UnconstrainedTree(UnconstrainedTree toCopy)
Method Detail |
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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 number
public 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 number
public double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter number
public double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter number
public Tree getCopy()
ParameterizedTree.ParameterizedTreeBase
getCopy
in interface Tree
getCopy
in class ParameterizedTree.ParameterizedTreeBase
public static final ParameterizedTree.Factory getParameterizedTreeFactory()
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