ClockTree

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pal.tree
Class ClockTree

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

All Implemented Interfaces:: java.io.Serializable, IdGroup, Parameterized, Units, UnitsProvider, ParameterizedTree, Tree

Direct Known Subclasses:: DemographicClockTree

public class ClockTree
extends ParameterizedTree.ParameterizedTreeBase
implements ParameterizedTree
extends ParameterizedTree.ParameterizedTreeBase
implements ParameterizedTree

provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)

Version:: $Id: ClockTree.java,v 1.16 2003/06/04 03:17:52 matt Exp $
Author:: Korbinian Strimmer, Alexei Drummond
See Also:: Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree
`ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase`

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
`protected double[]`	`parameter`

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

Constructor Summary
`ClockTree()`
`ClockTree(Tree t)` take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).

Method Summary
`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 Clock trees
`double`	`getUpperLimit(int n)` get upper parameter limit
`protected void`	`heights2parameters()`
`protected void`	`parameters2Heights()`
`void`	`setParameter(double param, int n)` set model parameter
`void`	`setParameterSE(double paramSE, int n)` set standard errors for model parameter
`void`	`update()` make clocktree consistent with branch lengths

Methods inherited from class pal.tree.ParameterizedTree.ParameterizedTreeBase
`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
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Methods inherited from interface pal.tree.ParameterizedTree
`getOrthogonalHints`

Methods inherited from interface pal.tree.Tree
`createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot`

Methods inherited from interface pal.misc.IdGroup
`getIdCount, getIdentifier, setIdentifier, whichIdNumber`

Field Detail

parameter

protected double[] parameter

Constructor Detail

ClockTree

public ClockTree()

ClockTree

public ClockTree(Tree t)

take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).

This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).

Method Detail

update

public void update()

make clocktree consistent with branch lengths