jebl.evolution.characterReconstruction
Class MLContinuousCharacterReconstructor

java.lang.Object
  jebl.evolution.characterReconstruction.MLContinuousCharacterReconstructor

public class MLContinuousCharacterReconstructor
extends Object

This is the main class that controls the ancestral calculations by the Schluter ML method The theoretical foundations are found in Schulter et al. 1997 Evolution.

Author:

Stephen A. Smith

Constructor Summary

MLContinuousCharacterReconstructor(ContinuousCharacter conchar, SimpleRootedTree tree)
a basic constructor which just defines the tree and character

Method Summary

Map<Node,Double>	getPhenotypes()
Map<Node,Double>	getPhenotypesSE()
void	reconstruct() initiates the analysis
void	setChar(ContinuousCharacter conchar)
void	setTree(SimpleRootedTree tree)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MLContinuousCharacterReconstructor

public MLContinuousCharacterReconstructor(ContinuousCharacter conchar,
                                          SimpleRootedTree tree)

a basic constructor which just defines the tree and character

Parameters:

conchar - the continuous character to reconstruct

tree - the tree on which to reconstruct the character

Method Detail

setTree

public void setTree(SimpleRootedTree tree)

Parameters:

tree - the tree for the analysis, unnecessary if using the same tree used from the constructor

setChar

public void setChar(ContinuousCharacter conchar)

Parameters:

chonchar - the character for the analsysis, unnecessary if using the same tree used from the constructor

reconstruct

public void reconstruct()

initiates the analysis

getPhenotypes

public Map<Node,Double> getPhenotypes()

Returns:

the phenotypes estimated from the analysis

getPhenotypesSE

public Map<Node,Double> getPhenotypesSE()

Returns:

the phenotype standard errors estimated from the analysis