jebl.evolution.distances
Class ModelBasedDistanceMatrix

java.lang.Object
  jebl.evolution.distances.ModelBasedDistanceMatrix

public class ModelBasedDistanceMatrix
extends Object

Author:

Joseph Heled

Field Summary

protected static double	freqR
protected static double	freqY
protected static double	MAX_DISTANCE

Constructor Summary

ModelBasedDistanceMatrix()

Method Summary

protected static double[]	getFrequencies(Alignment alignment)
protected static double[]	getFrequencies(List<Sequence> sequences) As a side effect, this method sets freqR and freqY if called on nucleotide sequences.
protected static double[]	getFrequenciesSafe(Alignment alignment)
protected static double[]	getFrequenciesSafe(List<Sequence> sequences) As a side effect, this method sets freqR and freqY if called on nucleotide sequences.

Methods inherited from class java.lang.Object

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

Field Detail

MAX_DISTANCE

protected static final double MAX_DISTANCE

See Also:

Constant Field Values

freqR

protected static double freqR

freqY

protected static double freqY

Constructor Detail

ModelBasedDistanceMatrix

public ModelBasedDistanceMatrix()

Method Detail

getFrequenciesSafe

protected static double[] getFrequenciesSafe(List<Sequence> sequences)

As a side effect, this method sets freqR and freqY if called on nucleotide sequences.

Parameters:

sequences - A list of sequences of the same type

Returns:

Approximation of the relative canonical state frequencies in the sequences; Each frequency is guaranteed to be > 0 (and therefore it can only be an approximation).

getFrequenciesSafe

protected static double[] getFrequenciesSafe(Alignment alignment)

getFrequencies

protected static double[] getFrequencies(List<Sequence> sequences)

As a side effect, this method sets freqR and freqY if called on nucleotide sequences.

Parameters:

sequences - A list of sequences of the same type

Returns:

Relative canonical state frequencies in the sequences;

getFrequencies

protected static double[] getFrequencies(Alignment alignment)