jebl.evolution.distances

Class BasicDistanceMatrix

java.lang.Object

jebl.evolution.distances.BasicDistanceMatrix

All Implemented Interfaces:

DistanceMatrix

Direct Known Subclasses:

F84DistanceMatrix, HKYDistanceMatrix, JukesCantorDistanceMatrix, SequenceAlignmentsDistanceMatrix, TamuraNeiDistanceMatrix

public class BasicDistanceMatrix
extends java.lang.Object
implements DistanceMatrix

Version:

$Id: BasicDistanceMatrix.java 842 2007-11-12 22:33:48Z twobeers $

Author:

Andrew Rambaut, Alexei Drummond

Constructor Summary

Constructors

Constructor and Description
BasicDistanceMatrix(java.util.Collection<Taxon> taxa, double[][] distances)

Method Summary

Methods

Modifier and Type	Method and Description
double	getDistance(int row, int column) Gets the distance at a particular row and column
double	getDistance(Taxon taxonRow, Taxon taxonColumn) Gets the distance between 2 taxa
double[][]	getDistances() Gets a 2-dimensional array containing the distances
int	getSize() Gets the size of the matrix (which is square), i.e., number of rows or columns.
DistanceMatrix	getSubmatrix(java.util.Collection<Taxon> taxonSubset) Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).
java.util.List<Taxon>	getTaxa()

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicDistanceMatrix

public BasicDistanceMatrix(java.util.Collection<Taxon> taxa,
                   double[][] distances)

Method Detail

getSize

public int getSize()

Gets the size of the matrix (which is square), i.e., number of rows or columns.

Specified by:

getSize in interface DistanceMatrix

Returns:

the size

getTaxa

public java.util.List<Taxon> getTaxa()

Specified by:

getTaxa in interface DistanceMatrix

Returns:

the list of taxa that the state values correspond to.

getDistance

public double getDistance(int row,
                 int column)

Gets the distance at a particular row and column

Specified by:

getDistance in interface DistanceMatrix

Parameters:

row - the row index

column - the column index

Returns:

the distance

getDistance

public double getDistance(Taxon taxonRow,
                 Taxon taxonColumn)

Gets the distance between 2 taxa

Specified by:

getDistance in interface DistanceMatrix

Parameters:

taxonRow -

taxonColumn -

Returns:

the distance

getSubmatrix

public DistanceMatrix getSubmatrix(java.util.Collection<Taxon> taxonSubset)

Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).

Specified by:

getSubmatrix in interface DistanceMatrix

Parameters:

taxonSubset -

Returns:

the new submatrix

getDistances

public double[][] getDistances()

Gets a 2-dimensional array containing the distances

Specified by:

getDistances in interface DistanceMatrix

Returns:

the distances