jebl.evolution.distances

Interface DistanceMatrix

All Known Implementing Classes:

BasicDistanceMatrix, F84DistanceMatrix, HKYDistanceMatrix, JukesCantorDistanceMatrix, SequenceAlignmentsDistanceMatrix, TamuraNeiDistanceMatrix

public interface DistanceMatrix

Version:

$Id: DistanceMatrix.java 186 2006-01-24 00:41:22Z pepster $

Author:

Andrew Rambaut, Alexei Drummond

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> taxa) 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()

Method Detail

getSize

int getSize()

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

Returns:

the size

getTaxa

java.util.List<Taxon> getTaxa()

Returns:

the list of taxa that the state values correspond to.

getDistance

double getDistance(int row,
                 int column)

Gets the distance at a particular row and column

Parameters:

row - the row index

column - the column index

Returns:

the distance

getDistance

double getDistance(Taxon taxonRow,
                 Taxon taxonColumn)

Gets the distance between 2 taxa

Parameters:

taxonRow -

taxonColumn -

Returns:

the distance

getSubmatrix

DistanceMatrix getSubmatrix(java.util.Collection<Taxon> taxa)

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

Parameters:

taxa -

Returns:

the new submatrix

getDistances

double[][] getDistances()

Gets a 2-dimensional array containing the distances

Returns:

the distances