DistanceMatrix (JEBL2 lib API)

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

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	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