BasicDistanceMatrix (JEBL2 lib API)

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 Description

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

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

Method Summary

All Methods Instance Methods Concrete 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> 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

Class BasicDistanceMatrix

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BasicDistanceMatrix

Method Detail

getSize

getTaxa

getDistance

getDistance

getSubmatrix

getDistances