jebl.evolution.distances
public class BasicDistanceMatrix extends java.lang.Object implements DistanceMatrix
Constructor and Description |
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BasicDistanceMatrix(java.util.Collection<Taxon> taxa,
double[][] distances) |
Modifier and Type | Method and Description |
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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() |
public BasicDistanceMatrix(java.util.Collection<Taxon> taxa, double[][] distances)
public int getSize()
getSize
in interface DistanceMatrix
public java.util.List<Taxon> getTaxa()
getTaxa
in interface DistanceMatrix
public double getDistance(int row, int column)
getDistance
in interface DistanceMatrix
row
- the row indexcolumn
- the column indexpublic double getDistance(Taxon taxonRow, Taxon taxonColumn)
getDistance
in interface DistanceMatrix
taxonRow
- taxonColumn
- public DistanceMatrix getSubmatrix(java.util.Collection<Taxon> taxonSubset)
getSubmatrix
in interface DistanceMatrix
taxonSubset
- public double[][] getDistances()
getDistances
in interface DistanceMatrix
http://code.google.com/p/jebl2/