Package 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
Modifier and TypeMethodDescriptiondouble
getDistance
(int row, int column) Gets the distance at a particular row and columndouble
getDistance
(Taxon taxonRow, Taxon taxonColumn) Gets the distance between 2 taxadouble[][]
Gets a 2-dimensional array containing the distancesint
getSize()
Gets the size of the matrix (which is square), i.e., number of rows or columns.getSubmatrix
(Collection<Taxon> taxa) Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).getTaxa()
-
Method Details
-
getSize
int getSize()Gets the size of the matrix (which is square), i.e., number of rows or columns.- Returns:
- the size
-
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 indexcolumn
- the column index- Returns:
- the distance
-
getDistance
Gets the distance between 2 taxa- Parameters:
taxonRow
-taxonColumn
-- Returns:
- the distance
-
getSubmatrix
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
-