Package jebl.evolution.distances

Class BasicDistanceMatrix

java.lang.Object
jebl.evolution.distances.BasicDistanceMatrix
All Implemented Interfaces:
DistanceMatrix
Direct Known Subclasses:
F84DistanceMatrix, HKYDistanceMatrix, JukesCantorDistanceMatrix, SequenceAlignmentsDistanceMatrix, TamuraNeiDistanceMatrix
public class BasicDistanceMatrix extends Object implements DistanceMatrix
Version:
$Id: BasicDistanceMatrix.java 842 2007-11-12 22:33:48Z twobeers $
Author:
Andrew Rambaut, Alexei Drummond

  • Constructor Details

    • BasicDistanceMatrix

      public BasicDistanceMatrix(Collection<Taxon> taxa, double[][] distances)

  • Method Details

    • 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 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(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