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 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(Collection<Taxon> taxa)
    Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).
    List<Taxon>
    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

      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(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