Package jebl.evolution.distances

Class BasicDistanceMatrix

    • Constructor Summary

      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