Interface DistanceMatrix

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