org.biojava.bio.dp.twohead

Interface CellCalculator

public interface CellCalculator

The interface for all functions that can calculate the 'scores' array for a given cell.

The methods in this interface work on a square matrix of cells. The cell at 0,0 is considered the 'target' cell to which data can be written. The other cells are the neighbours to this cell in the DP matrix.

Since:

1.2

Author:

Matthew Pocock

Method Summary

Methods

Modifier and Type	Method and Description
void	calcCell(Cell[][] cells) Calculate the 'scores' array in the cell at cells[0][0].
void	initialize(Cell[][] cells) Initialize the cell at [0][0] to the recursion initial parameters.

Method Detail

initialize

void initialize(Cell[][] cells)
                throws IllegalSymbolException,
                       IllegalAlphabetException,
                       IllegalTransitionException

Initialize the cell at [0][0] to the recursion initial parameters.

Parameters:

cells - the 2-D array of cells

Throws:

IllegalSymbolException

IllegalAlphabetException

IllegalTransitionException

calcCell

void calcCell(Cell[][] cells)
              throws IllegalSymbolException,
                     IllegalAlphabetException,
                     IllegalTransitionException

Calculate the 'scores' array in the cell at cells[0][0].

These objects implement the actual cell-by-cell recursions, such as forwards or viterbi.

Parameters:

cells - the array of cells to read from, with the cell to update at 0,0

Throws:

IllegalSymbolException

IllegalAlphabetException

IllegalTransitionException