/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.dp.twohead; import org.biojava.bio.dp.IllegalTransitionException; import org.biojava.bio.symbol.IllegalAlphabetException; import org.biojava.bio.symbol.IllegalSymbolException; /** *
* 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. *
* * @author Matthew Pocock * @since 1.2 */ public interface CellCalculator { /** * Initialize the cell at [0][0] to the recursion initial parameters. * * @param cells the 2-D array of cells */ public void initialize(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. *
* * @param cells the array of cells to read from, with the cell to update * at 0,0 */ public void calcCell(Cell [][] cells) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException; }