Package 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
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Method Summary
Modifier and TypeMethodDescriptionvoid
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.
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Method Details
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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
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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
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