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| Interface Summary | |
|---|---|
| CellCalculator | The interface for all functions that can calculate the 'scores' array for a given cell. |
| CellCalculatorFactory | |
| CellCalculatorFactoryMaker | The interface for all functions that can calculate the 'scores' array for a given cell. |
| PairDPCursor | A cursor over a DP matrix. |
| Class Summary | |
|---|---|
| AbstractMatrixPairDPCursor | |
| BackMatrixPairDPCursor | |
| Cell | A single cell in the DP matrix. |
| DPCompiler | This is an implementation of CellCalculatorFactoryMaker that compiles the HMM object down to Java byte-code that is equivalent in behaviour to the interpreter. |
| DPInterpreter | |
| DPInterpreter.Maker | |
| EmissionCache | Cache for columns of emission probabilities in pair-wise alignment algorithms. |
| LightPairDPCursor | A LIGHT implementation of PairDPCursor. |
| MatrixPairDPCursor | |
| PairDPMatrix | Storage structure for intermediate values from a pairwise dynamic programming run. |
| PairwiseDP | Algorithms for dynamic programming (alignments) between pairs of SymbolLists. |
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