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Interface Summary | |
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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 | |
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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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