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## Package org.biojava.bio.dp.twohead

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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