## 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.