Package org.biojava.bio.dp.twohead

Interface Summary

Interface	Description
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

Class	Description
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.