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.