Uses of Interface
org.biojava.bio.dp.DPMatrix
Packages that use DPMatrix
Package
Description
HMM and Dynamic Programming Algorithms.
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Uses of DPMatrix in org.biojava.bio.dp
Methods in org.biojava.bio.dp that return DPMatrixModifier and TypeMethodDescriptionabstract DPMatrix
DP.backwardMatrix
(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrix
DP.backwardMatrix
(SymbolList[] symList, ScoreType scoreType) abstract DPMatrix
DP.forwardMatrix
(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrix
DP.forwardMatrix
(SymbolList[] symList, ScoreType scoreType) DP.forwardsBackwards
(SymbolList[] symList, ScoreType scoreType) Methods in org.biojava.bio.dp with parameters of type DPMatrixModifier and TypeMethodDescriptionabstract DPMatrix
DP.backwardMatrix
(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrix
DP.forwardMatrix
(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) -
Uses of DPMatrix in org.biojava.bio.dp.onehead
Classes in org.biojava.bio.dp.onehead that implement DPMatrixModifier and TypeClassDescriptionclass
The dynamic programming matrix for a single sequence.Methods in org.biojava.bio.dp.onehead that return DPMatrixModifier and TypeMethodDescriptionSingleDP.backwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, ScoreType scoreType) Methods in org.biojava.bio.dp.onehead with parameters of type DPMatrixModifier and TypeMethodDescriptionSingleDP.backwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) -
Uses of DPMatrix in org.biojava.bio.dp.twohead
Classes in org.biojava.bio.dp.twohead that implement DPMatrixModifier and TypeClassDescriptionclass
Storage structure for intermediate values from a pairwise dynamic programming run.Methods in org.biojava.bio.dp.twohead that return DPMatrixModifier and TypeMethodDescriptionPairwiseDP.backwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.backwardMatrix
(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.forwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.forwardMatrix
(SymbolList[] seqs, ScoreType scoreType) Methods in org.biojava.bio.dp.twohead with parameters of type DPMatrixModifier and TypeMethodDescriptionPairwiseDP.backwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.forwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)