Uses of Interface
org.biojava.bio.dp.DPMatrix

Packages that use DPMatrix

Package	Description
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead
org.biojava.bio.dp.twohead

Uses of DPMatrix in org.biojava.bio.dp

Methods in org.biojava.bio.dp that return DPMatrix

Modifier and Type	Method and Description
abstract 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)
DPMatrix	DP.forwardsBackwards(SymbolList[] symList, ScoreType scoreType)

Methods in org.biojava.bio.dp with parameters of type DPMatrix

Modifier and Type	Method and Description
abstract 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 DPMatrix

Modifier and Type	Class and Description
class	SingleDPMatrix The dynamic programming matrix for a single sequence.

Methods in org.biojava.bio.dp.onehead that return DPMatrix

Modifier and Type	Method and Description
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType)

Methods in org.biojava.bio.dp.onehead with parameters of type DPMatrix

Modifier and Type	Method and Description
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	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 DPMatrix

Modifier and Type	Class and Description
class	PairDPMatrix Storage structure for intermediate values from a pairwise dynamic programming run.

Methods in org.biojava.bio.dp.twohead that return DPMatrix

Modifier and Type	Method and Description
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)

Methods in org.biojava.bio.dp.twohead with parameters of type DPMatrix

Modifier and Type	Method and Description
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)