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

Packages that use DPMatrix

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

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

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

class

SingleDPMatrix The dynamic programming matrix for a single sequence.

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

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

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

class

PairDPMatrix Storage structure for intermediate values from a pairwise dynamic programming run.

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

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

DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)