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)