Uses of Class
org.biojava.bio.dp.DP

Packages that use DP
org.biojava.bio.dp HMM and Dynamic Programming Algorithms. 
org.biojava.bio.dp.onehead   
org.biojava.bio.dp.twohead   
 

Uses of DP in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that return DP
 DP AbstractTrainer.getDP()
           
 DP TrainingAlgorithm.getDP()
           
 DP DPFactory.createDP(MarkovModel model)
           
 DP DPFactory.DefaultFactory.createDP(MarkovModel model)
           
 

Constructors in org.biojava.bio.dp with parameters of type DP
BaumWelchTrainer(DP dp)
           
AbstractTrainer(DP dp)
           
BaumWelchSampler(DP dp)
           
 

Uses of DP in org.biojava.bio.dp.onehead
 

Subclasses of DP in org.biojava.bio.dp.onehead
 class SingleDP
          An implementation of DP that aligns a single sequence against a single model.
 

Constructors in org.biojava.bio.dp.onehead with parameters of type DP
SingleDPMatrix(DP dp, SymbolList symList)
           
 

Uses of DP in org.biojava.bio.dp.twohead
 

Subclasses of DP in org.biojava.bio.dp.twohead
 class PairwiseDP
          Algorithms for dynamic programming (alignments) between pairs of SymbolLists.
 

Methods in org.biojava.bio.dp.twohead with parameters of type DP
 CellCalculatorFactory CellCalculatorFactoryMaker.make(DP dp)
           
 CellCalculatorFactory DPInterpreter.Maker.make(DP dp)
           
 CellCalculatorFactory DPCompiler.make(DP dp)
           
 java.lang.Class DPCompiler.generateForardClass(DP dp)
           
 java.lang.Class DPCompiler.generateBackwardClass(DP dp)
           
 java.lang.Class DPCompiler.generateViterbiClass(DP dp)
           
 

Constructors in org.biojava.bio.dp.twohead with parameters of type DP
PairDPMatrix(DP dp, SymbolList seq0, SymbolList seq1)
           
DPInterpreter(DP dp)