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

Packages that use DP

Package	Description
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

Modifier and Type	Method and Description
DP	DPFactory.createDP(MarkovModel model)
DP	DPFactory.DefaultFactory.createDP(MarkovModel model)
DP	TrainingAlgorithm.getDP()
DP	AbstractTrainer.getDP()

Constructors in org.biojava.bio.dp with parameters of type DP

Constructor and Description
AbstractTrainer(DP dp)
BaumWelchSampler(DP dp)
BaumWelchTrainer(DP dp)

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

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

Modifier and Type	Class and Description
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

Constructor and Description
SingleDPMatrix(DP dp, SymbolList symList)

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

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

Modifier and Type	Class and Description
class	PairwiseDP Algorithms for dynamic programming (alignments) between pairs of SymbolLists.

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

Modifier and Type	Method and Description
Class	DPCompiler.generateBackwardClass(DP dp)
Class	DPCompiler.generateForardClass(DP dp)
Class	DPCompiler.generateViterbiClass(DP dp)
CellCalculatorFactory	DPCompiler.make(DP dp)
CellCalculatorFactory	DPInterpreter.Maker.make(DP dp)
CellCalculatorFactory	CellCalculatorFactoryMaker.make(DP dp)

Constructors in org.biojava.bio.dp.twohead with parameters of type DP

Constructor and Description
DPInterpreter(DP dp)
PairDPMatrix(DP dp, SymbolList seq0, SymbolList seq1)