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

Packages that use MarkovModel

Package	Description
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead
org.biojava.bio.dp.twohead
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.

Uses of MarkovModel in org.biojava.bio.dp

Classes in org.biojava.bio.dp that implement MarkovModel

Modifier and Type	Class and Description
class	ProfileHMM
class	SimpleMarkovModel
class	WMAsMM Wraps a weight matrix up so that it appears to be a very simple HMM.

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

Modifier and Type	Method and Description
static MarkovModel	DP.flatView(MarkovModel model)
MarkovModel	ModelInState.getModel() The model that is inside this state.
MarkovModel	DP.getModel()
MarkovModel	SimpleModelInState.getModel()
MarkovModel	DPMatrix.model()
static MarkovModel	XmlMarkovModel.readModel(Element root)

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

Modifier and Type	Method and Description
static int[][]	DP.backwardTransitions(MarkovModel model, State[] states)
static double[][]	DP.backwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)
DP	DPFactory.createDP(MarkovModel model)
DP	DPFactory.DefaultFactory.createDP(MarkovModel model)
static MarkovModel	DP.flatView(MarkovModel model)
static int[][]	DP.forwardTransitions(MarkovModel model, State[] states) Returns a matrix for the specified States describing all valid Transitions between those States.
static double[][]	DP.forwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType) Compute the log(score) of all transitions between the specified States.
void	SimpleModelTrainer.registerModel(MarkovModel model)
void	ModelTrainer.registerModel(MarkovModel model) Registers an HMM with this trainer.
void	DP.setModel(MarkovModel model)
State[]	DP.stateList(MarkovModel mm)
static void	XmlMarkovModel.writeModel(MarkovModel model, PrintStream out)

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

Constructor and Description
DP(MarkovModel model)
SimpleHMMTrainer(MarkovModel model)
SimpleModelInState(MarkovModel model, String name)

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

Fields in org.biojava.bio.dp.onehead declared as MarkovModel

Modifier and Type	Field and Description
protected MarkovModel	SingleDPMatrix.model

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

Modifier and Type	Method and Description
MarkovModel	SingleDPMatrix.model()

Constructors in org.biojava.bio.dp.onehead with parameters of type MarkovModel

Constructor and Description
SingleDP(MarkovModel model)

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

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

Modifier and Type	Method and Description
MarkovModel	PairDPMatrix.model()

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

Modifier and Type	Method and Description
static String	DPCompiler.makeName(String prefix, MarkovModel model)

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

Constructor and Description
PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm)

Uses of MarkovModel in org.biojava.bio.program.hmmer

Classes in org.biojava.bio.program.hmmer that implement MarkovModel

Modifier and Type	Class and Description
class	FullHmmerProfileHMM This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
class	HmmerProfileHMM This is a class for representing HMMER generated Profile HMM.