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

Packages that use MarkovModel
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
`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
`static MarkovModel` `DP.flatView(MarkovModel model)`
`MarkovModel` `SimpleModelInState.getModel()`
`MarkovModel` `ModelInState.getModel()` The model that is inside this state.
`MarkovModel` `DP.getModel()`
`MarkovModel` `DPMatrix.model()`
`static MarkovModel` `XmlMarkovModel.readModel(Element root)`

Methods in org.biojava.bio.dp with parameters of type MarkovModel
`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
`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
`protected MarkovModel` `SingleDPMatrix.model`

Methods in org.biojava.bio.dp.onehead that return MarkovModel
`MarkovModel` `SingleDPMatrix.model()`

Constructors in org.biojava.bio.dp.onehead with parameters of type MarkovModel
`SingleDP(MarkovModel model)`

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

Methods in org.biojava.bio.dp.twohead that return MarkovModel
`MarkovModel` `PairDPMatrix.model()`

Methods in org.biojava.bio.dp.twohead with parameters of type MarkovModel
`static String` `DPCompiler.makeName(String prefix, MarkovModel model)`

Constructors in org.biojava.bio.dp.twohead with parameters of type MarkovModel
`PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm)`

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

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