Uses of Interface
org.biojava.bio.dp.MarkovModel
Packages that use MarkovModel
Package
Description
HMM and Dynamic Programming Algorithms.
Tools for working with profile Hidden Markov Models from the HMMer package.
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Uses of MarkovModel in org.biojava.bio.dp
Classes in org.biojava.bio.dp that implement MarkovModelModifier and TypeClassDescriptionclassclassclassWraps a weight matrix up so that it appears to be a very simple HMM.Methods in org.biojava.bio.dp that return MarkovModelModifier and TypeMethodDescriptionstatic MarkovModelDP.flatView(MarkovModel model) DP.getModel()ModelInState.getModel()The model that is inside this state.SimpleModelInState.getModel()DPMatrix.model()static MarkovModelMethods in org.biojava.bio.dp with parameters of type MarkovModelModifier and TypeMethodDescriptionstatic int[][]DP.backwardTransitions(MarkovModel model, State[] states) static double[][]DP.backwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType) DPFactory.createDP(MarkovModel model) DPFactory.DefaultFactory.createDP(MarkovModel model) static MarkovModelDP.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.voidModelTrainer.registerModel(MarkovModel model) Registers an HMM with this trainer.voidSimpleModelTrainer.registerModel(MarkovModel model) voidDP.setModel(MarkovModel model) State[]DP.stateList(MarkovModel mm) static voidXmlMarkovModel.writeModel(MarkovModel model, PrintStream out) Constructors in org.biojava.bio.dp with parameters of type MarkovModelModifierConstructorDescriptionDP(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 MarkovModelMethods in org.biojava.bio.dp.onehead that return MarkovModelConstructors in org.biojava.bio.dp.onehead with parameters of type MarkovModel -
Uses of MarkovModel in org.biojava.bio.dp.twohead
Methods in org.biojava.bio.dp.twohead that return MarkovModelMethods in org.biojava.bio.dp.twohead with parameters of type MarkovModelModifier and TypeMethodDescriptionstatic StringDPCompiler.makeName(String prefix, MarkovModel model) Constructors in org.biojava.bio.dp.twohead with parameters of type MarkovModel -
Uses of MarkovModel in org.biojava.bio.program.hmmer
Classes in org.biojava.bio.program.hmmer that implement MarkovModelModifier and TypeClassDescriptionclassThis is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).classThis is a class for representing HMMER generated Profile HMM.