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 TypeClassDescriptionclass
class
class
Wraps 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 MarkovModel
DP.flatView
(MarkovModel model) DP.getModel()
ModelInState.getModel()
The model that is inside this state.SimpleModelInState.getModel()
DPMatrix.model()
static MarkovModel
Methods 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 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
ModelTrainer.registerModel
(MarkovModel model) Registers an HMM with this trainer.void
SimpleModelTrainer.registerModel
(MarkovModel model) 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 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 String
DPCompiler.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 TypeClassDescriptionclass
This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).class
This is a class for representing HMMER generated Profile HMM.