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.