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
 MarkovModel DPMatrix.model()
           
 MarkovModel SimpleModelInState.getModel()
           
static MarkovModel DP.flatView(MarkovModel model)
           
 MarkovModel DP.getModel()
           
 MarkovModel ModelInState.getModel()
          The model that is inside this state.
static MarkovModel XmlMarkovModel.readModel(org.w3c.dom.Element root)
           
 

Methods in org.biojava.bio.dp with parameters of type MarkovModel
 void ModelTrainer.registerModel(MarkovModel model)
          Registers an HMM with this trainer.
 DP DPFactory.createDP(MarkovModel model)
           
 DP DPFactory.DefaultFactory.createDP(MarkovModel model)
           
static MarkovModel DP.flatView(MarkovModel model)
           
static State[] DP.stateList(MarkovModel mm)
           
static int[][] DP.forwardTransitions(MarkovModel model, State[] states)
           
static double[][] DP.forwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)
           
static int[][] DP.backwardTransitions(MarkovModel model, State[] states)
           
static double[][] DP.backwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)
           
 void SimpleModelTrainer.registerModel(MarkovModel model)
           
static void XmlMarkovModel.writeModel(MarkovModel model, java.io.PrintStream out)
           
 

Constructors in org.biojava.bio.dp with parameters of type MarkovModel
SimpleModelInState(MarkovModel model, java.lang.String name)
           
DP(MarkovModel model)
           
 

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

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 java.lang.String DPCompiler.makeName(java.lang.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.