Uses of Class
org.biojava.bio.dp.IllegalTransitionException

Packages that use IllegalTransitionException
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 IllegalTransitionException in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that throw IllegalTransitionException
 void TransitionTrainer.addCount(State from, State to, double count)
          Add 'count' to the transition from->to.
abstract  double DP.backward(SymbolList[] symList, ScoreType scoreType)
           
abstract  DPMatrix DP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
           
abstract  DPMatrix DP.backwardMatrix(SymbolList[] symList, ScoreType scoreType)
           
protected  void ProfileHMM.connectModel()
          This is called by constructor in setting up the allowed transitions in the model
abstract  double DP.forward(SymbolList[] symList, ScoreType scoreType)
           
abstract  DPMatrix DP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
           
abstract  DPMatrix DP.forwardMatrix(SymbolList[] symList, ScoreType scoreType)
           
 void SimpleMarkovModel.removeState(State toGo)
           
 void MarkovModel.removeState(State toGo)
          Remove a state from the model.
protected abstract  double AbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
           
protected  double BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
           
protected  double BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
           
protected  double BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType)
           
 State[] DP.stateList(MarkovModel mm)
           
abstract  StatePath DP.viterbi(SymbolList[] symList, ScoreType scoreType)
           
 

Constructors in org.biojava.bio.dp that throw IllegalTransitionException
DP(MarkovModel model)
           
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory)
          Deprecated.  
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)
          Create a new ProfileHMM.
 

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

Constructors in org.biojava.bio.dp.onehead that throw IllegalTransitionException
SingleDP(MarkovModel model)
           
 

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

Methods in org.biojava.bio.dp.twohead that throw IllegalTransitionException
 double PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)
           
 DPMatrix PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
           
 DPMatrix PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
           
 CellCalculator DPInterpreter.backwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.backwards(ScoreType scoreType)
           
 void CellCalculator.calcCell(Cell[][] cells)
           Calculate the 'scores' array in the cell at cells[0][0].
 double PairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType)
           
 DPMatrix PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
           
 DPMatrix PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)
           
 CellCalculator DPInterpreter.forwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.forwards(ScoreType scoreType)
           
 void CellCalculator.initialize(Cell[][] cells)
          Initialize the cell at [0][0] to the recursion initial parameters.
 CellCalculator DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
           
 CellCalculator CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)
           
 StatePath PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)
           
 

Constructors in org.biojava.bio.dp.twohead that throw IllegalTransitionException
PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm)
           
 

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

Methods in org.biojava.bio.program.hmmer that throw IllegalTransitionException
protected  void HmmerProfileHMM.connectModel()
          This is called by constructor in setting up the allowed transitions in the model
 

Constructors in org.biojava.bio.program.hmmer that throw IllegalTransitionException
HmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)