## 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 double` `BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)`
`protected double` `BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)`
`protected abstract double` `AbstractTrainer.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
`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)`