Uses of Class
org.biojava.bio.dp.IllegalTransitionException
Packages that use IllegalTransitionException
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 IllegalTransitionException in org.biojava.bio.dp
Methods in org.biojava.bio.dp that throw IllegalTransitionExceptionModifier and TypeMethodDescriptionvoidAdd 'count' to the transition from->to.abstract doubleDP.backward(SymbolList[] symList, ScoreType scoreType) abstract DPMatrixDP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrixDP.backwardMatrix(SymbolList[] symList, ScoreType scoreType) protected voidProfileHMM.connectModel()This is called by constructor in setting up the allowed transitions in the modelabstract doubleDP.forward(SymbolList[] symList, ScoreType scoreType) abstract DPMatrixDP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrixDP.forwardMatrix(SymbolList[] symList, ScoreType scoreType) voidMarkovModel.removeState(State toGo) Remove a state from the model.voidSimpleMarkovModel.removeState(State toGo) protected abstract doubleAbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList) protected doubleBaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList) protected doubleBaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType) protected doubleBaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList) State[]DP.stateList(MarkovModel mm) abstract StatePathDP.viterbi(SymbolList[] symList, ScoreType scoreType) Constructors in org.biojava.bio.dp that throw IllegalTransitionExceptionModifierConstructorDescriptionProfileHMM(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 -
Uses of IllegalTransitionException in org.biojava.bio.dp.twohead
Methods in org.biojava.bio.dp.twohead that throw IllegalTransitionExceptionModifier and TypeMethodDescriptiondoublePairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType) voidCalculate the 'scores' array in the cell at cells[0][0].doublePairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType) voidCellCalculator.initialize(Cell[][] cells) Initialize the cell at [0][0] to the recursion initial parameters.CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal) DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal) PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType) Constructors in org.biojava.bio.dp.twohead that throw IllegalTransitionException -
Uses of IllegalTransitionException in org.biojava.bio.program.hmmer
Methods in org.biojava.bio.program.hmmer that throw IllegalTransitionExceptionModifier and TypeMethodDescriptionprotected voidHmmerProfileHMM.connectModel()This is called by constructor in setting up the allowed transitions in the modelConstructors in org.biojava.bio.program.hmmer that throw IllegalTransitionExceptionModifierConstructorDescriptionprotectedHmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)