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

Packages that use IllegalTransitionException

Package	Description
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

Modifier and Type	Method and Description
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	MarkovModel.removeState(State toGo) Remove a state from the model.
void	SimpleMarkovModel.removeState(State toGo)
protected double	BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected double	BaumWelchTrainer.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

Constructor and Description
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

Constructor and Description
SingleDP(MarkovModel model)

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

Methods in org.biojava.bio.dp.twohead that throw IllegalTransitionException

Modifier and Type	Method and Description
double	PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
CellCalculator	CellCalculatorFactory.backwards(ScoreType scoreType)
CellCalculator	DPInterpreter.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	CellCalculatorFactory.forwards(ScoreType scoreType)
CellCalculator	DPInterpreter.forwards(ScoreType scoreType)
void	CellCalculator.initialize(Cell[][] cells) Initialize the cell at [0][0] to the recursion initial parameters.
CellCalculator	CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)
CellCalculator	DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
StatePath	PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)

Constructors in org.biojava.bio.dp.twohead that throw IllegalTransitionException

Constructor and Description
PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm)

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

Methods in org.biojava.bio.program.hmmer that throw IllegalTransitionException

Modifier and Type	Method and Description
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

Constructor and Description
HmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)