Uses of Interface
org.biojava.bio.dp.State
Packages that use State
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 State in org.biojava.bio.dp
Subinterfaces of State in org.biojava.bio.dpModifier and TypeInterfaceDescriptioninterface
A Dot state.interface
A state in a markov process that has an emission spectrum.interface
A state that contains an entire sub-model.Classes in org.biojava.bio.dp that implement StateModifier and TypeClassDescriptionfinal class
Start/end state for HMMs.class
A Dot state that you can make and use.class
class
Fields in org.biojava.bio.dp declared as StateModifier and TypeFieldDescriptionTrainerTransition.from
Transition.from
final State
BackPointer.state
The state with which this backpointer is associated.TrainerTransition.to
Transition.to
Methods in org.biojava.bio.dp that return StateModifier and TypeMethodDescriptionIllegalTransitionException.getFrom()
State[]
DP.getStates()
IllegalTransitionException.getTo()
State[]
DP.stateList
(MarkovModel mm) State[]
DPMatrix.states()
Methods in org.biojava.bio.dp with parameters of type StateModifier and TypeMethodDescriptionvoid
Add 'count' to the transition from->to.void
Adds a state to the model.void
void
static int[][]
DP.backwardTransitions
(MarkovModel model, State[] states) static double[][]
DP.backwardTransitionScores
(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType) boolean
MarkovModel.containsTransition
(State from, State to) Returns wether a transition exists or not.boolean
SimpleMarkovModel.containsTransition
(State from, State to) boolean
WMAsMM.containsTransition
(State from, State to) void
MarkovModel.createTransition
(State from, State to) Makes a transition between two states legal.void
SimpleMarkovModel.createTransition
(State from, State to) void
WMAsMM.createTransition
(State from, State to) void
MarkovModel.destroyTransition
(State from, State to) Breaks a transition between two states legal.void
SimpleMarkovModel.destroyTransition
(State from, State to) void
WMAsMM.destroyTransition
(State from, State to) static int[][]
DP.forwardTransitions
(MarkovModel model, State[] states) Returns a matrix for the specified States describing all valid Transitions between those States.static double[][]
DP.forwardTransitionScores
(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType) Compute the log(score) of all transitions between the specified States.MarkovModel.getWeights
(State source) Get a probability Distribution over the transition from 'source'.SimpleMarkovModel.getWeights
(State source) WMAsMM.getWeights
(State source) protected int
void
HMMTrainer.recordEmittedSymbol
(State state, Symbol symbol, double weight) record that the specified symbol was emitted from the specified state.void
SimpleHMMTrainer.recordEmittedSymbol
(State state, Symbol symbol, double weight) void
HMMTrainer.recordTransition
(State source, State dest, double weight) record that a transition was observed between the specified states.void
SimpleHMMTrainer.recordTransition
(State source, State dest, double weight) void
MarkovModel.removeState
(State toGo) Remove a state from the model.void
SimpleMarkovModel.removeState
(State toGo) void
WMAsMM.removeState
(State toAdd) void
MarkovModel.setWeights
(State source, Distribution dist) Set the probability distribution over the transitions from 'source'.void
SimpleMarkovModel.setWeights
(State source, Distribution dist) Use this methods to customize the transition probabilities.void
WMAsMM.setWeights
(State source, Distribution dist) MarkovModel.transitionsFrom
(State source) Returns the FiniteAlphabet of all states that have a transition from 'source'.SimpleMarkovModel.transitionsFrom
(State from) WMAsMM.transitionsFrom
(State from) MarkovModel.transitionsTo
(State dest) Returns the FiniteAlphabet of all states that have a transition to 'dest'.SimpleMarkovModel.transitionsTo
(State to) WMAsMM.transitionsTo
(State to) Constructors in org.biojava.bio.dp with parameters of type StateModifierConstructorDescriptionBackPointer
(State s) BackPointer
(State state, BackPointer back, double score) IllegalTransitionException
(State from, State to) IllegalTransitionException
(State from, State to, String message) TrainerTransition
(TransitionTrainer trainer, State from, State to) Transition
(State from, State to) -
Uses of State in org.biojava.bio.dp.onehead
Fields in org.biojava.bio.dp.onehead declared as StateMethods in org.biojava.bio.dp.onehead that return StateConstructors in org.biojava.bio.dp.onehead with parameters of type StateModifierConstructorDescriptionSmallCursor
(State[] states, SymbolList symList, Iterator symIterator) -
Uses of State in org.biojava.bio.dp.twohead
Methods in org.biojava.bio.dp.twohead that return StateConstructors in org.biojava.bio.dp.twohead with parameters of type StateModifierConstructorDescriptionEmissionCache
(Alphabet alpha, State[] states, int dsi, ScoreType scoreType) -
Uses of State in org.biojava.bio.program.hmmer
Classes in org.biojava.bio.program.hmmer that implement StateMethods in org.biojava.bio.program.hmmer with parameters of type StateModifier and TypeMethodDescriptiondouble
HmmerProfileHMM.transScore
(State from, State to, Symbol symFrom, Symbol symTo)