Uses of Interface
org.biojava.bio.dp.State

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

Subinterfaces of State in org.biojava.bio.dp
 interface DotState
           A Dot state.
 interface EmissionState
           A state in a markov process that has an emission spectrum.
 interface ModelInState
          A state that contains an entire sub-model.
 

Classes in org.biojava.bio.dp that implement State
 class MagicalState
          Start/end state for HMMs.
 class SimpleDotState
          A Dot state that you can make and use.
 class SimpleEmissionState
           
 class SimpleModelInState
           
 

Fields in org.biojava.bio.dp declared as State
 State TrainerTransition.from
           
 State Transition.from
           
 State BackPointer.state
          The state with which this backpointer is associated.
 State TrainerTransition.to
           
 State Transition.to
           
 

Methods in org.biojava.bio.dp that return State
 State IllegalTransitionException.getFrom()
           
 State[] DP.getStates()
           
 State IllegalTransitionException.getTo()
           
 State[] DP.stateList(MarkovModel mm)
           
 State[] DPMatrix.states()
           
 

Methods in org.biojava.bio.dp with parameters of type State
 void TransitionTrainer.addCount(State from, State to, double count)
          Add 'count' to the transition from->to.
 void WMAsMM.addState(State toAdd)
           
 void SimpleMarkovModel.addState(State toAdd)
           
 void MarkovModel.addState(State newState)
          Adds a state to the model.
static int[][] DP.backwardTransitions(MarkovModel model, State[] states)
           
static double[][] DP.backwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)
           
 boolean WMAsMM.containsTransition(State from, State to)
           
 boolean SimpleMarkovModel.containsTransition(State from, State to)
           
 boolean MarkovModel.containsTransition(State from, State to)
          Returns wether a transition exists or not.
 void WMAsMM.createTransition(State from, State to)
           
 void SimpleMarkovModel.createTransition(State from, State to)
           
 void MarkovModel.createTransition(State from, State to)
          Makes a transition between two states legal.
 void WMAsMM.destroyTransition(State from, State to)
           
 void SimpleMarkovModel.destroyTransition(State from, State to)
           
 void MarkovModel.destroyTransition(State from, State to)
          Breaks a transition between two states legal.
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.
 Distribution WMAsMM.getWeights(State source)
           
 Distribution SimpleMarkovModel.getWeights(State source)
           
 Distribution MarkovModel.getWeights(State source)
          Get a probability Distribution over the transition from 'source'.
protected  int WMAsMM.index(State s)
           
 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 WMAsMM.removeState(State toAdd)
           
 void SimpleMarkovModel.removeState(State toGo)
           
 void MarkovModel.removeState(State toGo)
          Remove a state from the model.
 void WMAsMM.setWeights(State source, Distribution dist)
           
 void SimpleMarkovModel.setWeights(State source, Distribution dist)
          Use this methods to customize the transition probabilities.
 void MarkovModel.setWeights(State source, Distribution dist)
          Set the probability distribution over the transitions from 'source'.
 FiniteAlphabet WMAsMM.transitionsFrom(State from)
           
 FiniteAlphabet SimpleMarkovModel.transitionsFrom(State from)
           
 FiniteAlphabet MarkovModel.transitionsFrom(State source)
          Returns the FiniteAlphabet of all states that have a transition from 'source'.
 FiniteAlphabet WMAsMM.transitionsTo(State to)
           
 FiniteAlphabet SimpleMarkovModel.transitionsTo(State to)
           
 FiniteAlphabet MarkovModel.transitionsTo(State dest)
          Returns the FiniteAlphabet of all states that have a transition to 'dest'.
 

Constructors in org.biojava.bio.dp with parameters of type State
BackPointer(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 State
protected  State[] SingleDPMatrix.states
           
 

Methods in org.biojava.bio.dp.onehead that return State
 State[] SingleDPMatrix.states()
           
 

Constructors in org.biojava.bio.dp.onehead with parameters of type State
SmallCursor(State[] states, SymbolList symList, Iterator symIterator)
           
 

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

Methods in org.biojava.bio.dp.twohead that return State
 State[] PairDPMatrix.states()
           
 

Constructors in org.biojava.bio.dp.twohead with parameters of type State
EmissionCache(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 State
 class ProfileEmissionState
          A state in a HMMer model.
 

Methods in org.biojava.bio.program.hmmer with parameters of type State
 double HmmerProfileHMM.transScore(State from, State to, Symbol symFrom, Symbol symTo)