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 Transition.from
           
 State Transition.to
           
 State TrainerTransition.from
           
 State TrainerTransition.to
           
 State BackPointer.state
           
 

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

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

Constructors in org.biojava.bio.dp with parameters of type State
Transition(State from, State to)
           
IllegalTransitionException(State from, State to, java.lang.String message)
           
IllegalTransitionException(State from, State to)
           
TrainerTransition(TransitionTrainer trainer, State from, State to)
           
BackPointer(State state, BackPointer back, double score)
           
BackPointer(State s)
           
 

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

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

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)