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

Packages that use State

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 State in org.biojava.bio.dp

Subinterfaces of State in org.biojava.bio.dp

Modifier and Type	Interface and Description
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

Modifier and Type	Class and Description
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

Modifier and Type	Field and Description
State	Transition.from
State	TrainerTransition.from
State	BackPointer.state The state with which this backpointer is associated.
State	Transition.to
State	TrainerTransition.to

Methods in org.biojava.bio.dp that return State

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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	SimpleHMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight)
void	HMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight) record that the specified symbol was emitted from the specified state.
void	SimpleHMMTrainer.recordTransition(State source, State dest, double weight)
void	HMMTrainer.recordTransition(State source, State dest, double weight) record that a transition was observed between the specified states.
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

Constructor and Description
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

Modifier and Type	Field and Description
protected State[]	SingleDPMatrix.states

Methods in org.biojava.bio.dp.onehead that return State

Modifier and Type	Method and Description
State[]	SingleDPMatrix.states()

Constructors in org.biojava.bio.dp.onehead with parameters of type State

Constructor and Description
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

Modifier and Type	Method and Description
State[]	PairDPMatrix.states()

Constructors in org.biojava.bio.dp.twohead with parameters of type State

Constructor and Description
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

Modifier and Type	Class and Description
class	ProfileEmissionState A state in a HMMer model.

Methods in org.biojava.bio.program.hmmer with parameters of type State

Modifier and Type	Method and Description
double	HmmerProfileHMM.transScore(State from, State to, Symbol symFrom, Symbol symTo)