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Packages that use State | |
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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 |
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Subinterfaces of State in org.biojava.bio.dp | |
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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 | |
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class |
MagicalState
Start/end state for HMMs. |
class |
SimpleDotState
A Dot state that you can make and use. |
class |
SimpleEmissionState
|
class |
SimpleModelInState
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Fields in org.biojava.bio.dp declared as State | |
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State |
Transition.from
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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 | |
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State |
IllegalTransitionException.getFrom()
|
State[] |
DP.getStates()
|
State |
IllegalTransitionException.getTo()
|
State[] |
DP.stateList(MarkovModel mm)
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State[] |
DPMatrix.states()
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Methods in org.biojava.bio.dp with parameters of type State | |
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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 | |
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BackPointer(State s)
|
|
BackPointer(State state,
BackPointer back,
double score)
|
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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 |
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Fields in org.biojava.bio.dp.onehead declared as State | |
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protected State[] |
SingleDPMatrix.states
|
Methods in org.biojava.bio.dp.onehead that return State | |
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State[] |
SingleDPMatrix.states()
|
Constructors in org.biojava.bio.dp.onehead with parameters of type State | |
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SmallCursor(State[] states,
SymbolList symList,
Iterator symIterator)
|
Uses of State in org.biojava.bio.dp.twohead |
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Methods in org.biojava.bio.dp.twohead that return State | |
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State[] |
PairDPMatrix.states()
|
Constructors in org.biojava.bio.dp.twohead with parameters of type State | |
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EmissionCache(Alphabet alpha,
State[] states,
int dsi,
ScoreType scoreType)
|
Uses of State in org.biojava.bio.program.hmmer |
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Classes in org.biojava.bio.program.hmmer that implement State | |
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class |
ProfileEmissionState
A state in a HMMer model. |
Methods in org.biojava.bio.program.hmmer with parameters of type State | |
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double |
HmmerProfileHMM.transScore(State from,
State to,
Symbol symFrom,
Symbol symTo)
|
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