Uses of Interface
calhoun.analysis.crf.io.InputSequence

Packages that use InputSequence

calhoun.analysis.crf	the interface, main Conrad class, and solver for the Conrad engine.
calhoun.analysis.crf.features.generic	features useful across different models
calhoun.analysis.crf.features.interval13	mdoel definition and setup for the interval13 model
calhoun.analysis.crf.features.interval29
calhoun.analysis.crf.features.supporting	utility classes used by feature managers in gene calling models
calhoun.analysis.crf.features.supporting.phylogenetic	utility classes for phylogenetic analysis
calhoun.analysis.crf.features.tricycle13	basic features and model for the tricycle13 gene calling model
calhoun.analysis.crf.io	handles input and output of gene calling formats
calhoun.analysis.crf.solver	training and inference algorithms used in the CRF engine
calhoun.analysis.crf.test

Uses of InputSequence in calhoun.analysis.crf

Methods in calhoun.analysis.crf with parameters of type InputSequence

void	FeatureManagerEdge.evaluateEdge(InputSequence<? extends InputType> seq, int pos, int prevState, int state, FeatureList result) Evaluates the set of features managed by this object for the given arguments.
void	CompositeFeatureManager.evaluateEdge(InputSequence seq, int pos, int prevState, int state, FeatureList result)
void	FeatureManagerEdgeExplicitLength.evaluateEdgeLength(InputSequence<? extends InputType> seq, int pos, int length, int prevState, int state, FeatureList result)
void	CompositeFeatureManager.evaluateEdgeLength(InputSequence seq, int pos, int length, int prevState, int state, FeatureList result)
void	FeatureManagerNode.evaluateNode(InputSequence<? extends InputType> seq, int pos, int state, FeatureList result) Evaluates the set of features managed by this object for the given arguments.
void	CompositeFeatureManager.evaluateNode(InputSequence seq, int pos, int state, FeatureList result)
void	FeatureManagerNodeExplicitLength.evaluateNodeLength(InputSequence<? extends InputType> seq, int pos, int length, int state, FeatureList result)
void	CompositeFeatureManager.evaluateNodeLength(InputSequence seq, int pos, int length, int state, FeatureList result)
CRFInference.InferenceResult	Conrad.predict(InputSequence data) preforms inference on the input sequence and determines the best labeling for the sequence using the configured inference algorithm.
CRFInference.InferenceResult	CRFInference.predict(ModelManager mm, InputSequence<?> data, double[] weights) Return the labelling that maximizes the conditional probability P(y|x).

Uses of InputSequence in calhoun.analysis.crf.features.generic

Methods in calhoun.analysis.crf.features.generic with parameters of type InputSequence

void	WeightedStateChanges.evaluateEdge(InputSequence<?> seq, int pos, int prevState, int state, FeatureList result)
void	WeightedEdges.evaluateEdge(InputSequence<?> seq, int pos, int prevState, int state, FeatureList result)
void	IndicatorEdges.evaluateEdge(InputSequence seq, int pos, int prevState, int state, FeatureList result)
void	StartFeatures.evaluateNode(InputSequence<?> seq, int pos, int state, FeatureList result)
void	EndFeatures.evaluateNode(InputSequence<?> seq, int pos, int state, FeatureList result)

Uses of InputSequence in calhoun.analysis.crf.features.interval13

Methods in calhoun.analysis.crf.features.interval13 with parameters of type InputSequence

void	StateTransitionsInterval13.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)
void	PWMInterval13.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int previousState, int state, FeatureList result)
void	GeneConstraintsInterval13.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)
void	ESTInterval13.evaluateEdge(InputSequence<? extends CompositeInput> seq, int pos, int prevState, int state, FeatureList result)
void	ReferenceBasePredictorInterval13Base.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)
void	GeneConstraintsInterval13.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)
void	ESTInterval13.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)
void	BlastInterval13.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)
void	PhylogeneticLogprobInterval13.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	GapFeaturesInterval13.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	FootprintsInterval13.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	StateLengthLogprobInterval13.evaluateNodeLength(InputSequence<? extends java.lang.Character> seq, int pos, int length, int state, FeatureList result)

Uses of InputSequence in calhoun.analysis.crf.features.interval29

Methods in calhoun.analysis.crf.features.interval29 with parameters of type InputSequence

void	StateTransitionsInterval29.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)
void	PWMInterval29.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int previousState, int state, FeatureList result)
void	GeneConstraintsInterval29.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)
void	ESTInterval29.evaluateEdge(InputSequence<? extends CompositeInput> seq, int pos, int prevState, int state, FeatureList result)
void	ReferenceBasePredictorInterval29Base.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)
void	GeneConstraintsInterval29.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)
void	ESTInterval29.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)
void	GapFeaturesInterval29.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	FootprintsInterval29.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	StateLengthLogprobInterval29.evaluateNodeLength(InputSequence<? extends java.lang.Character> seq, int pos, int length, int state, FeatureList result)

Uses of InputSequence in calhoun.analysis.crf.features.supporting

Methods in calhoun.analysis.crf.features.supporting with parameters of type InputSequence

void	PWMLookup.increment(InputSequence<? extends java.lang.Character> seq, int pos, boolean isPlus)
void	LogProbLookup.increment(InputSequence<? extends java.lang.Character> seq, int pos, boolean isPlus)
float	MarkovPredictorLogprob.logprob(int state, InputSequence<? extends java.lang.Character> seq, int pos)
double	PWMLookup.lookup(InputSequence<? extends java.lang.Character> seq, int pos, boolean isPlus)
double	LogProbLookup.lookup(InputSequence<? extends java.lang.Character> seq, int pos, boolean isPlus)

Uses of InputSequence in calhoun.analysis.crf.features.supporting.phylogenetic

Methods in calhoun.analysis.crf.features.supporting.phylogenetic with parameters of type InputSequence

double

ColumnConditionalLogProbability.condLogProb(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state)

Uses of InputSequence in calhoun.analysis.crf.features.tricycle13

Methods in calhoun.analysis.crf.features.tricycle13 with parameters of type InputSequence

void	PositionWeightMatrixFeatures.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int previousState, int state, FeatureList result)
void	MaxentMotifFeatures.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int previousState, int state, FeatureList result)
void	GeneConstraints.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)
void	CodingStopFeature.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int ix, int prevState, int state, FeatureList result)
void	PWM_evolution.evaluateEdge(InputSequence<? extends CompositeInput> seq, int pos, int previousState, int state, FeatureList result)
void	ESTEdge.evaluateEdge(InputSequence<? extends CompositeInput> seq, int pos, int prevState, int state, FeatureList result)
void	KmerFeatures.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)
void	EmissionMarkovFeature.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)
void	PfamPhase.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)
void	PfamGenic.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)
void	ESTIntron.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)
void	ESTExon.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)
void	ESTEdge.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)
void	IntervalPresenceFeatures.evaluateNode(InputSequence<? extends IntervalInputSequence.IntervalPosition> seq, int pos, int state, FeatureList result)
void	GapConjunctionFeatures.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	FelsensteinFeatures.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	IntronLengthFeature.evaluateNodeLength(InputSequence seq, int pos, int length, int state, FeatureList result)
java.lang.String	KmerFeatures.getKmer(InputSequence<? extends java.lang.Character> seq, int pos, int[] def)

Uses of InputSequence in calhoun.analysis.crf.io

Classes in calhoun.analysis.crf.io that implement InputSequence

class	InputSequenceBoolean an input sequence where the elements of the sequence are boolean values.
class	InputSequenceCharacter an input sequence where the elements of the sequence are string characters.
class	InputSequenceComposite a composite input sequence made up of individual components.
class	InputSequenceInt an input sequence where the elements of the sequence are integer values.
class	InputSequenceObject<T> an input sequence where the elements of the sequence are objects.
class	IntervalInputSequence an input sequence made up of intervals of constant valued features.
class	MultipleAlignmentInputSequence an input sequence where each element represents one column of a multiple alignment.
class	NameInputSequence input sequence that captures the 'name' of a sequence.
class	TrainingSequence<A> represents an input sequence that also contains a sequence of hidden states.

Methods in calhoun.analysis.crf.io that return InputSequence

InputSequence<?>	TrainingSequence.getComponent(java.lang.String name)
InputSequence<?>	NameInputSequence.getComponent(java.lang.String name)
InputSequence<?>	MultipleAlignmentInputSequence.getComponent(java.lang.String name)
InputSequence	IntervalInputSequence.getComponent(java.lang.String name)
InputSequence<?>	InputSequenceObject.getComponent(java.lang.String name)
InputSequence<?>	InputSequenceInt.getComponent(java.lang.String name)
InputSequence<?>	InputSequenceComposite.getComponent(java.lang.String name)
InputSequence<?>	InputSequenceCharacter.getComponent(java.lang.String name)
InputSequence<?>	InputSequenceBoolean.getComponent(java.lang.String name)
InputSequence<?>	InputSequence.getComponent(java.lang.String name) For input sequences that are a composite of several different input objects, returns a particular component of the input.
InputSequence<? extends A>	TrainingSequence.getInputSequence() gets the underlying input sequence
InputSequence<? extends T>	IteratorAdapterTrainingSequenceInput.next()
InputSequence<java.lang.String>	NameInputSequence.subSequence(int start, int end)
InputSequence<MultipleAlignmentInputSequence.MultipleAlignmentColumn>	MultipleAlignmentInputSequence.subSequence(int start, int end)
InputSequence<T>	InputSequenceObject.subSequence(int start, int end)
InputSequence<java.lang.Integer>	InputSequenceInt.subSequence(int start, int end)
InputSequence<java.lang.Character>	InputSequenceCharacter.subSequence(int start, int end)
InputSequence<java.lang.Boolean>	InputSequenceBoolean.subSequence(int start, int end)
InputSequence<A>	InputSequence.subSequence(int start, int end) tTakes a subinterval of the input sequence with given start-end coordinates which are relative coordinates, 1-based, and inclusive.

Methods in calhoun.analysis.crf.io that return types with arguments of type InputSequence

java.util.Map<java.lang.String,InputSequence<?>>	InputSequenceComposite.getComponents() returns all of components of this input sequence.
java.util.Map<java.lang.String,InputSequence<?>>	IteratorAdapterInputComponent.next()
java.util.Iterator<? extends InputSequence<?>>	InputHandlerInterleaved.readInputData(java.lang.String location)
java.util.Iterator<? extends InputSequence<?>>	InputHandlerFile.readInputData(java.lang.String location)
java.util.Iterator<? extends InputSequence<?>>	InputHandlerDirectory.readInputData(java.lang.String location)
java.util.Iterator<? extends InputSequence<?>>	InputHandler.readInputData(java.lang.String location) returns the input data read from the specified location.
java.util.Iterator<? extends InputSequence<?>>	CompositeInput.LegacyInputHandler.readInputData(java.lang.String inputLocation)

Methods in calhoun.analysis.crf.io with parameters of type InputSequence

void	InputSequenceComposite.addComponent(java.lang.String name, InputSequence<?> seq) adds a new component input sequence to this composite.
void	OutputHandlerWriter.writeOutput(InputSequence<?> sequence, int[] hiddenStates)
void	OutputHandlerGeneCallStats.writeOutput(InputSequence<?> sequence, int[] hiddenStates)
void	OutputHandlerGeneCallPredict.writeOutput(InputSequence<?> sequence, int[] hiddenStates)
void	OutputHandlerComposite.writeOutput(InputSequence<?> sequence, int[] hiddenStates)
void	OutputHandler.writeOutput(InputSequence<?> sequence, int[] hiddenStates) Writes out a set of predicted hidden states.
void	OutputHandlerWriter.writeTestOutput(InputSequence<?> sequence, int[] truePath, int[] hiddenStates)
void	OutputHandlerGeneCallStatsInterval29.writeTestOutput(InputSequence<?> sequence, int[] truePath, int[] hiddenStates)
void	OutputHandlerGeneCallStats.writeTestOutput(InputSequence<?> sequence, int[] truePath, int[] hiddenStates)
void	OutputHandlerGeneCallPredict.writeTestOutput(InputSequence<?> sequence, int[] truePath, int[] hiddenStates)
void	OutputHandlerComposite.writeTestOutput(InputSequence<?> sequence, int[] truePath, int[] hiddenStates)
void	OutputHandler.writeTestOutput(InputSequence<?> sequence, int[] truePath, int[] hiddenStates) Writes out a set of hidden states compared with a known true path.

Method parameters in calhoun.analysis.crf.io with type arguments of type InputSequence

void	InputSequenceComposite.addComponents(java.util.Map<java.lang.String,InputSequence<?>> data) adds all input sequences in the given map as components.
boolean	StringInput.read(java.io.BufferedReader r, java.util.Map<java.lang.String,InputSequence<?>> output)
boolean	NameInput.read(java.io.BufferedReader r, java.util.Map<java.lang.String,InputSequence<?>> output)
boolean	MultipleAlignmentInput.read(java.io.BufferedReader r, java.util.Map<java.lang.String,InputSequence<?>> output)
boolean	IntInput.read(java.io.BufferedReader r, java.util.Map<java.lang.String,InputSequence<?>> output)
boolean	IntervalInput.read(java.io.BufferedReader r, java.util.Map<java.lang.String,InputSequence<?>> output)
boolean	InterleavedInputComponent.read(java.io.BufferedReader r, java.util.Map<java.lang.String,InputSequence<?>> output) Read the contents of the sequence in from a reader.
boolean	BooleanInput.read(java.io.BufferedReader r, java.util.Map<java.lang.String,InputSequence<?>> output)
void	InterleavedInputComponentBase.readInputSequences(java.lang.String location, java.util.List<java.util.Map<java.lang.String,InputSequence<?>>> inputs)
void	InputComponentIO.readInputSequences(java.lang.String location, java.util.List<java.util.Map<java.lang.String,InputSequence<?>>> inputs) reads input sequences from this location.
void	FastaInput.readInputSequences(java.lang.String location, java.util.List<java.util.Map<java.lang.String,InputSequence<?>>> inputs)
void	FastaAlignmentInput.readInputSequences(java.lang.String location, java.util.List<java.util.Map<java.lang.String,InputSequence<?>>> inputs)
void	AlignmentTree.readInputSequences(java.lang.String location, java.util.List<java.util.Map<java.lang.String,InputSequence<?>>> inputs)
void	StringInput.write(java.io.Writer w, java.util.Map<java.lang.String,? extends InputSequence<?>> data)
void	NameInput.write(java.io.Writer w, java.util.Map<java.lang.String,? extends InputSequence<?>> data)
void	MultipleAlignmentInput.write(java.io.Writer w, java.util.Map<java.lang.String,? extends InputSequence<?>> data)
void	IntInput.write(java.io.Writer w, java.util.Map<java.lang.String,? extends InputSequence<?>> data)
void	IntervalInput.write(java.io.Writer w, java.util.Map<java.lang.String,? extends InputSequence<?>> data)
void	InterleavedInputComponent.write(java.io.Writer w, java.util.Map<java.lang.String,? extends InputSequence<?>> data) Output this sequence to the given writer.
void	BooleanInput.write(java.io.Writer w, java.util.Map<java.lang.String,? extends InputSequence<?>> data)
void	InputHandlerInterleaved.writeInputData(java.lang.String location, java.util.Iterator<? extends InputSequence<?>> data)
void	InputHandlerFile.writeInputData(java.lang.String location, java.util.Iterator<? extends InputSequence<?>> data)
void	InputHandlerDirectory.writeInputData(java.lang.String location, java.util.Iterator<? extends InputSequence<?>> data)
void	InputHandler.writeInputData(java.lang.String location, java.util.Iterator<? extends InputSequence<?>> data) writes input data to the specified location.
void	InterleavedInputComponentBase.writeInputSequences(java.lang.String location, java.util.List<? extends java.util.Map<java.lang.String,? extends InputSequence<?>>> inputComponents)
void	InputComponentIO.writeInputSequences(java.lang.String location, java.util.List<? extends java.util.Map<java.lang.String,? extends InputSequence<?>>> inputComponents) writes input sequences to this location.
void	FastaInput.writeInputSequences(java.lang.String location, java.util.List<? extends java.util.Map<java.lang.String,? extends InputSequence<?>>> inputComponents)
void	FastaAlignmentInput.writeInputSequences(java.lang.String location, java.util.List<? extends java.util.Map<java.lang.String,? extends InputSequence<?>>> inputComponents)
void	AlignmentTree.writeInputSequences(java.lang.String location, java.util.List<? extends java.util.Map<java.lang.String,? extends InputSequence<?>>> inputComponents)

Constructors in calhoun.analysis.crf.io with parameters of type InputSequence

TrainingSequence(InputSequence<? extends A> xArg)
constructs a training sequence using just the input sequence.

TrainingSequence(InputSequence<? extends A> xArg, int[] yArg)
constructs a training sequence using these input and hidden sequences

Constructor parameters in calhoun.analysis.crf.io with type arguments of type InputSequence

InputSequenceComposite(java.util.Map<java.lang.String,InputSequence<?>> data)
constructor that initializes the sequence with a set of components.

IteratorAdapterInputComponent(java.util.Iterator<? extends InputSequence<?>> parent)
constructs an iterator that separates out the input components of the parent iterator

Uses of InputSequence in calhoun.analysis.crf.solver

Methods in calhoun.analysis.crf.solver with parameters of type InputSequence

CRFInference.InferenceResult	Viterbi.predict(ModelManager fm, InputSequence<?> seq, double[] lambda)
CRFInference.InferenceResult	SemiMarkovViterbiNoCache.predict(ModelManager fm, InputSequence<?> seq, double[] lambda)
CRFInference.InferenceResult	SemiMarkovViterbi.predict(ModelManager fm, InputSequence<?> seq, double[] lambda)
void	CacheProcessorBasic.setInputData(ModelManager fm, InputSequence<?> seq)
void	CacheProcessor.setInputData(ModelManager fm, InputSequence<?> data)

Uses of InputSequence in calhoun.analysis.crf.test

Methods in calhoun.analysis.crf.test with parameters of type InputSequence

void	TestFeatures.ExplicitHalfExponentialLengthFeature.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)
void	TestFeatures.ExponentialLengthFeature.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)
void	TestFeatures.HalfExponentialLengthFeature.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)
void	GeneConstraintsToy.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)
void	ConstraintTest.FixedEdges.evaluateEdge(InputSequence seq, int pos, int prevState, int state, FeatureList result)
void	TestFeatures.EmissionFeature.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)
void	TestFeatures.GaussianLengthFeature.evaluateNodeLength(InputSequence<? extends java.lang.Character> seq, int pos, int length, int state, FeatureList result)
void	TestFeatures.ExplicitHalfExponentialLengthFeature.evaluateNodeLength(InputSequence<? extends java.lang.Character> seq, int pos, int length, int state, FeatureList result)
void	FeatureTest.writeFeatures(Conrad runner, java.lang.String file, InputSequence data)