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## 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)`

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