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## Package calhoun.analysis.crf.io

handles input and output of gene calling formats

See:
Description

Interface Summary
FilenameMapper | An interface used to map filenames.
InputComponentIO | interface to read or write `InputSequence` components to or from a file.
InputHandler | interface to classes that handle reading and writing of input data for the CRF.
InputSequence<A> | represents the observed inputs.
InterleavedInputComponent | an input component that can be used with the `InputHandlerInterleaved`.
OutputHandler | handles outputting of results from predictions.
TrainingSequenceIO | Interface for reading a training sequence from the specified location.

Class Summary
AlignmentTree |
AllIntergenicHiddenStateReader |
BooleanInput | reads in an input consisting of a string of 1's and 0's that correspond to binary values.
CompositeInput | Deprecated.
CompositeInput.InputComponent |
CompositeInput.LegacyInputHandler | legacy `InputHandler` that mirrors the original XML config file behavior.
ExtensionMapper | an implementation of `FilenameMapper` that changes file extensions or add a new file extension onto the source file.
FastaAlignmentInput |
FastaInput |
GTFInputInterval13 |
GTFInputInterval29 |
InputHandlerBase | Utility class to abstract out some of the common behavior for `InputHandler`s.
InputHandlerDirectory | an `InputHandler` used when the input is in several files within a single directory.
InputHandlerFile | an `InputHandler` used when all of the input is in a single file.
InputHandlerInterleaved | an `InputHandler` for handling input files that consist of multiple different sequences interleaved together in a file.
InputSequenceBoolean | an input sequence where the elements of the sequence are boolean values.
InputSequenceCharacter | an input sequence where the elements of the sequence are string characters.
InputSequenceComposite | a composite input sequence made up of individual components.
InputSequenceInt | an input sequence where the elements of the sequence are integer values.
InputSequenceObject<T> | an input sequence where the elements of the sequence are objects.
InterleavedInputComponentBase | base class for `InterleavedInputComponent`s.
Interval21HiddenSequenceTranslator |
IntervalInput | an input component used to read in values that are similar for long intervals.
IntervalInputSequence | an input sequence made up of intervals of constant valued features.
IntervalInputSequence.IntervalRangeMapValue |
IntInput | reads in an input consisting of a list of ints that correspond to binary values.
IntInputInterval29 |
IteratorAdapterInputComponent | utility adapter class for creating an iterator of input components from an `InputSequenceComposite` iterator.
IteratorAdapterTrainingSequenceInput<T> | utility class to convert an iterator over training sequences into an iterator over the underlying input sequences
MultipleAlignmentInput | an input component that reads in multiple alignment sequences.
MultipleAlignmentInputSequence | an input sequence where each element represents one column of a multiple alignment.
NameInput | an input component that reads in a name for each sequence.
NameInputSequence | input sequence that captures the 'name' of a sequence.
OutputHandlerComposite | an output handler that allows multiple output handlers to be configured.
OutputHandlerGeneCallPredict | A legacy output handler that computes basic stats, gene calling statsm and then writes out a GTF file.
OutputHandlerGeneCallPredict.Results |
OutputHandlerGeneCallStats | A legacy output handler that computes basic stats, gene calling statsm and then writes out a GTF file.
OutputHandlerGeneCallStats.Results |
OutputHandlerGeneCallStatsInterval29 |
OutputHandlerWriter | writes output to a file using a `TrainingSequenceIO`.
SequenceConverter | used for converting between different encodings of gene structure in a hidden sequence.
StringInput | reads in an input consisting of a string.
TrainingSequence<A> | represents an input sequence that also contains a sequence of hidden states.

## Package calhoun.analysis.crf.io Description

handles input and output of gene calling formats

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