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## Uses of Package
calhoun.analysis.crf.io

Packages that use calhoun.analysis.crf.io
calhoun.analysis.crf | the interface, main `Conrad` class, and solver for the Conrad engine.
calhoun.analysis.crf.executables.viewer | prototype of a viewing utility for examiining the results of inference.
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.scoring | local similarity functions used in gene calling models
calhoun.analysis.crf.solver | training and inference algorithms used in the CRF engine
calhoun.analysis.crf.solver.semimarkov |
calhoun.analysis.crf.test |

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf
InputHandler interface to classes that handle reading and writing of input data for the CRF.
InputSequence represents the observed inputs.
OutputHandler handles outputting of results from predictions.
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.executables.viewer
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.features.generic
InputSequence represents the observed inputs.
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.features.interval13
CompositeInput Deprecated.
InputSequence represents the observed inputs.
MultipleAlignmentInputSequence.MultipleAlignmentColumn represents the column of the alignment at a given position on the reference sequence
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.features.interval29
CompositeInput Deprecated.
InputSequence represents the observed inputs.
MultipleAlignmentInputSequence.MultipleAlignmentColumn represents the column of the alignment at a given position on the reference sequence
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.features.supporting
InputSequence represents the observed inputs.
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.features.supporting.phylogenetic
InputSequence represents the observed inputs.
MultipleAlignmentInputSequence.MultipleAlignmentColumn represents the column of the alignment at a given position on the reference sequence
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.features.tricycle13
CompositeInput Deprecated.
InputSequence represents the observed inputs.
IntervalInputSequence.IntervalPosition provides interval based queries for a particular position in the input sequence for an IntervalInputSequence.
MultipleAlignmentInputSequence.MultipleAlignmentColumn represents the column of the alignment at a given position on the reference sequence
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.io
CompositeInput.InputComponent Deprecated.
FilenameMapper An interface used to map filenames.
GTFInputInterval13
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.
InputHandlerBase Utility class to abstract out some of the common behavior for `InputHandler`s.
InputSequence represents the observed inputs.
InputSequenceComposite a composite input sequence made up of individual components.
InterleavedInputComponent an input component that can be used with the `InputHandlerInterleaved`.
InterleavedInputComponentBase base class for `InterleavedInputComponent`s.
IntervalInputSequence an input sequence made up of intervals of constant valued features.
IntervalInputSequence.IntervalPosition provides interval based queries for a particular position in the input sequence for an IntervalInputSequence.
IntInput reads in an input consisting of a list of ints that correspond to binary values.
MultipleAlignmentInputSequence an input sequence where each element represents one column of a multiple alignment.
MultipleAlignmentInputSequence.MultipleAlignmentColumn represents the column of the alignment at a given position on the reference sequence
OutputHandler handles outputting of results from predictions.
OutputHandlerGeneCallStats A legacy output handler that computes basic stats, gene calling statsm and then writes out a GTF file.
TrainingSequence represents an input sequence that also contains a sequence of hidden states.
TrainingSequenceIO Interface for reading a training sequence from the specified location.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.scoring
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.solver
InputSequence represents the observed inputs.
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.solver.semimarkov
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

Classes in calhoun.analysis.crf.io used by calhoun.analysis.crf.test
InputSequence represents the observed inputs.
TrainingSequence represents an input sequence that also contains a sequence of hidden states.

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