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 InputHandlers.

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 InterleavedInputComponents.

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.