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 InputHandlers.
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 InterleavedInputComponents.
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