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## Uses of Interface
calhoun.analysis.crf.io.TrainingSequenceIO

Packages that use TrainingSequenceIO
calhoun.analysis.crf.io | handles input and output of gene calling formats

Uses of TrainingSequenceIO in calhoun.analysis.crf.io

Classes in calhoun.analysis.crf.io that implement TrainingSequenceIO
`class` | `AllIntergenicHiddenStateReader`
`class` | `GTFInputInterval13`
`class` | `GTFInputInterval29`
`class` | `Interval21HiddenSequenceTranslator`
`class` | `IntInput` reads in an input consisting of a list of ints that correspond to binary values.
`class` | `IntInputInterval29`

Methods in calhoun.analysis.crf.io that return TrainingSequenceIO
`TrainingSequenceIO` | `CompositeInput.getHiddenSequenceReader()` Deprecated.
`TrainingSequenceIO` | `InputHandlerFile.getHiddenStateReader()` gets the reader used to read in results for training data.
`TrainingSequenceIO` | `InputHandlerDirectory.getHiddenStateReader()` gets the reader used to read in results for training data.
`TrainingSequenceIO` | `OutputHandlerWriter.getResultHandler()` gets the result handler which will be used to handle the output sequence

Methods in calhoun.analysis.crf.io with parameters of type TrainingSequenceIO
`void` | `CompositeInput.setHiddenSequenceReader(TrainingSequenceIO hiddenSequenceReader)` Deprecated.
`void` | `InputHandlerFile.setHiddenStateReader(TrainingSequenceIO hiddenStateReader)` sets the reader used to get hidden sequences.
`void` | `InputHandlerDirectory.setHiddenStateReader(TrainingSequenceIO hiddenStateReader)` sets the reader used to get hidden sequences.
`void` | `OutputHandlerWriter.setResultHandler(TrainingSequenceIO resultHandler)` sets the result handler which will be used to handle the output sequence

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