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

Packages that use InputHandler
calhoun.analysis.crf | the interface, main `Conrad` class, and solver for the Conrad engine.
calhoun.analysis.crf.io | handles input and output of gene calling formats

Uses of InputHandler in calhoun.analysis.crf

Methods in calhoun.analysis.crf that return InputHandler
`InputHandler` | `Conrad.getInputHandler()` returns the configured input handler.

Methods in calhoun.analysis.crf with parameters of type InputHandler
`void` | `Conrad.setInputHandler(InputHandler inputHandler)` sets the configured input handler.

Uses of InputHandler in calhoun.analysis.crf.io

Classes in calhoun.analysis.crf.io that implement InputHandler
`static class` | `CompositeInput.LegacyInputHandler` Deprecated. legacy `InputHandler` that mirrors the original XML config file behavior.
`class` | `InputHandlerBase` Utility class to abstract out some of the common behavior for `InputHandler`s.
`class` | `InputHandlerDirectory` an `InputHandler` used when the input is in several files within a single directory.
`class` | `InputHandlerFile` an `InputHandler` used when all of the input is in a single file.
`class` | `InputHandlerInterleaved` an `InputHandler` for handling input files that consist of multiple different sequences interleaved together in a file.

Methods in calhoun.analysis.crf.io that return InputHandler
`InputHandler` | `OutputHandlerGeneCallStats.getInputHandler()` retursn the input handler used to write out the input sequences
`InputHandler` | `OutputHandlerGeneCallPredict.getInputHandler()` retursn the input handler used to write out the input sequences

Methods in calhoun.analysis.crf.io with parameters of type InputHandler
`void` | `OutputHandlerGeneCallStats.setInputHandler(InputHandler inputHandler)` sets the inputHandler used to write out the input sequences
`void` | `OutputHandlerGeneCallPredict.setInputHandler(InputHandler inputHandler)` sets the inputHandler used to write out the input sequences

Constructors in calhoun.analysis.crf.io with parameters of type InputHandler
`OutputHandlerGeneCallPredict(ModelManager manager, InputHandler inputHandler)` creates an output handler using this model and input handler
`OutputHandlerGeneCallStats(ModelManager manager, InputHandler inputHandler)` creates an output handler using this model and input handler

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