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 InputHandlers.
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