All Classes

Class	Description
CommandLineOptionsParser	Command line options parser.
FileOutputWriter	Writer for writing output to a file.
GenePrioritizedOutputFormatWriterFactory	A factory for Gene prioritized PrioritizedOutputFormatWriters.
OrderedGenesOutputFormatWriter	A very basic ordered genes output writer.
OutputFormatWriter	Abstract class defining a complete writer (using OutputWriter as target to write to).
OutputWriter	Superclass for the different types of output writers.
PrioritizedOutputFormatWriter<T extends BiologicalEntity>	An OutputFormatWriter that writes in a specific format: where the results are prioritized based on a BiologicalEntity.
PrioritizedOutputFormatWriterFactory<T extends BiologicalEntity>	Interface describing the required methods for all PrioritizedOutputFormatWriter factories.
ResultsPerGeneSeparatedValuesOutputFormatWriter	Writer for writing Gene to a CSV file where a single line represent a Gene.
ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds	A ResultsPerGeneSeparatedValuesOutputFormatWriter where Entity.getId() is used for generating the output.
ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris	A ResultsPerGeneSeparatedValuesOutputFormatWriter where Entity.getUri() is used for generating the output.
RunMode	Describes what the application should do.
StdoutOutputWriter	Writer for writing output to stdout.
ValuesSeparator	Defines possible separators to be used.
VibeApplication	The main application class.
VibeOptions	Abstract class to be used for options parsing.
VibeProperties	Properties (parsed by VibePropertiesLoader) stored in application.properties accessible anywhere in the app (so VibePropertiesLoader should always be used first to parse the properties).
VibePropertiesLoader	Loads the properties stored in application.properties for usage by VibeProperties.