Package biolockj.module

Pipeline modules are loaded based on the BioModules listed in the Config file.
All modules (i.e., implement BioModule) are contained within this package or its sub-packages.

See: Description

Interface Summary

Interface	Description
BioModule	Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
DatabaseModule	Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database directory to map to the container /db volume.
JavaModule	Classes that implement this interface are pure Java modules.
OutsidePipelineWriter	Implementing modules get to have write permissions outside of the pipeline.
ReadCounter	Identifies modules that can report the number of reads per file in the metadata.
ScriptModule	Classes that implement this interface are
SeqModule	Classes that implement this interface requires sequence files for input.

Class Summary

Class	Description
BioModuleImpl	Superclass for standard BioModules (classifiers, parsers, etc).
JavaModuleImpl	Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModuleImpl	Superclass for Java BioModules that will be called in separate instances of the application.
SeqModuleImpl	Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.
Stop	Stop a pipeline.

Package biolockj.module Description

Pipeline modules are loaded based on the BioModules listed in the Config file.
All modules (i.e., implement BioModule) are contained within this package or its sub-packages.