Uses of Package
biolockj.node

Packages that use biolockj.node

Package	Description
biolockj.module.implicit.parser	This package contains Parser BioModules in the r16s and WGS sub-packages that are paired with a ClassifierModule via BioModule.getPostRequisiteModules() to run immediately after the classifier.
biolockj.module.implicit.parser.r16s	This package contains Parser BioModules that convert the 16S taxonomy reports generated by 16S classifiers (such as RDP and QIIME) into standardized OTU abundance tables.
biolockj.module.implicit.parser.wgs	This package contains Parser BioModules that convert the WGS taxonomy reports generated by WGS classifiers (such as Kraken, Kraken2 Metaphlan2, or Humann2) into standardized OTU abundance tables.
biolockj.module.report	This package contains BioModules that normalize OTU abundance tables output by Parser modules, merges them with the metadata, and generates various reports and notifications.
biolockj.node	Package biolockj.node contains core classes instantiated by the ParserModule to hold Sample ID-(OTU name/count) data read in from ClassifierModule output.
biolockj.node.r16s	Package contains RDP and QIIME specific OtuNodes that represent the OTUs (operational taxonomy units) assigned by 16S ClassifierModules
biolockj.node.wgs	Package contains Kraken, Kraken2, and MetaPhlAn2 specific OtuNodes that represent the OTUs (operational taxonomy units) assigned by WGS ClassifierModules

Classes in biolockj.node used by biolockj.module.implicit.parser

Class and Description
OtuNode Classes that implement this interface store taxonomy assignment info for one sequence, as output by a classifier.
ParsedSample ParserModules create and store one ParsedSample, with OTU assignments and counts, for each sample.

Classes in biolockj.node used by biolockj.module.implicit.parser.r16s

Class and Description
OtuNode Classes that implement this interface store taxonomy assignment info for one sequence, as output by a classifier.

Classes in biolockj.node used by biolockj.module.implicit.parser.wgs

Class and Description
OtuNode Classes that implement this interface store taxonomy assignment info for one sequence, as output by a classifier.

Classes in biolockj.node used by biolockj.module.report

Class and Description
JsonNode Each JsonNode holds an OTU, count, and link to its parent node.

Classes in biolockj.node used by biolockj.node

Class and Description
JsonNode Each JsonNode holds an OTU, count, and link to its parent node.
OtuNode Classes that implement this interface store taxonomy assignment info for one sequence, as output by a classifier.
ParsedSample ParserModules create and store one ParsedSample, with OTU assignments and counts, for each sample.

Classes in biolockj.node used by biolockj.node.r16s

Class and Description
OtuNode Classes that implement this interface store taxonomy assignment info for one sequence, as output by a classifier.
OtuNodeImpl The default implementation of OtuNode is also the superclass for all WGS and 16S OtuNode classes.

Classes in biolockj.node used by biolockj.node.wgs

Class and Description
OtuNode Classes that implement this interface store taxonomy assignment info for one sequence, as output by a classifier.
OtuNodeImpl The default implementation of OtuNode is also the superclass for all WGS and 16S OtuNode classes.