Uses of Interface
biolockj.node.OtuNode

Packages that use OtuNode

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.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

Uses of OtuNode in biolockj.module.implicit.parser

Methods in biolockj.module.implicit.parser with parameters of type OtuNode

Modifier and Type	Method and Description
void	ParserModuleImpl.addOtuNode(OtuNode node)
void	ParserModule.addOtuNode(OtuNode node) Each sample with taxonomic assignments from a ClassifierModule is parsed by ParserModule.parseSamples() to produce a ParsedSample.
protected boolean	ParserModuleImpl.isValid(OtuNode node) Some ClassifierModules can include taxonomy level identifiers without an OTU name in the sample report files.

Uses of OtuNode in biolockj.module.implicit.parser.r16s

Methods in biolockj.module.implicit.parser.r16s with parameters of type OtuNode

Modifier and Type	Method and Description
protected boolean	RdpParser.isValid(OtuNode node) If RdpNode.getScore() is above the Config., continue with the standard OtuNode validation.

Uses of OtuNode in biolockj.node

Classes in biolockj.node that implement OtuNode

Modifier and Type	Class and Description
class	OtuNodeImpl The default implementation of OtuNode is also the superclass for all WGS and 16S OtuNode classes.

Methods in biolockj.node with parameters of type OtuNode

Modifier and Type	Method and Description
void	ParsedSample.addNode(OtuNode node) Add the OtuNode to the ParsedSample.
int	OtuNodeImpl.compareTo(OtuNode node) The sort order of the TreeSet(OtuNode) is absolutely required for proper processing in OtuNodeImpl.addTaxa(String, String) and OtuNodeImpl.getTaxaMap().

Constructors in biolockj.node with parameters of type OtuNode

Constructor and Description
ParsedSample(OtuNode node) Construct a new ParsedSample with it's 1st OtuNode.

Uses of OtuNode in biolockj.node.r16s

Classes in biolockj.node.r16s that implement OtuNode

Modifier and Type	Class and Description
class	QiimeNode This class holds the OTU assignments from one line of QiimeClassifier output.
class	RdpNode This class represents one line of RdpClassifier output.

Uses of OtuNode in biolockj.node.wgs

Classes in biolockj.node.wgs that implement OtuNode

Modifier and Type	Class and Description
class	Kraken2Node This class represents one line of Kraken2Classifier output.
class	KrakenNode This class represents one line of KrakenClassifier output.
class	MetaphlanNode This class represents one line of Metaphlan2Classifier output.