Uses of Interface
biolockj.module.JavaModule

Packages that use JavaModule

Package	Description
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.
biolockj.module.implicit	The modules in this package are implicitly added to pipelines as needed. These modules cannot be directly added to any pipeline unless overridden via pipeline.disableImplicitModules=Y.
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.module.report.humann2
biolockj.module.report.otu
biolockj.module.report.taxa
biolockj.module.seq	BioModules used to prepare sequence files or update the metadata prior to classification.

Uses of JavaModule in biolockj.module

Classes in biolockj.module that implement JavaModule

Modifier and Type	Class and Description
class	JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.

Uses of JavaModule in biolockj.module.implicit

Classes in biolockj.module.implicit that implement JavaModule

Modifier and Type	Class and Description
class	Demultiplexer This BioModule splits multiplexed data into a separate file or pair of files (for paired reads) for each sample.
class	RegisterNumReads This BioModule parses sequence file to count the number of reads per sample.

Uses of JavaModule in biolockj.module.implicit.parser

Subinterfaces of JavaModule in biolockj.module.implicit.parser

Modifier and Type	Interface and Description
interface	ParserModule This interface defines the required methods to parse ClassifierModule output.

Classes in biolockj.module.implicit.parser that implement JavaModule

Modifier and Type	Class and Description
class	ParserModuleImpl Parser BioModules read ClassifierModule output to build standardized OTU count tables.

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

Classes in biolockj.module.implicit.parser.r16s that implement JavaModule

Modifier and Type	Class and Description
class	QiimeParser This BioModules parses QiimeClassifier output reports to build standard OTU abundance tables.
class	RdpParser This BioModule parses RDP output files to build standard OTU abundance tables.

Uses of JavaModule in biolockj.module.implicit.parser.wgs

Classes in biolockj.module.implicit.parser.wgs that implement JavaModule

Modifier and Type	Class and Description
class	Humann2Parser This BioModules parses Humann2Classifier output reports to build standard OTU abundance tables. Samples IDs are found in the column headers starting with the 2nd column. The count type depends on the HumanN2 config properties.
class	Kraken2Parser This BioModules parses KrakenClassifier output reports to build standard OTU abundance tables.
class	KrakenParser This BioModules parses KrakenClassifier output reports to build standard OTU abundance tables.
class	Metaphlan2Parser This BioModules parses Metaphlan2Classifier output reports to build standard OTU abundance tables.

Uses of JavaModule in biolockj.module.report

Classes in biolockj.module.report that implement JavaModule

Modifier and Type	Class and Description
class	JsonReport This BioModule is used to build a JSON file (summary.json) compiled from all OTUs in the dataset.

Uses of JavaModule in biolockj.module.report.humann2

Classes in biolockj.module.report.humann2 that implement JavaModule

Modifier and Type	Class and Description
class	AddMetadataToPathwayTables This BioModule is used to add metadata columns to the HumanN2 pathway abundance, pathway coverage, and gene family tables.
class	Humann2CountModule This abstract superclass is extended by all other modules in this package. Shared method implementations are defined to ensure uniform adoption of dependencies and prerequisites.
class	RemoveLowPathwayCounts This BioModule set low Pathway counts below a configured threshold to zero. These low sample counts are assumed to be miscategorized or genomic contamination.
class	RemoveScarcePathwayCounts This BioModule removes scarce pathways not found in enough samples. Each pathway must be found in a configurable percentage of samples to be retained.

Uses of JavaModule in biolockj.module.report.otu

Classes in biolockj.module.report.otu that implement JavaModule

Modifier and Type	Class and Description
class	CompileOtuCounts This BioModule compiles the counts from all OTU count files into a single summary OTU count file containing OTU counts for the entire dataset.
class	OtuCountModule OtuCount modules reads OTU count assignment tables (1 file/sample) with 2 columns. Col1: Full OTU pathway spanning top to bottom level Col2: Count (# of reads) for the sample.
class	RarefyOtuCounts This BioModule applies a mean iterative post-OTU classification rarefication algorithm so that each output sample will have approximately the same number of OTUs.
class	RemoveLowOtuCounts This BioModule set low OTU counts below a configured threshold to zero. These low sample counts are assumed to be miscategorized or contaminents.
class	RemoveScarceOtuCounts This BioModule removes scarce OTUs not found in enough samples. The OTU must be found in a configurable percentage of samples.

Uses of JavaModule in biolockj.module.report.taxa

Classes in biolockj.module.report.taxa that implement JavaModule

Modifier and Type	Class and Description
class	AddMetadataToTaxaTables This BioModule is used to add metadata columns to the OTU abundance tables.
class	BuildTaxaTables Many R BioModules expect separate tables containing log-normalized taxa counts for each taxonomy level.
class	LogTransformTaxaTables This utility is used to log-transform the raw OTU counts on Log10 or Log-e scales.
class	NormalizeTaxaTables This utility is used to normalize and/or log-transform the raw OTU counts using the formulas: Normalized OTU count formula = (RC/n)*((SUM(x))/N)+1 Relative abundance formula = Log(log_base) [ (RC/n)*((SUM(x))/N)+1 ] The code implementation supports (log_base = e) and (log_base = 10) which is configured via Constants.REPORT_LOG_BASE property.
class	TaxaCountModule TBD

Uses of JavaModule in biolockj.module.seq

Classes in biolockj.module.seq that implement JavaModule

Modifier and Type	Class and Description
class	Multiplexer This BioModule will merge sequence files into a single combined sequence file, with either the sample ID or an identifying bar-code (if defined in the metatata) is stored in the sequence header. BioLockJ is designed to run on demultiplexed data so this must be the last module to run in its branch.
class	RarefySeqs This BioModule imposes a minimum and/or maximum number of reads per sample.
class	SeqFileValidator This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.
class	TrimPrimers This BioModule removes sequence primers from demultiplexed files. The primers are defined using regular expressions in a separate file.