Uses of Package
biolockj.exception

Packages that use biolockj.exception

Package	Description
biolockj	The root biolockj package contains core classes used by all BioLockJ pipelines.
biolockj.exception	This package contains Exception subclasses specific to BioLockJ.
biolockj.launch
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.assembly
biolockj.module.classifier	This package contains Classifier specific BioModules that build bash scripts to generate taxonomy reports from the sequences files.
biolockj.module.classifier.r16s	This package contains RDP and QIIME classifier modules that assign taxonomy to 16s sequences. Output file formats are classifier specific so classifier requires a unique post-requisite ParserModule.
biolockj.module.classifier.wgs	This package contains Kraken, Kraken2, Humann2, MetaPhlAn classifier modules that assign taxonomy to WGS data. As with all BioLockJ classifiers, these modules generate raw classifier output files from the sequence data. Include the corresponding ParserModule in the Config file to generate standardized OTU abundance tables.
biolockj.module.diy
biolockj.module.getData.sra
biolockj.module.hello_world
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.qiime	This package contains BioModules that are implicitly added to QIIME pipeline as needed.
biolockj.module.report.r	This package contains BioModules that build pipeline reports from the standard OTU abundance tables by generating R scripts to produce the summary statistics and data visualizations output to PDF files.
biolockj.module.rnaseq
biolockj.module.seq	BioModules used to prepare sequence files or update the metadata prior to classification.
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.pipelines
biolockj.util	Static utilities centralize and organize reusable core methods.
biolockj.util.paths

Classes in biolockj.exception used by biolockj

Class and Description
BioLockJException Superclass for all BioLockJ exception used to ensure message uniformity.
ConfigFormatException ConfigFormatException is thrown if property is defined but the format is invalid.
ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
DockerVolCreationException
SpecialPropertiesException This type of exception is thrown if an error occurs while processing a special type of property such as "exe." properties or defaultProps.

Classes in biolockj.exception used by biolockj.exception

Class and Description
BioLockJException Superclass for all BioLockJ exception used to ensure message uniformity.
ConfigException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
DockerVolumeException
IntentionalStop Parent exception for BioLockJ Exception that arise when the user explicitly intended to make the pipeline stop.
MetadataException MetadataException is thrown if errors occur processing Metadata files.

Classes in biolockj.exception used by biolockj.launch

Class and Description
BioLockJException Superclass for all BioLockJ exception used to ensure message uniformity.
BioLockJStatusException
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
DockerVolCreationException
InvalidPipelineException

Classes in biolockj.exception used by biolockj.module

Class and Description
ConfigException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
ConfigFormatException ConfigFormatException is thrown if property is defined but the format is invalid.
ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
DockerVolCreationException
PipelineFormationException PipelineFormationException is thrown when there is a problem in setting up the modules to run.
SequnceFormatException SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.

Classes in biolockj.exception used by biolockj.module.assembly

Class and Description
ConfigException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.

Classes in biolockj.exception used by biolockj.module.classifier

Class and Description
ConfigException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
DockerVolCreationException

Classes in biolockj.exception used by biolockj.module.classifier.r16s

Class and Description
ConfigException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
ConfigFormatException ConfigFormatException is thrown if property is defined but the format is invalid.
ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
DockerVolCreationException

Classes in biolockj.exception used by biolockj.module.classifier.wgs

Class and Description
ConfigException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
DockerVolCreationException

Classes in biolockj.exception used by biolockj.module.diy

Class and Description
ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.

Classes in biolockj.exception used by biolockj.module.getData.sra

Class and Description
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
DockerVolCreationException

Classes in biolockj.exception used by biolockj.module.hello_world

Class and Description
ConfigFormatException ConfigFormatException is thrown if property is defined but the format is invalid.

Classes in biolockj.exception used by biolockj.module.implicit

Class and Description
BioLockJException Superclass for all BioLockJ exception used to ensure message uniformity.
SequnceFormatException SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.

Classes in biolockj.exception used by biolockj.module.implicit.qiime

Class and Description
ConfigException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.

Classes in biolockj.exception used by biolockj.module.report.r

Class and Description
BioLockJException Superclass for all BioLockJ exception used to ensure message uniformity.
ConfigFormatException ConfigFormatException is thrown if property is defined but the format is invalid.

Classes in biolockj.exception used by biolockj.module.rnaseq

Class and Description
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
DockerVolCreationException

Classes in biolockj.exception used by biolockj.module.seq

Class and Description
ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
SequnceFormatException SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.

Classes in biolockj.exception used by biolockj.node

Class and Description
ConfigFormatException ConfigFormatException is thrown if property is defined but the format is invalid.

Classes in biolockj.exception used by biolockj.pipelines

Class and Description
BioLockJStatusException
InvalidPipelineException

Classes in biolockj.exception used by biolockj.util

Class and Description
BioLockJException Superclass for all BioLockJ exception used to ensure message uniformity.
BioLockJStatusException
ConfigException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
ConfigFormatException ConfigFormatException is thrown if property is defined but the format is invalid.
ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
ConfigViolationException ConfigViolationException is thrown at runtime due to application state violations caused by invalid module I/O (sequences or metadata) as defined by Config properties.
DockerVolCreationException
DockerVolumeException
MetadataException MetadataException is thrown if errors occur processing Metadata files.
OtuFileException OtuFileException is thrown if errors occur processing OTU files.
PipelineScriptException PipelineScriptException is thrown by BashScriptBuilder if errors occur writing MASTER & WORKER scripts.
RuntimeParamException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
SequnceFormatException SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.
SpecialPropertiesException This type of exception is thrown if an error occurs while processing a special type of property such as "exe." properties or defaultProps.

Classes in biolockj.exception used by biolockj.util.paths

Class and Description
BioLockJException Superclass for all BioLockJ exception used to ensure message uniformity.
DockerVolCreationException