Uses of Class
biolockj.api.API_Exception

Packages that use API_Exception

Package	Description
biolockj	The root biolockj package contains core classes used by all BioLockJ pipelines.
biolockj.api
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.diy
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.report.taxa
biolockj.util	Static utilities centralize and organize reusable core methods.

Uses of API_Exception in biolockj

Methods in biolockj that throw API_Exception

Modifier and Type	Method and Description
static String	Properties.getDescription(String prop)
static HashMap<String,String>	Properties.getPropDescMap() Allow the API to access the list of properties and descriptions.
static String	Properties.getPropertyType(String prop)
static HashMap<String,String>	Properties.getPropTypeMap() Allow the API to access the list of properties and descriptions.
static Boolean	Properties.isValidProp(String property) Check if a property has a value in a valid format.
static void	Properties.registerProp(String prop, String type, String desc) Allow utility classes to keep their props private but still register them with Properties for API.
(package private) static void	Constants.registerProps() Register properties with the Properties class for API access.

Uses of API_Exception in biolockj.api

Methods in biolockj.api that throw API_Exception

Modifier and Type	Method and Description
static String	BuildDocs.copyFromFile(File file)
static String	BuildDocs.copyFromModuleResource(BioModule module, String name)
String	ApiModule.getDescription(String prop) Describe a given property / how it is used (including how it is used by a super class)
String	ApiModule.getDetails() A extension of getDescription.
String	ApiModule.getPropType(String prop) Get the type for a given property.
static List<String>	BioLockJ_API.listProps()
static String	BioLockJ_API.propDescModule(String prop, String module)
static String	BioLockJ_API.propTypeModule(String prop, String module) Returns a string describing the format type that required for the value of the property given.

Uses of API_Exception in biolockj.module

Methods in biolockj.module that throw API_Exception

Modifier and Type	Method and Description
String	BioModuleImpl.getDescription(String prop)
String	BioModuleImpl.getDetails()
String	BioModuleImpl.getPropType(String prop)

Uses of API_Exception in biolockj.module.diy

Methods in biolockj.module.diy that throw API_Exception

Modifier and Type	Method and Description
String	ForEachLoop.getDetails()
String	ForEachFile.getDetails()
String	ForEachLevel.getDetails() Deprecated.
String	ForEachSample.getDetails()
String	GenMod.getDetails()
String	Rmarkdown.getDetails()

Uses of API_Exception in biolockj.module.implicit

Methods in biolockj.module.implicit that throw API_Exception

Modifier and Type	Method and Description
String	Demultiplexer.getDetails()

Constructors in biolockj.module.implicit that throw API_Exception

Constructor and Description
Demultiplexer()

Uses of API_Exception in biolockj.module.report.taxa

Methods in biolockj.module.report.taxa that throw API_Exception

Modifier and Type	Method and Description
String	AddMetadataToTaxaTables.getDetails()
String	NormalizeByReadsPerMillion.getDetails()
String	NormalizeTaxaTables.getDetails()
String	TaxaCountModule.getDetails() All child classes from this class have this pre-req.

Uses of API_Exception in biolockj.util

Methods in biolockj.util that throw API_Exception

Modifier and Type	Method and Description
static void	DockerUtil.registerProps() Register properties with the Properties class for API access.
static void	MetaUtil.registerProps()
static void	BashScriptBuilder.registerProps() Register properties with the Properties class for API access.
static void	NextflowUtil.registerProps() Register properties with the Properties class for API access.
static void	RMetaUtil.registerProps()
static void	ValidationUtil.registerProps()
static void	DemuxUtil.registerProps()