Package | Description |
---|---|
biolockj |
The root biolockj package contains core classes used by all BioLockJ pipelines.
|
biolockj.api | |
biolockj.module | |
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.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
String |
BioModuleImpl.getDescription(String prop) |
String |
BioModuleImpl.getDetails() |
String |
BioModuleImpl.getPropType(String prop) |
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() |
Modifier and Type | Method and Description |
---|---|
String |
Demultiplexer.getDetails() |
Constructor and Description |
---|
Demultiplexer() |
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.
|
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() |