Uses of Class
biolockj.exception.ConfigFormatException

Packages that use ConfigFormatException

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

Uses of ConfigFormatException in biolockj

Methods in biolockj that throw ConfigFormatException

Modifier and Type	Method and Description
static void	Config.checkDependencies(BioModule module)
static boolean	Config.getBoolean(BioModule module, String property) Parse property value (Y or N) to return boolean, if not found, return false;
static Double	Config.getDoubleVal(BioModule module, String property) Parse property for numeric (double) value
static Integer	Config.getIntegerProp(BioModule module, String property) Parse property value as integer
static Integer	Config.getNonNegativeInteger(BioModule module, String property) Parse property as non-negative integer value
static Double	Config.getPositiveDoubleVal(BioModule module, String property) Parse property as positive double value
static Integer	Config.getPositiveInteger(BioModule module, String property) Parse property as positive integer value
static boolean	Config.requireBoolean(BioModule module, String property) Required to return a valid boolean or
static Double	Config.requireDoubleVal(BioModule module, String property) Requires valid double value
static Integer	Config.requireInteger(BioModule module, String property) Requires valid integer value
static Double	Config.requirePositiveDouble(BioModule module, String property) Require valid positive double value
static Integer	Config.requirePositiveInteger(BioModule module, String property) Require valid positive integer value

Uses of ConfigFormatException in biolockj.module

Methods in biolockj.module that throw ConfigFormatException

Modifier and Type	Method and Description
Integer	ScriptModuleImpl.getTimeout() Default behavior is for scripts to run indefinitely (no timeout).
Integer	ScriptModule.getTimeout() ScriptModule that run scripts can opt to set a timeout (such as used by the R script).

Uses of ConfigFormatException in biolockj.module.classifier.r16s

Methods in biolockj.module.classifier.r16s that throw ConfigFormatException

Modifier and Type	Method and Description
(package private) String	RdpClassifier.getConfThreshold()

Uses of ConfigFormatException in biolockj.module.hello_world

Methods in biolockj.module.hello_world that throw ConfigFormatException

Modifier and Type	Method and Description
protected String	Step5.howExciting() Accesses the "hello.excitmentLevel" and creates a string with that many !s.
protected String	Hello_Friends.howExciting() Accesses the "hello.excitmentLevel" and creates a string with that many !s, or just "." if the value is null.
protected String	Step5.makeMessage() Create a message based on the modules properties.
protected String	Hello_Friends.makeMessage() Create a message based on the modules properties.

Uses of ConfigFormatException in biolockj.module.report.r

Methods in biolockj.module.report.r that throw ConfigFormatException

Modifier and Type	Method and Description
Integer	R_Module.getTimeout() The R Script should run quickly, timeout = 10 minutes appears to work well.

Uses of ConfigFormatException in biolockj.node

Methods in biolockj.node that throw ConfigFormatException

Modifier and Type	Method and Description
Map<String,String>	OtuNodeImpl.getTaxaMap() This implementation ensures all levels between top and bottom taxonomy levels are complete.
protected void	OtuNodeImpl.populateInBetweenTaxa() Populate missing OTUs if top level taxa is defined and there is a level gap between the top level and the bottom level.
protected static boolean	OtuNodeImpl.reportUnclassifiedTaxa()

Uses of ConfigFormatException in biolockj.util

Methods in biolockj.util that throw ConfigFormatException

Modifier and Type	Method and Description
static void	BashScriptBuilder.checkDependencies(BioModule module)
static boolean	BioLockJUtil.copyInputFiles() Copy input files into an internal folder within the pipeline root direction named "input"
static Integer	ModuleUtil.getMinSamplesPerWorker(BioModule module) Return the min number of samples that can be processed per worker script.
static Integer	ModuleUtil.getNumWorkers(BioModule module) Get the actual number of worker scripts generated for a given module, minimum value = 1.
static String	SeqUtil.getSampleId(File file)
protected static String	BashScriptBuilder.getWorkerScriptPath(ScriptModule module) Build the file path for the numbered worker script.
static boolean	MetaUtil.hasMetaColToSampleIdMap()
static List<String>	TaxaUtil.initTaxaLevels() Set taxonomy levels ordered by level, from highest to lowest.
static Boolean	SeqUtil.isMultiplexed() Check current state of sequence data.
protected static List<String>	BashScriptBuilder.passEnvironmentVarVals(ScriptModule module)
static boolean	MetaUtil.setSampleId(File file, String sampleId)
static boolean	MetaUtil.setSampleId(String filename, String sampleId)