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.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 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.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.util

Methods in biolockj.util that throw ConfigFormatException

Modifier and Type	Method and Description
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.