- LabeledSpinner - Class in biolockj.launch
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- LabeledSpinner(String) - Constructor for class biolockj.launch.LabeledSpinner
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- Launcher - Class in biolockj.launch
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- Launcher() - Constructor for class biolockj.launch.Launcher
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- LAUNCHER - Static variable in class biolockj.module.diy.GenMod
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Config
property: "genMod.launcher"
- LaunchProcess - Class in biolockj.launch
-
- LaunchProcess(String[]) - Constructor for class biolockj.launch.LaunchProcess
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- LIMIT_DEBUG_CLASSES - Static variable in class biolockj.Constants
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- LIST_TYPE - Static variable in class biolockj.Properties
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- listApiModules() - Static method in class biolockj.api.BioLockJ_API
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Like listModules, but only include modules that implement the ApiModule interface.
- listModuleProps(String) - Static method in class biolockj.api.BioLockJ_API
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- listModules(String) - Static method in class biolockj.api.BioLockJ_API
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Return a list of all the modules on the class path.
- listModules() - Static method in class biolockj.api.BioLockJ_API
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- listMounts(String) - Static method in class biolockj.api.BioLockJ_API
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- listProps() - Method in interface biolockj.api.ApiModule
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List properties that this module uses, including those called by any super class.
- listProps() - Static method in class biolockj.api.BioLockJ_API
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- listProps() - Method in class biolockj.module.BioModuleImpl
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- listProps() - Static method in class biolockj.util.BashScriptBuilder
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Let modules see property names.
- listProps() - Static method in class biolockj.util.DockerUtil
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Let modules see property names.
- listSamples() - Method in class biolockj.module.report.taxa.TaxaLevelTable
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- listTaxa() - Method in class biolockj.module.report.taxa.TaxaLevelTable
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- listUploads(String) - Static method in class biolockj.api.BioLockJ_API
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- load(FileInputStream) - Method in class biolockj.Properties
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Load properties, adding escape characters where necessary.
- loadModules(ScriptModule) - Static method in class biolockj.util.BashScriptBuilder
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- loadProperties(File) - Static method in class biolockj.Properties
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- Log - Class in biolockj
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- LOG_10 - Static variable in class biolockj.module.report.taxa.LogTransformTaxaTables
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- LOG_APPEND - Static variable in class biolockj.Log
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- LOG_DIR - Static variable in interface biolockj.module.BioModule
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Name of the temporary sub-directory: "log"
- LOG_E - Static variable in class biolockj.module.report.taxa.LogTransformTaxaTables
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- LOG_EXT - Static variable in class biolockj.Constants
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BioLockJ log file extension: ".log"
- LOG_EXT - Static variable in class biolockj.module.BioModuleImpl
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BioLockJ log file extension constant: ".log"
- LOG_FILE - Static variable in class biolockj.Log
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- LOG_FORMAT - Static variable in class biolockj.Log
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- LOG_LEVEL_PROPERTY - Static variable in class biolockj.Constants
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Config
property used to set log sensitivity in
log4j.properties
log4j.rootLogger=${pipeline.logLevel}, file, stdout
DEBUG - Log all messages
INFO - Log info, warning and error messages
WARN - Log warning and error messages
ERROR - Log error messages only
- LOG_SPACER - Static variable in class biolockj.Constants
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Spacer used to improve log file readability
- logConfig() - Static method in class biolockj.Log
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Prints
Config
properties to the Java log file.
- logFatalError(String[], Exception) - Static method in class biolockj.exception.FatalExceptionHandler
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Print the
Log
messages and the exception stack trace info to the $USER $HOME directory.
- logLowCountOtus(TreeMap<String, TreeSet<String>>) - Method in class biolockj.module.report.otu.RemoveLowOtuCounts
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Save a list of low count OTUs to the module temp directory.
- logLowCountPathways(TreeMap<String, TreeSet<String>>) - Method in class biolockj.module.report.humann2.RemoveLowPathwayCounts
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Save a list of low count pathways to the module temp directory.
- logScarceData(TreeMap<String, TreeSet<String>>, File) - Method in class biolockj.module.report.humann2.RemoveScarcePathwayCounts
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Save a list of low count pathways or samples to the module temp directory.
- logScarceOtus(Set<String>) - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts
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Save a list of scarce OTUs to the module temp directory.
- logsEnabled() - Static method in class biolockj.Log
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Check status of boolean toggle variable used to enable/disable log messages.
- logToSystemOut() - Static method in class biolockj.util.RuntimeParamUtil
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Return TRUE if runtime parameters indicate Logs should be written to system.out
- LogTransformTaxaTables - Class in biolockj.module.report.taxa
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This utility is used to log-transform the raw OTU counts on Log10 or Log-e scales.
- LogTransformTaxaTables() - Constructor for class biolockj.module.report.taxa.LogTransformTaxaTables
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- LogUtil - Class in biolockj.util
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This util adds auxiliary log info to BioLockJ log file
- LogUtil() - Constructor for class biolockj.util.LogUtil
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- logWelcomeMsg() - Static method in class biolockj.Log
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- LOW_ABUNDANT_CUTOFF - Static variable in class biolockj.module.report.otu.RarefyOtuCounts
-
Config
Posivite Double property to define minimum percentage of samples that must contain an
OTU.