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LabeledSpinner - Class in biolockj.launch
 
LabeledSpinner(String) - Constructor for class biolockj.launch.LabeledSpinner
 
Launcher - Class in biolockj.launch
 
Launcher() - Constructor for class biolockj.launch.Launcher
 
LAUNCHER - Static variable in class biolockj.module.diy.GenMod
Config property: "genMod.launcher"
LaunchProcess - Class in biolockj.launch
 
LaunchProcess(String[]) - Constructor for class biolockj.launch.LaunchProcess
 
LIMIT_DEBUG_CLASSES - Static variable in class biolockj.Constants
Config property used to limit classes that log debug statements when "pipeline.logLevel"="Y" TODO: make this clearer.
LIST_TYPE - Static variable in class biolockj.Properties
 
listApiModules() - Static method in class biolockj.api.BioLockJ_API
Like listModules, but only include modules that implement the ApiModule interface.
listModuleProps(String) - Static method in class biolockj.api.BioLockJ_API
 
listModules(String) - Static method in class biolockj.api.BioLockJ_API
Return a list of all the modules on the class path.
listModules() - Static method in class biolockj.api.BioLockJ_API
 
listMounts(String) - Static method in class biolockj.api.BioLockJ_API
 
listProps() - Method in interface biolockj.api.ApiModule
List properties that this module uses, including those called by any super class.
listProps() - Static method in class biolockj.api.BioLockJ_API
 
listProps() - Method in class biolockj.module.BioModuleImpl
 
listProps() - Static method in class biolockj.util.BashScriptBuilder
Let modules see property names.
listProps() - Static method in class biolockj.util.DockerUtil
Let modules see property names.
listSamples() - Method in class biolockj.module.report.taxa.TaxaLevelTable
 
listTaxa() - Method in class biolockj.module.report.taxa.TaxaLevelTable
 
listUploads(String) - Static method in class biolockj.api.BioLockJ_API
 
load(FileInputStream) - Method in class biolockj.Properties
Load properties, adding escape characters where necessary.
loadModules(ScriptModule) - Static method in class biolockj.util.BashScriptBuilder
Return lines to script that load cluster modules based on Config."cluster.modules"
loadProperties(File) - Static method in class biolockj.Properties
Log - Class in biolockj
Simple Logging Facade for Java (SLF4J) implementation using Log4J
Log4J Configuration: log4j.properties
Every Java class that prints to the Java log file, will do so by calling: Log.out(Class).Log.out(Class).debug( logMessage ) Log.out(Class).Log.out(Class).info( logMessage ) Log.out(Class).Log.out(Class).warn( logMessage ) Log.out(Class).Log.out(Class).error( logMessage, exception )
LOG_10 - Static variable in class biolockj.module.report.taxa.LogTransformTaxaTables
Log 10 display string a supported value for: "report.logBase"
LOG_APPEND - Static variable in class biolockj.Log
Set in Log.initialize(String) to true only if executing pipeline restart.
Used by log4j.properties
log4j.appender.file.Append=${LOG_APPEND}
LOG_DIR - Static variable in interface biolockj.module.BioModule
Name of the temporary sub-directory: "log"
LOG_E - Static variable in class biolockj.module.report.taxa.LogTransformTaxaTables
Log e display string a supported value for: "report.logBase"
LOG_EXT - Static variable in class biolockj.Constants
BioLockJ log file extension: ".log"
LOG_EXT - Static variable in class biolockj.module.BioModuleImpl
BioLockJ log file extension constant: ".log"
LOG_FILE - Static variable in class biolockj.Log
Set in Log.initialize(String) to file path of pipeline Java log file
Used by log4j.properties
log4j.appender.file.File=${LOG_FILE}
LOG_FORMAT - Static variable in class biolockj.Log
Set in Log.initialize(String) to proper layout based on pipeline is direct or note
Used by log4j.properties
log4j.appender.file.layout.ConversionPattern=${LOG_FORMAT}
LOG_LEVEL_PROPERTY - Static variable in class biolockj.Constants
Config property used to set log sensitivity in log4j.properties
log4j.rootLogger=${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
Spacer used to improve log file readability
logConfig() - Static method in class biolockj.Log
Prints Config properties to the Java log file.
logFatalError(String[], Exception) - Static method in class biolockj.exception.FatalExceptionHandler
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
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
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
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
Save a list of scarce OTUs to the module temp directory.
logsEnabled() - Static method in class biolockj.Log
Check status of boolean toggle variable used to enable/disable log messages.
logToSystemOut() - Static method in class biolockj.util.RuntimeParamUtil
Return TRUE if runtime parameters indicate Logs should be written to system.out
LogTransformTaxaTables - Class in biolockj.module.report.taxa
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
 
LogUtil - Class in biolockj.util
This util adds auxiliary log info to BioLockJ log file
LogUtil() - Constructor for class biolockj.util.LogUtil
 
logWelcomeMsg() - Static method in class biolockj.Log
Print welcome message.
Message includes BioLockJ version BioLockJUtil.getVersion(), lab citation, and freeware blurb.
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.
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