A B C D E F G H I J K L M N O P Q R S T U V W X Y

L

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

Instantiate Properties via Properties.buildConfig(File)

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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