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UNCLASSIFIED - Static variable in class biolockj.Constants
Unclassified taxa prefix: "Unclassified"
UNUSED_PROPS_ARG - Static variable in class biolockj.launch.LaunchProcess
 
UNUSED_PROPS_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
Flag argument; if presetn, BioLockJ will run check dependencies for ALL modules to determine unused properties from the primary config.
UNVERIFIED_PROPS_FILE - Static variable in class biolockj.Constants
 
unzip(File, String) - Static method in class biolockj.module.seq.AwkFastaConverter
Build script line to decompress gzipped sequence file.
UpdateJavaDocs - Class in biolockj.util
This class has a main() method as it is designed to be called as a stand-alone class.
This utility updates the JavaDocs to add additional header options.
These headers are added to almost every class when the JavaDoc command is run so an automated solution was needed.
UpdateJavaDocs() - Constructor for class biolockj.util.UpdateJavaDocs
 
updateNodeStats(LinkedHashMap<String, TreeSet<JsonNode>>, File, String, String) - Method in class biolockj.module.report.JsonReport
Add stats from R_CalculateStats into all of the JsonNodes.
updateNumAttempts() - Static method in class biolockj.util.SummaryUtil
Update the number of attempts in the summary file (called from restart)
updateRConfig(BioModule) - Static method in class biolockj.util.RMetaUtil
Get updated R config props
updateStats(String, Double) - Method in class biolockj.node.JsonNode
Update stats, add val to key name.
USE_EVERY_ROW - Static variable in class biolockj.util.MetaUtil
Config Boolean property: "metadata.useEveryRow"
useHumann2RawCount(BioModule) - Static method in class biolockj.util.PathwayUtil
Determine if humann2 provided most recent raw count data, used to determine getPreReq modules.
USER_PROFILE - Static variable in class biolockj.Constants
Config File property: "pipeline.userProfile"
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