- UNCLASSIFIED - Static variable in class biolockj.Constants
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Unclassified taxa prefix: "Unclassified"
- UNUSED_PROPS_ARG - Static variable in class biolockj.launch.LaunchProcess
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- UNUSED_PROPS_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
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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
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- unzip(File, String) - Static method in class biolockj.module.seq.AwkFastaConverter
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Build script line to decompress gzipped sequence file.
- UpdateJavaDocs - Class in biolockj.util
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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
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- updateNodeStats(LinkedHashMap<String, TreeSet<JsonNode>>, File, String, String) - Method in class biolockj.module.report.JsonReport
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- updateNumAttempts() - Static method in class biolockj.util.SummaryUtil
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Update the number of attempts in the summary file (called from restart)
- updateRConfig(BioModule) - Static method in class biolockj.util.RMetaUtil
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Get updated R config props
- updateStats(String, Double) - Method in class biolockj.node.JsonNode
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Update stats, add val to key name.
- USE_EVERY_ROW - Static variable in class biolockj.util.MetaUtil
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Config Boolean property: "metadata.useEveryRow"
- useHumann2RawCount(BioModule) - Static method in class biolockj.util.PathwayUtil
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Determine if humann2 provided most recent raw count data, used to determine getPreReq modules.
- USER_PROFILE - Static variable in class biolockj.Constants
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Config File property: "pipeline.userProfile"