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T

t - Static variable in class biolockj.launch.ProgressUtil
 
TAB_DELIM - Static variable in class biolockj.Constants
BioLockJ tab character: "\t"
TAB_DELIM - Static variable in class biolockj.module.BioModuleImpl
BioLockJ tab character constant: "\t"
tapSampleAssignmentMap() - Static method in class biolockj.util.MetaUtil
A care-free wrapper for saveSampleAssignmentMap().
TAXA_TABLE - Static variable in class biolockj.util.TaxaUtil
Included in the file name of each file output.
TaxaCountModule - Class in biolockj.module.report.taxa
TBD
TaxaCountModule() - Constructor for class biolockj.module.report.taxa.TaxaCountModule
 
TaxaLevelTable - Class in biolockj.module.report.taxa
 
TaxaLevelTable(String) - Constructor for class biolockj.module.report.taxa.TaxaLevelTable
 
TaxaUtil - Class in biolockj.util
This utility helps work individual Taxa names, not full OTU path files which need OtuUtil.
Taxa files containing sample taxa counts for a given taxonomy level as output by BuildTaxaTables.
TEMP_DIR - Static variable in interface biolockj.module.BioModule
Name of the temporary sub-directory: "temp"
topTaxaLevel() - Static method in class biolockj.util.TaxaUtil
Return the top configured taxonomy level from Config."report.taxonomyLevels"
toString() - Method in class biolockj.module.BioModuleImpl
 
toString() - Method in class biolockj.node.OtuNodeImpl
 
touchDockerInfo() - Static method in class biolockj.util.DockerUtil
Save a file with info about the current docker container.
touchSystemInfo() - Static method in class biolockj.util.SummaryUtil
Save information about the system, such as OS name and version.
transferMarkdown() - Method in class biolockj.module.diy.Rmarkdown
 
transferResources() - Method in class biolockj.module.diy.GenMod
 
transferResources() - Method in class biolockj.module.diy.Rmarkdown
 
transferScript() - Method in class biolockj.module.diy.GenMod
 
transform(TaxaLevelTable, List<String>, List<String>) - Method in class biolockj.module.diversity.ShannonDiversity
 
transform(TaxaLevelTable, List<String>, List<String>) - Method in class biolockj.module.report.taxa.AddPseudoCount
 
transform(TaxaLevelTable, List<String>, List<String>) - Method in class biolockj.module.report.taxa.LogTransformTaxaTables
Log transform the data
transform(TaxaLevelTable, List<String>, List<String>) - Method in class biolockj.module.report.taxa.NormalizeByReadsPerMillion
 
transform(TaxaLevelTable, List<String>, List<String>) - Method in class biolockj.module.report.taxa.NormalizeTaxaTables
Populate normalized counts with the formula: (RC/n)*((SUM(x))/N)+1
transform(TaxaLevelTable, List<String>, List<String>) - Method in class biolockj.module.report.taxa.TransformTaxaTables
Transform a table of values.
TransformTaxaTables - Class in biolockj.module.report.taxa
This utility is used to normalize, log-transform or othewise transfrom data that is stored as taxa counts.
TransformTaxaTables() - Constructor for class biolockj.module.report.taxa.TransformTaxaTables
 
TrimPrimers - Class in biolockj.module.seq
This BioModule removes sequence primers from demultiplexed files.
The primers are defined using regular expressions in a separate file.
TrimPrimers() - Constructor for class biolockj.module.seq.TrimPrimers
 
TRUE - Static variable in class biolockj.Constants
Boolean Config property value option: "Y"
TSV_EXT - Static variable in class biolockj.Constants
BioLockJ tab delimited text file extension: ".tsv"
TSV_EXT - Static variable in class biolockj.module.BioModuleImpl
BioLockJ tab delimited text file extension constant: ".tsv"
TXT_EXT - Static variable in class biolockj.Constants
BioLockJ standard text file extension: ".txt"
TXT_EXT - Static variable in class biolockj.module.BioModuleImpl
BioLockJ tab delimited text file extension constant: ".txt"
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