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T

TAB_DELIM - Static variable in class biolockj.Constants

BioLockJ tab character constant: "\t"

TAB_DELIM - Static variable in class biolockj.module.BioModuleImpl

BioLockJ tab character constant: "\t"

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

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

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

transform(File) - Method in class biolockj.module.report.taxa.LogTransformTaxaTables

Log transform the data

transform(File) - Method in class biolockj.module.report.taxa.NormalizeTaxaTables

Populate normalized OTU counts with the formula: (RC/n)*((SUM(x))/N)+1

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 constant: ".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 constant: ".txt"

TXT_EXT - Static variable in class biolockj.module.BioModuleImpl

BioLockJ tab delimited text file extension constant: ".txt"

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