- 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
-
- 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"