- FAIL - Static variable in class biolockj.util.ValidationUtil
-
- FALSE - Static variable in class biolockj.Constants
-
Boolean
Config property value option: "N"
- FAMILY - Static variable in class biolockj.Constants
-
- FAMILY_DELIM - Static variable in class biolockj.node.OtuNodeImpl
-
Standard classifier output level delimiter for FAMILY
- FASTA - Static variable in class biolockj.Constants
-
File extension for fasta files = "fasta"
- FASTA_HEADER_DEFAULT_DELIM - Static variable in class biolockj.util.SeqUtil
-
Default 1st character for a FASTA file: ">"
- FASTQ - Static variable in class biolockj.Constants
-
File extension for fastq files: "fastq"
- FatalExceptionHandler - Class in biolockj.exception
-
FatalExceptionHandler saves logs somewhere the user can access if failures occur before the log file is generated.
- FatalExceptionHandler() - Constructor for class biolockj.exception.FatalExceptionHandler
-
- FG_ARG - Static variable in class biolockj.launch.LaunchProcess
-
- fieldValuesAreUnique(String, boolean) - Static method in class biolockj.util.MetaUtil
-
Determine if the given field has only unique values.
- FILE - Static variable in exception biolockj.exception.ConfigPathException
-
One of 2 BioLockJ file path types that can be passed to the constructor "file".
- FILE_EXT - Static variable in class biolockj.util.TaxaUtil
-
- FILE_PATH - Static variable in class biolockj.Properties
-
- FILE_PATH_LIST - Static variable in class biolockj.Properties
-
- fileExt(File) - Static method in class biolockj.util.BioLockJUtil
-
Return the file extension - but ignore
".gz".
- FileWithoutMetadataException - Exception in biolockj.exception
-
- FileWithoutMetadataException(File) - Constructor for exception biolockj.exception.FileWithoutMetadataException
-
- fillEmptyVals() - Method in class biolockj.module.report.taxa.TaxaLevelTable
-
Replace all null values in the maps with 0.
- fillEmptyVals(Double) - Method in class biolockj.module.report.taxa.TaxaLevelTable
-
Replace all null values in the maps with the given value.
- filterByProcessLevel(List<File>) - Static method in class biolockj.module.report.taxa.TaxaCountModule
-
Pipelines may include taxa tables + normalized taxa tables (or log normalized taxa tables).
- filterSamples(TaxaLevelTable) - Method in class biolockj.module.report.taxa.TransformTaxaTables
-
Filter out any samples in which all values are 0.
- filterTaxa(TaxaLevelTable) - Method in class biolockj.module.diversity.ShannonDiversity
-
- filterTaxa(TaxaLevelTable) - Method in class biolockj.module.report.taxa.TransformTaxaTables
-
- findModuleInputFiles() - Method in class biolockj.module.BioModuleImpl
-
- findModuleInputFiles() - Method in class biolockj.module.rnaseq.DESeq2
-
- findModuleInputFiles() - Method in class biolockj.module.rnaseq.EdgeR
-
- findScarceOtus(TreeSet<String>, TreeMap<String, TreeSet<String>>) - Static method in class biolockj.module.report.otu.RemoveScarceOtuCounts
-
Find the scarce OTUs that contain the key values in scarceTaxa.
- findScarceTaxa(TreeMap<String, TreeMap<String, Long>>, TreeSet<String>) - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts
-
- findUniqueOtus(TreeMap<String, TreeMap<String, Long>>) - Static method in class biolockj.util.OtuUtil
-
Find every unique OTU across all samples.
- findUniqueTaxa(TreeSet<String>, String) - Static method in class biolockj.util.TaxaUtil
-
Extract taxonomy names at the given level from all given OTUs.
- ForEachFile - Class in biolockj.module.diy
-
- ForEachFile() - Constructor for class biolockj.module.diy.ForEachFile
-
- ForEachLevel - Class in biolockj.module.diy
-
Deprecated.
- ForEachLevel() - Constructor for class biolockj.module.diy.ForEachLevel
-
Deprecated.
- ForEachLoop - Class in biolockj.module.diy
-
- ForEachLoop() - Constructor for class biolockj.module.diy.ForEachLoop
-
- ForEachSample - Class in biolockj.module.diy
-
- ForEachSample() - Constructor for class biolockj.module.diy.ForEachSample
-
- formatConfigPath(String) - Method in class biolockj.util.paths.BasicDockerMapper
-
Give a path as it appears in the config file, convert it to a form suitable for matching to map keys.
- formatConfigPath(String) - Method in class biolockj.util.paths.CommonDockerMapper
-
- formatDigits(Integer, Integer) - Static method in class biolockj.util.BioLockJUtil
-
This method formats the input number to have a length of at least numDigits.
Simply add leading zeros until numDigits is reached.
- formatHostPath(String) - Method in class biolockj.util.paths.BasicDockerMapper
-
Given a path as it appears in the Docker inspect Mount host info, convert the path to a form suitable for the map as a key.
- formatHostPath(String) - Method in class biolockj.util.paths.CommonDockerMapper
-
In the docker json file, the host path is sometimes represented as the exact path that the user might see on
their host machine, and sometimes it is pre-prended with /host_mnt/, and other other differences.
- formatHostPath(String) - Method in class biolockj.util.paths.SimpleDockerMapper
-
- formatInnerPath(String) - Method in class biolockj.util.paths.BasicDockerMapper
-
Given a path as it appears in the target portion of a Mount entry, convert the path to a form suitable for the map a value.
- formatMetaId(String) - Method in class biolockj.module.implicit.ImportMetadata
-
Format the metadata ID to remove problematic invisible characters (particularly converted Excel files).
- formatNumericOutput(Long, boolean) - Static method in class biolockj.util.BioLockJUtil
-
This method formats the input number by adding commas.
- formatPercentage(long, long) - Static method in class biolockj.util.BioLockJUtil
-
Build the percentage display string for the num/denom ratio as "##.##%"
- foundNewPipeline() - Method in class biolockj.launch.LaunchProcess
-
- FUNCTION_ASSEMBLY - Static variable in class biolockj.module.assembly.GenomeAssembly
-
Name of the metaspades function used to assemble reads: "runAssembly"
- FUNCTION_CONVERT_454 - Static variable in class biolockj.module.seq.AwkFastaConverter
-
Name of the bash function used to conver 454 format to BioLockJ friendly Illumina format:
"convert454"
- FUNCTION_CONVERT_TO_FASTA - Static variable in class biolockj.module.seq.AwkFastaConverter
-
Name of the bash function that converts the file format to Fasta: "convertToFastA"
- FUNCTION_CREATE_BATCH_MAPPING - Static variable in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier
-
Name of the bash function that prepares a batch of seqs for processing: "createBatchMapping"
- FUNCTION_GUNZIP - Static variable in class biolockj.module.seq.AwkFastaConverter
-
Name of the bash function used to decompress gzipped files: "decompressGzip"
- FUNCTION_GUNZIP - Static variable in class biolockj.module.seq.Gunzipper
-
Name of the bash function used to decompress gzipped files: "openZip"
- FUNCTION_KRAKEN - Static variable in class biolockj.module.classifier.wgs.Kraken2Classifier
-
Name of the kraken function used to assign taxonomy: "runKraken2"
- FUNCTION_KRAKEN - Static variable in class biolockj.module.classifier.wgs.KrakenClassifier
-
Name of the kraken function used to assign taxonomy: "runKraken"
- FUNCTION_PEAR_MERGE - Static variable in class biolockj.module.seq.PearMergeReads
-
Name of the bash function that merges files with PEAR: "mergeReads"
- FUNCTION_RDP - Static variable in class biolockj.module.classifier.r16s.RdpClassifier
-
Name of the RdpClassifier bash script function used to assign taxonomy: "runRdp"
- FUNCTION_REORDER_FIELDS - Static variable in class biolockj.module.implicit.qiime.BuildQiimeMapping
-
Name of the bash function that reorders metadata columns: "reorderColumns"
- FUNCTION_SANATIZE - Static variable in class biolockj.module.seq.KneadData
-
Name of the bash function used to decompress gzipped files: "sanatizeData"
- FUNCTION_TRANSLATE - Static variable in class biolockj.module.classifier.wgs.KrakenClassifier
-
Name of the translate function used to convert mpa-format to standard format: "translate"