A B C D E F G H I J K L M N O P Q R S T U V W

F

FALSE - Static variable in class biolockj.Constants

Boolean Config property value option: "N"

FAMILY - Static variable in class biolockj.Constants

Config option for "report.taxonomyLevels": "family"

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"

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".

fileExt(File) - Static method in class biolockj.util.BioLockJUtil

Return the file extension - but ignore ".gz".

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).

filterZeroSampleIDs(List<String>, Set<Integer>) - Static method in class biolockj.module.report.taxa.NormalizeTaxaTables

Filter Sample IDs with all zero rows

findAllZeroIndex(List<List<Long>>) - Static method in class biolockj.module.report.taxa.NormalizeTaxaTables

Return the table index for rows with all zer count values

findModuleInputFiles() - Method in class biolockj.module.BioModuleImpl

Called upon first access of input files to return sorted list of files from all Config."input.dirPaths"
Hidden files (starting with ".") are ignored
Call BioModuleImpl.isValidInputModule(BioModule) on each previous module until acceptable input files are found

findScarceOtus(TreeMap<String, TreeMap<String, Long>>, 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

Find scarce taxa found in less samples than the cutoff percentage: Config."report.scarceCountCutoff".

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.

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.

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 "##.##%"

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_EXECUTE - Static variable in class biolockj.util.BashScriptBuilder

Worker script function to execute 1 line of a worker script.

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_RUN_JOB - Static variable in class biolockj.util.BashScriptBuilder

Main script function to submit jobs on the cluster

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"

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