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F

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
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"
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
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
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
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.
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"
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