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

C

cacheInputFiles(Collection<File>) - Method in class biolockj.module.BioModuleImpl

Cache the input files for quick access on subsequent calls to BioModuleImpl.getInputFiles()

calcTimeout(List<File>) - Method in class biolockj.module.report.r.R_Module

Use this to estimate the max time needed to process a given list of inputs.

cancel() - Method in class biolockj.launch.LabeledSpinner

catchFirstResponse(Process) - Method in class biolockj.launch.LaunchProcess

checkBasicArgCompatibility() - Method in class biolockj.launch.LaunchProcess

checkDependencies(BioModule) - Static method in class biolockj.Config

checkDependencies() - Method in class biolockj.module.assembly.GenomeAssembly

Samples must be paired reads since metaspades currently doesn't support single reads.

checkDependencies() - Method in interface biolockj.module.BioModule

During pipeline initialization, all configured BioModules will run this method to validate dependencies.

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

If restarting or running a direct pipeline execute the cleanup for completed modules.

checkDependencies() - Method in class biolockj.module.classifier.ClassifierModuleImpl

Validate module dependencies: Call ClassifierModuleImpl.getClassifierExe() to verify the executable Call ClassifierModuleImpl.getClassifierParams() to verify the runtime parameters are valid Call ClassifierModuleImpl.validateModuleOrder() to validate module configuration order.

checkDependencies() - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier

Call QiimeClassifier checkOtuPickingDependencies() method to verify OTU picking script parameters.

checkDependencies() - Method in class biolockj.module.classifier.r16s.QiimeDeNovoClassifier

Call QiimeClassifier checkOtuPickingDependencies() method to verify OTU picking script parameters.

checkDependencies() - Method in class biolockj.module.classifier.r16s.QiimeOpenRefClassifier

Call QiimeClassifier checkOtuPickingDependencies() method to verify OTU picking script parameters.

checkDependencies() - Method in class biolockj.module.classifier.r16s.RdpClassifier

checkDependencies() - Method in class biolockj.module.classifier.wgs.Humann2Classifier

Verify that none of the derived command line parameters are included in Config."exe.humann2".

checkDependencies() - Method in class biolockj.module.classifier.wgs.Kraken2Classifier

Verify that none of the derived command line parameters are included in Config."exe.kraken2".

checkDependencies() - Method in class biolockj.module.classifier.wgs.KrakenClassifier

Verify that none of the derived command line parameters are included in Config."exe.kraken".

checkDependencies() - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Verify none of the derived command line parameters are included in Config."exe.metaphlan2"

checkDependencies() - Method in class biolockj.module.diy.ForEachLoop

checkDependencies() - Method in class biolockj.module.diy.GenMod

checkDependencies() - Method in class biolockj.module.diy.Rmarkdown

checkDependencies() - Method in class biolockj.module.getData.sra.SraDownload

checkDependencies() - Method in class biolockj.module.getData.sra.SraMetaData

checkDependencies() - Method in class biolockj.module.getData.sra.SraMetaDB

checkDependencies() - Method in class biolockj.module.hello_world.Hello_Friends

Be sure to touch any / all properties your module uses.

checkDependencies() - Method in class biolockj.module.hello_world.Step3

Be sure to touch any / all properties your module uses.

checkDependencies() - Method in class biolockj.module.hello_world.Step5

Test anything that might cause your module to fail; especially user input.

checkDependencies() - Method in class biolockj.module.implicit.Demultiplexer

Validate module dependencies: If Config."demultiplexer.strategy" indicates use of barcodes to demultiplexer, validate metadata column named Config."metadata.barcodeColumn" exists Call DemuxUtil.setMultiplexedConfig() to set multiplexed Config if needed If Config."demultiplexer.barcodeCutoff" defined, validate between 0.0 - 1.0

checkDependencies() - Method in class biolockj.module.implicit.ImportMetadata

checkDependencies() - Method in class biolockj.module.implicit.parser.ParserModuleImpl

Execute ParserModuleImpl.validateModuleOrder() to validate module configuration order.

checkDependencies() - Method in class biolockj.module.implicit.parser.r16s.RdpHierParser

checkDependencies() - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser

checkDependencies() - Method in class biolockj.module.implicit.qiime.MergeQiimeOtuTables

Verify the previous module = QiimeClosedRefClassifier

checkDependencies() - Method in class biolockj.module.implicit.qiime.QiimeClassifier

checkDependencies() - Method in class biolockj.module.report.Email

Verify required email Config properties exist and are properly formatted.

checkDependencies() - Method in class biolockj.module.report.humann2.Humann2CountModule

checkDependencies() - Method in class biolockj.module.report.humann2.RemoveLowPathwayCounts

checkDependencies() - Method in class biolockj.module.report.humann2.RemoveScarcePathwayCounts

checkDependencies() - Method in class biolockj.module.report.otu.RarefyOtuCounts

checkDependencies() - Method in class biolockj.module.report.otu.RemoveLowOtuCounts

checkDependencies() - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts

checkDependencies() - Method in class biolockj.module.report.r.R_CalculateStats

Validate configuration file properties used to build the R report: super.checkDependencies() Require "r_CalculateStats.pAdjustScope" Require "r_CalculateStats.pAdjustMethod"

checkDependencies() - Method in class biolockj.module.report.r.R_Module

checkDependencies() - Method in class biolockj.module.report.r.R_PlotEffectSize

At least one of the available plot types should NOT be disabled.

checkDependencies() - Method in class biolockj.module.report.r.R_PlotMds

Require Config."r_PlotMds.numAxis" set to integer greater than 2

checkDependencies() - Method in class biolockj.module.report.r.R_PlotOtus

checkDependencies() - Method in class biolockj.module.report.r.R_PlotPvalHistograms

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

Verify Config."report.logBase" property is valid (if defined) with a value = (e or 10).

checkDependencies() - Method in class biolockj.module.rnaseq.DESeq2

checkDependencies() - Method in class biolockj.module.rnaseq.EdgeR

checkDependencies() - Method in class biolockj.module.ScriptModuleImpl

Validate module dependencies: Require Config. exists Require Config. is positive integer Require Config. is positive integer Verify Config. is positive integer if set Start the AWS DB sync to S3 if a novel DB has been configure and "aws.copyDbToS3" is enabled

checkDependencies() - Method in class biolockj.module.seq.KneadData

checkDependencies() - Method in class biolockj.module.seq.Multiplexer

Validate module dependencies: Validate this is the last module to run (excluding Email) If this module was completed on a previous run, update the property: Config."internal.multiplexed" = "Y"

checkDependencies() - Method in class biolockj.module.seq.PearMergeReads

Validate module dependencies Verify input files are in fastq format Verify matching paired reads are found Validate required Config.PearMergeReads.EXE_PEAR property If running a restarted pipeline that already merged reads, set paired indicator to false

checkDependencies() - Method in class biolockj.module.seq.RarefySeqs

Validate module dependencies Validate Config.RarefySeqs.INPUT_RAREFYING_MIN is a non-negative integer Validate Config.RarefySeqs.INPUT_RAREFYING_MAX is a positive integer that is greater than or equal to Config.RarefySeqs.INPUT_RAREFYING_MIN (if defined)

checkDependencies() - Method in class biolockj.module.seq.SeqFileValidator

checkDependencies() - Method in class biolockj.module.seq.TrimPrimers

Validates the file that defines the REGEX primers.

checkDependencies() - Method in class biolockj.module.Stop

checkDependencies(BioModule) - Static method in class biolockj.util.BashScriptBuilder

checkDependencies(BioModule) - Static method in class biolockj.util.DockerUtil

checkDependencies(BioModule) - Static method in class biolockj.util.ValidationUtil

This method calls the methods that are used by executeTask to get the validation input.

checkModuleDependencies() - Static method in class biolockj.Pipeline

Initialization occurs by calling BioModule methods on configured modules
Create module sub-directories under "internal.pipelineDir" as ordered in Config file.
Reset the SummaryUtil module so previous summary descriptions can be used for completed modules Delete incomplete module contents if restarting a failed pipeline "output" directory
Call Pipeline.refreshRCacheIfNeeded() to cache R fields after 1st R module runs
Verify dependencies with BioModule.checkDependencies()

checkOneModulesDependencies(BioModule) - Static method in class biolockj.Pipeline

checkVersion() - Static method in class biolockj.util.BioLockJUtil

CITE_QIIME - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

CLASS - Static variable in class biolockj.Constants

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

CLASS_DELIM - Static variable in class biolockj.node.OtuNodeImpl

Standard classifier output level delimiter for CLASS

ClassifierModule - Interface in biolockj.module.classifier

Classifier BioModules build one or more bash scripts to call the application on sequence files.

ClassifierModuleImpl - Class in biolockj.module.classifier

This is the superclass for all WGS and 16S biolockj.module.classifier BioModules.

ClassifierModuleImpl() - Constructor for class biolockj.module.classifier.ClassifierModuleImpl

classifyReportableMetadata(BioModule) - Static method in class biolockj.util.RMetaUtil

Classify and verify the R filter and reportable metadata fields listed in the Config file.
All metadata fields are reported unless specific fields are listed in: Config."r.reportFields".

cleanUp() - Method in interface biolockj.module.BioModule

This method executes after execution to update Config modified by the module or other cleanup operations.

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

If metadata exists in module output directory, refresh MetaUtil.

cleanUp() - Method in class biolockj.module.classifier.wgs.Humann2Classifier

cleanUp() - Method in class biolockj.module.getData.sra.SraDownload

cleanUp() - Method in class biolockj.module.getData.sra.SrpSrrConverter

cleanUp() - Method in class biolockj.module.implicit.Demultiplexer

Update SeqUtil to indicate data has been demultiplexed.

cleanUp() - Method in class biolockj.module.implicit.ImportMetadata

Verify the metadata fields configured for R reports.

cleanUp() - Method in class biolockj.module.implicit.parser.r16s.QiimeParser

cleanUp() - Method in class biolockj.module.implicit.qiime.QiimeClassifier

The cleanUp operation builds a new metadata file if alpha diversity metrics were generated by this module.

cleanUp() - Method in class biolockj.module.report.humann2.AddMetadataToPathwayTables

For R to report HumanN2 reports instead of taxa levels

cleanUp() - Method in class biolockj.module.report.otu.RarefyOtuCounts

Update ParserModuleImpl OTU_COUNT field name.

cleanUp() - Method in class biolockj.module.report.otu.RemoveLowOtuCounts

Update ParserModuleImpl OTU_COUNT field name.

cleanUp() - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts

Set the number of hits field.

cleanUp() - Method in class biolockj.module.report.r.R_Module

cleanUp() - Method in class biolockj.module.report.taxa.AddMetadataToTaxaTables

For R to report taxa levels (not HumanN2 reports)

cleanUp() - Method in class biolockj.module.seq.AwkFastaConverter

Set Config."internal.seqType" = "fasta"
Set Config."internal.seqHeaderChar" = SeqUtil.FASTA_HEADER_DEFAULT_DELIM

cleanUp() - Method in class biolockj.module.seq.PearMergeReads

Set Config."internal.pairedReads" = "N" and register number of reads.

cleanUp() - Method in class biolockj.module.seq.RarefySeqs

Set "Num_Rarefied_Reads" as the number of reads field.

cleanUp() - Method in class biolockj.module.seq.SeqFileValidator

Set "Num_Valid_Reads" as the number of reads field.

cleanUp() - Method in class biolockj.module.seq.TrimPrimers

Set "Num_Trimmed_Reads" as the number of reads field.

clear() - Static method in class biolockj.launch.ProgressUtil

Use with caution.

clearDemuxConfig() - Static method in class biolockj.util.DemuxUtil

Clear demultiplexer related fields

clearStatus(File) - Static method in class biolockj.pipelines.PipelineUtil

Remove the current status flag of a given directory

clearStatus(String) - Static method in class biolockj.pipelines.PipelineUtil

Remove the current status flag of a given directory

CLUSTER_BATCH_COMMAND - Static variable in class biolockj.util.BashScriptBuilder

Config String property: "cluster.batchCommand"

CLUSTER_HAS_BATCH_IDS - Static variable in class biolockj.util.BashScriptBuilder

Config Boolean property: "cluster.returnsBatchIds"

CLUSTER_HOST - Static variable in class biolockj.Constants

Config "string" property: "cluster.host"

CLUSTER_MODULES - Static variable in class biolockj.util.BashScriptBuilder

Config List property: "cluster.modules"

CLUSTER_NUM_PROCESSORS - Static variable in class biolockj.util.BashScriptBuilder

One parameter of the Config String property "cluster.jobHeader" to set number of cores.

CLUSTER_PROLOGUE - Static variable in class biolockj.util.BashScriptBuilder

Config String property: "cluster.prologue"

CLUSTER_STATUS_COMMAND - Static variable in class biolockj.util.BashScriptBuilder

Config String property: "cluster.statusCommand"

CODE_LINE - Static variable in class biolockj.module.diy.GenMod

COMBINED_FNA - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Multiplexed fasta file produced by QIIME "add_qiime_labels.py" script: "combined_seqs.fna"

command - Variable in class biolockj.launch.LaunchProcess

COMMON_CAUSES - Static variable in exception biolockj.exception.PipelineScriptException

CommonDockerMapper - Class in biolockj.util.paths

Introduced with BioLockJ v1.3.18.

CommonDockerMapper() - Constructor for class biolockj.util.paths.CommonDockerMapper

COMPARE_ON - Static variable in class biolockj.util.ValidationUtil

Config set property giving the file metrics to use in comparing to the expectation.

compareTo(BioModule) - Method in class biolockj.module.BioModuleImpl

compareTo(JsonNode) - Method in class biolockj.node.JsonNode

compareTo(OtuNode) - Method in class biolockj.node.OtuNodeImpl

The sort order of the TreeSet(OtuNode) is absolutely required for proper processing in OtuNodeImpl.addTaxa(String, String) and OtuNodeImpl.getTaxaMap().

compareTo(ParsedSample) - Method in class biolockj.node.ParsedSample

CompileOtuCounts - Class in biolockj.module.report.otu

This BioModule compiles the counts from all OTU count files into a single summary OTU count file containing OTU counts for the entire dataset.

CompileOtuCounts() - Constructor for class biolockj.module.report.otu.CompileOtuCounts

compileOtuCounts(Collection<File>) - Method in class biolockj.module.report.otu.CompileOtuCounts

Compile OTU counts from the individual sample OTU count files

compileSampleOtuCounts(File) - Static method in class biolockj.util.OtuUtil

Compile OTU counts from an individual sample OTU count file

Config - Class in biolockj

Provides type-safe, validated methods for storing/accessing system properties.
Initially populated by the properties in the Config file, several additional properties are created and stored in the the Config (to save system determined info such as: pipeline directory and name, has paired reads?, has multiplexed reads?, etc.).

Config() - Constructor for class biolockj.Config

CONFIG_ARG - Static variable in class biolockj.launch.LaunchProcess

CONFIG_FILE - Static variable in class biolockj.util.RuntimeParamUtil

Config file path runtime parameter switch: "-config"

ConfigConflictException - Exception in biolockj.exception

ConfigConflictException(String) - Constructor for exception biolockj.exception.ConfigConflictException

ConfigConflictException(String, String) - Constructor for exception biolockj.exception.ConfigConflictException

ConfigConflictException(String[], String) - Constructor for exception biolockj.exception.ConfigConflictException

ConfigException - Exception in biolockj.exception

ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.

ConfigException(String) - Constructor for exception biolockj.exception.ConfigException

Abstract Config exception calls super to instantiate using the superclass Exception implementation

ConfigException(String, String) - Constructor for exception biolockj.exception.ConfigException

Abstract Config exception calls ConfigException.buildMessage(String, String) to generate a standard error message for Configuration file errors, passing an empty string for the msg parameter.

ConfigFormatException - Exception in biolockj.exception

ConfigFormatException is thrown if property is defined but the format is invalid.

ConfigFormatException(String, String) - Constructor for exception biolockj.exception.ConfigFormatException

ConfigFormatException is thrown if property is defined but the format is invalid.

ConfigNotFoundException - Exception in biolockj.exception

ConfigNotFoundException is thrown if a required Config property is undefined.

ConfigNotFoundException(String) - Constructor for exception biolockj.exception.ConfigNotFoundException

ConfigNotFoundException is thrown if a required Config property is undefined.

ConfigNotFoundException(String, String) - Constructor for exception biolockj.exception.ConfigNotFoundException

ConfigNotFoundException is thrown if a required Config property is undefined.

ConfigPathException - Exception in biolockj.exception

ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.

ConfigPathException(File) - Constructor for exception biolockj.exception.ConfigPathException

ConfigPathException is thrown if the filePath parameter does not exist on the file system.

ConfigPathException(File, String) - Constructor for exception biolockj.exception.ConfigPathException

ConfigPathException is thrown if the filePath parameter does not exist on the file system.

ConfigPathException(String, String) - Constructor for exception biolockj.exception.ConfigPathException

ConfigPathException is thrown if the path does not exist or is not the proper file type: "file" or "directory".

ConfigViolationException - Exception in biolockj.exception

ConfigViolationException is thrown at runtime due to application state violations caused by invalid module I/O (sequences or metadata) as defined by Config properties.

ConfigViolationException(String) - Constructor for exception biolockj.exception.ConfigViolationException

Generic exception message.

ConfigViolationException(String, String) - Constructor for exception biolockj.exception.ConfigViolationException

ConfigViolationException is thrown application detects a violation due to a Config property setting, such as finding Sample IDs with no corresponding sequence file enforced by Config."metadata.useEveryRow" = "Y"

Constants - Class in biolockj

Single Java class to hold shared constant values referenced my multiple classes.

Constants() - Constructor for class biolockj.Constants

CONTAINER_BLJ_DIR - Static variable in class biolockj.util.DockerUtil

Docker container blj dir: "/app/biolockj"

CONTAINER_ID_KEY - Static variable in class biolockj.util.DockerUtil

containerizePath(String) - Static method in class biolockj.util.DockerUtil

If running in docker mode, convert this path to the form that can be used inside the docker container.

containerizePath(File) - Static method in class biolockj.util.DockerUtil

DockerUtil.containerizePath(String)

containsHn2ParserOutput(Collection<File>) - Static method in class biolockj.util.PathwayUtil

Check pipeline input contains Humann2Parser module output.

convertRelativePath(String, File) - Static method in class biolockj.Config

Given a relative path (ie, one that starts with "."), get the absolute path---even when runnig in docker.

convertWindowsPath(String) - Method in class biolockj.util.paths.CommonDockerMapper

convertWindowsPathForDocker(String) - Static method in class biolockj.Config

copyBatchOtuTableToOutputDir(File, Integer) - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier

The method returns 1 bash script line that will copy the batch "otu_table.biom" from the batchDir to the output directory.

copyDEseqScript() - Method in class biolockj.module.rnaseq.DESeq2

copyEdgeRScript() - Method in class biolockj.module.rnaseq.EdgeR

copyFileToPipelineRoot(File) - Static method in class biolockj.BioLockJ

Copy file to pipeline root directory.

copyFromFile(File) - Static method in class biolockj.api.BuildDocs

copyFromModuleResource(BioModule, String) - Static method in class biolockj.api.BuildDocs

copyInputData() - Static method in class biolockj.BioLockJ

Create a copy of the sequence files in property "input.dirPaths", output to a directory named "internal.pipelineDir"/input.

copyInputFiles() - Static method in class biolockj.util.BioLockJUtil

Copy input files into an internal folder within the pipeline root direction named "input"

copyTempOtuTableToOutputDir() - Method in class biolockj.module.classifier.r16s.QiimeDeNovoClassifier

The method returns 1 bash script line that will copy the batch "otu_table.biom" from the batchDir to the output directory.

countNumReads(File) - Static method in class biolockj.util.SeqUtil

Method counts number of reads in the given sequence file by counting the number of lines and dividing by the number of lines/sample (fasta=2, fastq=4)

createCmd() - Method in class biolockj.launch.DockerLaunchProcess

createCmd() - Method in class biolockj.launch.JavaLaunchProcess

createCmd() - Method in class biolockj.launch.LaunchProcess

createFile(String) - Static method in class biolockj.util.BioLockJUtil

Used to save status files for modules and the pipeline.

createModuleInstance(String) - Static method in class biolockj.util.ModuleUtil

Construct a BioModule based on its className to add it to the pipeline.

createScript(ScriptModule, String, List<String>) - Static method in class biolockj.util.BashScriptBuilder

Create the script.

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