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main(String[]) - Static method in class biolockj.BioLockJ

BioLockJ is the BioLockj.jar Main-Class, and is the first method executed.
Execution summary:
Call BioLockJ.initBioLockJ(String[]) to assign pipeline root dir and log file If change password pipeline, call Email.encryptAndStoreEmailPassword() Otherwise execute BioLockJ.runPipeline()

main(String[]) - Static method in class biolockj.util.UpdateJavaDocs

Main method updates the JavaDocs to replace undesirable auto-generated text.

MAIN_SCRIPT_PREFIX - Static variable in interface biolockj.module.BioModule

Script prefix appended to start of file name to indicate the main script in the script directory.

makeRunAllScript(List<BioModule>) - Static method in class biolockj.util.DownloadUtil

This script allows a user to run all R scripts together from a single script.

MAPPING_FILE - Static variable in class biolockj.util.DemuxUtil

Config String property "demultiplexer.mapping" lists the path to the mapping file to match sequence headers to barcodes.

markComplete(BioModule) - Static method in class biolockj.util.ModuleUtil

Method creates a file named "biolockjComplete" in module root directory to document module has completed successfully.

markProjectStatus(String) - Static method in class biolockj.BioLockJ

Create indicator file in pipeline root directory, with name = status parameter.

markStarted(BioModule) - Static method in class biolockj.util.ModuleUtil

Method creates a file named "biolockjStarted" in module root directory to document module has completed successfully.

markStatus(String) - Method in class biolockj.module.JavaModuleImpl

This method sets the module status by saving the indicator file to the module root dir.

MASTER_PREFIX - Static variable in class biolockj.Constants

Prefix added to the master Config file: "MASTER_"

MemoryUtil - Class in biolockj.util

This Java memory report utility can be used to help identify memory leaks in the application.

MemoryUtil() - Constructor for class biolockj.util.MemoryUtil

MergeQiimeOtuTables - Class in biolockj.module.implicit.qiime

This BioModule will run immediately after QiimeClosedRefClassifier if multiple otu_table.biom files were created.

MergeQiimeOtuTables() - Constructor for class biolockj.module.implicit.qiime.MergeQiimeOtuTables

META_BARCODE_COLUMN - Static variable in class biolockj.util.MetaUtil

Config property "metadata.barcodeColumn" defines metadata column with identifying barcode

META_COLUMN_DELIM - Static variable in class biolockj.util.MetaUtil

Config property that defines how metadata columns are separated: "metadata.columnDelim" Typically files are tab or comma separated.

META_COMMENT_CHAR - Static variable in class biolockj.util.MetaUtil

Config property to set metadata file comment indicator: "metadata.commentChar"
Empty string is a valid option indicating no comments in metadata file

META_DIR_FLAG - Static variable in class biolockj.util.RuntimeParamUtil

Metadata file directory path runtime parameter switch: "m"

META_FILE_PATH - Static variable in class biolockj.util.MetaUtil

Config String property: "metadata.filePath"
If absolute file path, use file as metadata.
If directory path, must find exactly 1 file within, to use as metadata.

META_FILENAME_COLUMN - Static variable in class biolockj.util.MetaUtil

Config property "metadata.fileNameColumn" defines metadata column with input file names

META_MERGED - Static variable in class biolockj.module.report.taxa.AddMetadataToTaxaTables

File suffix added to OTU table file name once merged with metadata.

META_NULL_VALUE - Static variable in class biolockj.util.MetaUtil

Config property to set metadata file empty cell: "metadata.nullValue"

META_REQUIRED - Static variable in class biolockj.util.MetaUtil

Config Boolean property: "metadata.required"
If Y, require metadata row for each sample with sequence data in "input.dirPaths".
If N, samples without metadata are ignored.

METAPHLAN2_DB - Static variable in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Config Directory property containing alternate database: "metaphlan2.db"
Must always be paired with "metaphlan2.mpa_pkl"

METAPHLAN2_MPA_PKL - Static variable in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Config File property containing path to the mpa_pkl file used to reference an alternate DB "metaphlan2.mpa_pkl"
Must always be paired with "metaphlan2.db"

Metaphlan2Classifier - Class in biolockj.module.classifier.wgs

This BioModule builds the bash scripts used to execute metaphlan2.py to classify WGS sequences with MetaPhlAn2.

Metaphlan2Classifier() - Constructor for class biolockj.module.classifier.wgs.Metaphlan2Classifier

Metaphlan2Parser - Class in biolockj.module.implicit.parser.wgs

This BioModules parses Metaphlan2Classifier output reports to build standard OTU abundance tables.

Metaphlan2Parser() - Constructor for class biolockj.module.implicit.parser.wgs.Metaphlan2Parser

MetaphlanNode - Class in biolockj.node.wgs

This class represents one line of Metaphlan2Classifier output.

MetaphlanNode(String, String) - Constructor for class biolockj.node.wgs.MetaphlanNode

Build the OtuNode by extracting the OTU names for each level from the line.

MetaUtil - Class in biolockj.util

This utility is used to read, modify, or create a metadata file for the sequence data.

MODULE_SEQ_PACKAGE - Static variable in class biolockj.Constants

BioLockJ SEQ module package: "biolockj.module.seq"

MODULE_WGS_CLASSIFIER_PACKAGE - Static variable in class biolockj.Constants

BioLockJ WGS Classifier module package: "biolockj.module.classifier.wgs"

moduleComplete() - Method in interface biolockj.module.JavaModule

This method will create the success flag file so the next module can run.

moduleComplete() - Method in class biolockj.module.JavaModuleImpl

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

Check if a module was in the pipeline at least once.

moduleFailed() - Method in interface biolockj.module.JavaModule

This method will create the fail flag file so the pipeline can move on..

moduleFailed() - Method in class biolockj.module.JavaModuleImpl

ModuleUtil - Class in biolockj.util

This utility holds general methods useful for BioModule interaction and management.

multiplex(File) - Method in class biolockj.module.seq.Multiplexer

Add file sequences to the multiplexed file.

Multiplexer - Class in biolockj.module.seq

This BioModule will merge sequence files into a single combined sequence file, with either the sample ID or an identifying bar-code (if defined in the metatata) is stored in the sequence header.
BioLockJ is designed to run on demultiplexed data so this must be the last module to run in its branch.

Multiplexer() - Constructor for class biolockj.module.seq.Multiplexer

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