- DatabaseModule - Interface in biolockj.module
-
Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database
directory to map to the container /db volume.
- DEBUG - Static variable in class biolockj.Log
-
DEBUG log message type
- debug(Class<?>, String) - Static method in class biolockj.Log
-
Print log level DEBUG message.
Do not print
MetaUtil debug since these will always print since the Logger isn't
initialized yet and logMesseges will print them as INFO after Log file initializes.
- DEFAULT_COL_DELIM - Static variable in class biolockj.util.MetaUtil
-
Default column delimiter = tab character
- DEFAULT_COMMENT_CHAR - Static variable in class biolockj.util.MetaUtil
-
Default comment character for any new metadata file created by a BioModule: ""
- DEFAULT_DOCKER_HUB_USER - Static variable in class biolockj.util.DockerUtil
-
Name of the BioLockJ Docker account ID: "biolockj"
- DEFAULT_FORMAT - Static variable in class biolockj.Log
-
Standard BioLockJ log format includes date, time, severity type, and calling class before the msg.
- DEFAULT_MOD_DEMUX - Static variable in class biolockj.Constants
-
Config String property: Java class name for default module used to demultiplex data:
"pipeline.defaultDemultiplexer"
- DEFAULT_MOD_FASTA_CONV - Static variable in class biolockj.Constants
-
Config String property: Java class name for default module used to convert files into fasta:
"pipeline.defaultFastaConverter" format
- DEFAULT_MOD_SEQ_MERGER - Static variable in class biolockj.Constants
-
Config String property: Java class name for default module used combined paired read files:
"pipeline.defaultSeqMerger"
- DEFAULT_NULL_VALUE - Static variable in class biolockj.util.MetaUtil
-
Default field value to represent null-value: "NA"
- DEFAULT_STATS_MODULE - Static variable in class biolockj.Constants
-
Config String property: Java class name for default module used generate p-value and other
stats: "pipeline.defaultStatsModule"
- deleteIncompleteModule(BioModule) - Static method in class biolockj.Pipeline
-
Delete and recreate incomplete module directory.
- deleteWithRetry(File, int) - Static method in class biolockj.util.BioLockJUtil
-
Delete file or directory with retry.
- DELIM_SEP - Static variable in class biolockj.Constants
-
In an otu string for multiple levels, each separated by
"|", each otu has a level prefix ending
with "__"
- delimToLevelMap() - Method in interface biolockj.node.OtuNode
-
- delimToLevelMap() - Method in class biolockj.node.OtuNodeImpl
-
- delimToLevelMap() - Method in class biolockj.node.r16s.QiimeNode
-
- demultiplex(Map<String, Set<String>>) - Method in class biolockj.module.implicit.Demultiplexer
-
Demultiplex the file into separate small temp files, with
2000000 lines each for
processing.
- Demultiplexer - Class in biolockj.module.implicit
-
This BioModule splits multiplexed data into a separate file or pair of files (for paired reads) for each sample.
- Demultiplexer() - Constructor for class biolockj.module.implicit.Demultiplexer
-
- DEMUX_STRATEGY - Static variable in class biolockj.util.DemuxUtil
-
Config property "demultiplexer.strategy" tells BioLockJ how to match sequences with Sample
IDs.
Options: barcode_in_header, barcode_in_mapping, barcode_in_seq, id_in_header, do_not_demux.
If using barcodes, metadata column
"metadata.barcodeColumn" is required.
- DemuxUtil - Class in biolockj.util
-
This utility contains standard methods used to handle multiplexed data.
- DemuxUtil() - Constructor for class biolockj.util.DemuxUtil
-
- demuxWithBarcode() - Static method in class biolockj.util.DemuxUtil
-
Return TRUE if barcode column is defined in the Config file and is populated in the metadata file
- DETACH_JAVA_MODULES - Static variable in class biolockj.Constants
-
Config Boolean property: "pipeline.detachJavaModules"
If
"Y" Java modules do not run with main BioLockJ Java application
- DIRECT_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
-
Direct mode runtime parameter switch: "d"
- DIRECT_FORMAT - Static variable in class biolockj.Log
-
Direct BioLockJ log prefix includes only the msg.
- DIRECTORY - Static variable in exception biolockj.exception.ConfigPathException
-
One of 2 BioLockJ file path types that can be passed to the constructor "directory".
- DISABLE_ADD_IMPLICIT_MODULES - Static variable in class biolockj.Constants
-
Config Boolean property: "pipeline.disableAddImplicitModules"
If set to
"Y", implicit modules will not be added to the pipeline.
- DISABLE_PRE_REQ_MODULES - Static variable in class biolockj.Constants
-
Config Boolean property: "pipeline.disableAddPreReqModules"
If set to
"Y", prerequisite modules will not be added to the pipeline.
- displayID(BioModule) - Static method in class biolockj.util.ModuleUtil
-
Return the module ID as a 2 digit display number (add leading zero if needed).
- DO_GZIP - Static variable in class biolockj.module.seq.Multiplexer
-
Config boolean property that if enabled will gzip the multiplexed output: "multiplexer.gzip":
- doAddNextBatch(int) - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier
-
Return true if the sample count indicates we have a full batch
- doChangePassword() - Static method in class biolockj.util.RuntimeParamUtil
-
Return TRUE if runtime parameters indicate change password request
- DOCKER_CONFIG_PATH - Static variable in class biolockj.Constants
-
- DOCKER_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
-
Docker mode runtime parameter switch: "-docker"
- DOCKER_HUB_USER - Static variable in class biolockj.util.DockerUtil
-
Config name of the Docker Hub user with the BioLockJ containers: "docker.user"
Docker Hub URL:
https://hub.docker.com
By default the "biolockj" user is used to pull the standard modules, but advanced users can deploy their own
versions of these modules and add new modules in their own Docker Hub account.
- DOCKER_ROOT_HOME - Static variable in class biolockj.util.DockerUtil
-
Docker container root user $HOME directory
- DockerUtil - Class in biolockj.util
-
DockerUtil for Docker integration.
- DockerUtil() - Constructor for class biolockj.util.DockerUtil
-
- doDebug() - Static method in class biolockj.Log
-
Return TRUE if = DEBUG.
- doDemux() - Static method in class biolockj.util.DemuxUtil
-
Return TRUE if Config is setup to demultiplex the sequence data.
- DOMAIN - Static variable in class biolockj.Constants
-
- DOMAIN_DELIM - Static variable in class biolockj.node.OtuNodeImpl
-
Standard classifier output level delimiter for DOMAIN
- doRestart() - Static method in class biolockj.util.RuntimeParamUtil
-
Return TRUE if runtime parameters indicate attempt to restart pipeline
- DOWNLOAD_DIR - Static variable in class biolockj.util.DownloadUtil
-
Config String property: "pipeline.downloadDir"
Sets the local directory targeted by the scp command.
- DOWNLOAD_LIST - Static variable in class biolockj.util.DownloadUtil
-
Name of the file holding the list of pipeline files to include when running
DownloadUtil
- DownloadUtil - Class in biolockj.util
-
This utility is used to validate the metadata to help ensure the format is valid R script input.