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S

SAMPLE_ID_SUFFIX_TRIM_DEFAULT - Static variable in class biolockj.util.DemuxUtil
Multiplexed files created by BioLockJ may add sample ID to the sequence header if no barcode is provided.
If sample ID is added, it is immediately followed by the character: "_"
This value can be used then to set Config."input.trimSuffix"
sampleIdInHeader() - Static method in class biolockj.util.DemuxUtil
Return TRUE if Config is setup to demultiplex the sequence data based on Sample IDs in the sequence headers.
sampleIdToQiimeIdMap - Static variable in class biolockj.module.implicit.parser.r16s.QiimeParser
Convenience map, to convert Sample ID to Qiime ID
sanitizeMasterConfig() - Static method in class biolockj.util.MasterConfigUtil
Remove unused properties from the MASTER config file.
SAVE_CONTAINER_ON_EXIT - Static variable in class biolockj.util.DockerUtil
Config Boolean property: "docker.saveContainerOnExit"
saveEfsDataToS3() - Static method in class biolockj.util.NextflowUtil
Save EFS data to S3 based on pipeline Config.
saveMasterConfig() - Static method in class biolockj.util.MasterConfigUtil
Save a single version of the Config file with all inherited properties for the default config (if any exist).
saveMasterConfig(Map<String, String>) - Static method in class biolockj.util.MasterConfigUtil
Save a single version of the Config file with all inherited properties for the default config (if any exist).
saveModuleProps(BioModule) - Static method in class biolockj.Config
 
saveNextflowLog() - Static method in class biolockj.util.NextflowUtil
Save a copy of the Nextflow log file to the Pipeline root directory
saveNextflowSuccessFlag() - Static method in class biolockj.util.NextflowUtil
Save success flag, so after pipeline bash start script can stop/terminate S3 instances if successful.
saveSummary(String) - Static method in class biolockj.util.SummaryUtil
Save the summary generated to the pipeline root directory.
scanFirstLine(BufferedReader, File) - Static method in class biolockj.util.SeqUtil
This method returns the 1st non-empty line and moves the BufferedReader pointer to this line.
scanForKeys(String) - Method in class biolockj.launch.DockerLaunchProcess
 
scanForKeys(String) - Method in class biolockj.launch.LaunchProcess
Scan string for specific keys which warrant specific actions.
SCRIPT - Static variable in class biolockj.module.diy.GenMod
Config property: "genMod.scriptPath"
SCRIPT_ADD_ALPHA_DIVERSITY - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
QIIME script to add "alphaDiversity.txt" to the metadata file: "add_alpha_to_mapping_file.py"
SCRIPT_ADD_LABELS - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
QIIME script that produces "combined_seqs.fna", the multiplexed fasta file: "add_qiime_labels.py"
SCRIPT_CALC_ALPHA_DIVERSITY - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
QIIME script that creates alpha diversity metrics file in output/"alphaDiversity.txt": "alpha_diversity.py"
SCRIPT_DEFAULT_HEADER - Static variable in class biolockj.Constants
SCRIPT_DEFAULT_HEADER_DESC - Static variable in class biolockj.Constants
 
SCRIPT_DELAY_FOR_FILE_UPDATES - Static variable in class biolockj.Constants
Config List property: "script.fileRefreshDelay"
In some cases, especially with virtualization, there may be delays between before the program is able to register file system changes made by another container/node/host.
SCRIPT_DIR - Static variable in class biolockj.Constants
Name of the script sub-directory: "script"
SCRIPT_FAILURES - Static variable in class biolockj.Constants
File suffix appended to failed scripts: "Failures"
SCRIPT_FILTER_OTUS - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
QIIME script used to remove chimeras detected by "exe.vsearch": "filter_otus_from_otu_table.py"
SCRIPT_JOB_HEADER - Static variable in class biolockj.util.BashScriptBuilder
Config String property: "cluster.jobHeader"
SCRIPT_MERGE_OTU_TABLES - Static variable in class biolockj.module.implicit.qiime.MergeQiimeOtuTables
QIIME script to merge multiple OTU tables in biom format.
SCRIPT_NUM_THREADS - Static variable in class biolockj.Constants
SCRIPT_NUM_THREADS_DESC - Static variable in class biolockj.Constants
 
SCRIPT_NUM_WORKERS - Static variable in class biolockj.Constants
SCRIPT_NUM_WORKERS_DESC - Static variable in class biolockj.Constants
 
SCRIPT_PERMISSIONS - Static variable in class biolockj.Constants
Config String property: "script.permissions"
"Used as chmod permission parameter (ex: 774)"
SCRIPT_PERMISSIONS_DESC - Static variable in class biolockj.Constants
 
SCRIPT_PRINT_CONFIG - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
QIIME script to print environment configuration to qsub output file: "print_qiime_config.py"
SCRIPT_STARTED - Static variable in class biolockj.Constants
File suffix appended to started script: "Started"
SCRIPT_SUCCESS - Static variable in class biolockj.Constants
File suffix appended to successful scripts: "Success"
SCRIPT_SUMMARIZE_BIOM - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
Produces output/"otuSummary.txt" summarizing dataset: "biom summarize-table"
SCRIPT_SUMMARIZE_TAXA - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
QIIME script used to produce taxonomy-level reports in the module output directory: "summarize_taxa.py"
SCRIPT_TIMEOUT - Static variable in class biolockj.Constants
SCRIPT_TIMEOUT_DESC - Static variable in class biolockj.Constants
 
SCRIPT_VALIDATE_MAPPING - Static variable in class biolockj.module.implicit.qiime.BuildQiimeMapping
QIIME script used to validate the QIIME mapping file format
ScriptModule - Interface in biolockj.module
Classes that implement this interface are
ScriptModuleImpl - Class in biolockj.module
Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModuleImpl() - Constructor for class biolockj.module.ScriptModuleImpl
 
sendHostInfo(File) - Static method in class biolockj.util.SummaryUtil
Write the system host info.
SeqFileValidator - Class in biolockj.module.seq
This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.
SeqFileValidator() - Constructor for class biolockj.module.seq.SeqFileValidator
 
SeqModule - Interface in biolockj.module
Classes that implement this interface requires sequence files for input.
SeqModuleImpl - Class in biolockj.module
Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.
SeqModuleImpl() - Constructor for class biolockj.module.SeqModuleImpl
 
SequenceReadArchive - Class in biolockj.module.getData.sra
 
SequenceReadArchive() - Constructor for class biolockj.module.getData.sra.SequenceReadArchive
 
SequnceFormatException - Exception in biolockj.exception
SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.
SequnceFormatException(File, String) - Constructor for exception biolockj.exception.SequnceFormatException
Create standard error to throw for fasta/fastq sequence file parsing errors.
SequnceFormatException(String) - Constructor for exception biolockj.exception.SequnceFormatException
Create standard error to throw for fasta/fastq sequence file parsing errors.
SeqUtil - Class in biolockj.util
This utility helps interact with FastA and FastQ sequence files.
SET_SEED - Static variable in class biolockj.Constants
Config property "pipeline.setSeed"
setAlias(String) - Method in interface biolockj.module.BioModule
 
setAlias(String) - Method in class biolockj.module.BioModuleImpl
 
setConfigProperty(String, Collection<?>, BioModule) - Static method in class biolockj.Config
Sets a property value in the props cache as a list
setConfigProperty(String, Collection<?>) - Static method in class biolockj.Config
Sets a property value in the props cache as a list
setConfigProperty(String, String, BioModule) - Static method in class biolockj.Config
Sets a property value in the props cache
setConfigProperty(String, String) - Static method in class biolockj.Config
Sets a property value in the props cache
setCount(long) - Method in interface biolockj.node.OtuNode
Set the number of reads for a sample ID that have this OTU assignment.
setCount(long) - Method in class biolockj.node.OtuNodeImpl
 
setDbCache(File) - Method in class biolockj.module.classifier.ClassifierModuleImpl
Set DB cache directory path on 1st access
setFile(File) - Static method in class biolockj.util.MetaUtil
Set a new metadata file.
setFilePathProperty(String, String, BioModule) - Static method in class biolockj.Config
 
setFilePathProperty(String, String) - Static method in class biolockj.Config
 
setFilePermissions(String, String) - Static method in class biolockj.Processor
Set file permissions by executing chmod "script.permissions" on generated bash scripts.
setLevel(String) - Method in class biolockj.node.JsonNode
Setter method for level
setLine(String) - Method in interface biolockj.node.OtuNode
Set the classifier report line parsed to build this OTU node.
setLine(String) - Method in class biolockj.node.OtuNodeImpl
Set line only if in DEBUG mode, so we can print OtuNode constructor inputs.
setMasterConfig() - Method in class biolockj.pipelines.OtherPipelineImpl
Used to initial set the masterProps file object.
setMultiplexedConfig() - Static method in class biolockj.util.DemuxUtil
Set the Config properties needed to read the sample IDs from a multiplexed file if no barcode is provided
Set Config."input.trimPrefix" = 1st sequence header character.
Set Config."input.trimSuffix" ="_"
setNumHitsFieldName(String) - Static method in class biolockj.module.implicit.parser.ParserModuleImpl
When a module modifies the number of hits, the new counts must replace the old count fields.
setNumReadFieldName(String) - Static method in class biolockj.module.implicit.RegisterNumReads
When a module modifies the number of reads, the new counts must replace the old count fields.
setOrderedQiimeIDs(File) - Method in class biolockj.module.implicit.parser.r16s.QiimeParser
Qiime IDs are read in from the header line, converted to the sampleId, and saved to QiimeParser.orderedQiimeIDs.
setOtuCounts(Map<String, Long>) - Method in class biolockj.node.ParsedSample
Directly assign OtuCounts
setParent(JsonNode) - Method in class biolockj.node.JsonNode
Setter method for parent
setPipedir(File) - Method in class biolockj.launch.LaunchProcess
 
setPipelineId() - Method in class biolockj.pipelines.OtherPipelineImpl
 
setProjectName() - Method in class biolockj.pipelines.OtherPipelineImpl
 
setSampleId(String) - Method in interface biolockj.node.OtuNode
Set the sample ID, parsed from file name or sequence header, to which this taxonomy assignment belongs.
setSampleId(String) - Method in class biolockj.node.OtuNodeImpl
 
setSampleId(String, String) - Static method in class biolockj.util.MetaUtil
 
setSampleId(File, String) - Static method in class biolockj.util.MetaUtil
 
setTaxa(String) - Method in class biolockj.node.JsonNode
Setter method for taxa
setVerbose(boolean) - Static method in class biolockj.api.BioLockJ_API
 
SH_EXT - Static variable in class biolockj.Constants
BioLockJ shell script file extension: ".sh"
SH_EXT - Static variable in class biolockj.module.BioModuleImpl
BioLockJ shell script file extension constant: ".sh"
SHANNON_COLUMN - Static variable in class biolockj.module.diversity.ShannonDiversity
 
ShannonDiversity - Class in biolockj.module.diversity
 
ShannonDiversity() - Constructor for class biolockj.module.diversity.ShannonDiversity
 
showArgs(String, String[]) - Static method in class biolockj.launch.LaunchProcess
 
showFileContents(File) - Static method in class biolockj.launch.ProgressUtil
 
showFileContents(File, int, int) - Static method in class biolockj.launch.ProgressUtil
 
showInfo(String[]) - Static method in class biolockj.util.BioLockJUtil
Print basic version or help info if requested.
Called by 1st line BioLockJ.java main() method
showMap(TreeMap<String, String>) - Method in exception biolockj.exception.DockerVolumeException
 
showUnusedProps() - Static method in class biolockj.Config
 
showUserUpdates(String) - Static method in class biolockj.launch.ProgressUtil
Pass BioLockJ out/err stream lines.
showValue(String) - Static method in exception biolockj.exception.ConfigException
 
SILVA_CLASS_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
Silva class taxonomy level delimiter: "D_2__"
SILVA_DOMAIN_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
Silva domain taxonomy level delimiter: "D_0__"
SILVA_FAMILY_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
Silva family taxonomy level delimiter: "D_4__"
SILVA_GENUS_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
Silva genus taxonomy level delimiter: "D_5__"
SILVA_ORDER_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
Silva order taxonomy level delimiter: "D_3__"
SILVA_PHYLUM_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
Silva phylum taxonomy level delimiter: "D_1__"
SILVA_SPECIES_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
Silva species taxonomy level delimiter: "D_6__"
SimpleDockerMapper - Class in biolockj.util.paths
Introduced with BioLockJ v1.3.18.
SimpleDockerMapper() - Constructor for class biolockj.util.paths.SimpleDockerMapper
 
SIZE - Static variable in class biolockj.util.ValidationUtil
 
SIZE_WITHIN_PERCENT - Static variable in class biolockj.util.ValidationUtil
Config property "validation.sizeWithinPercent" giving the percentage by which size is allow to deviate and still be considered a valid match for the expectation.
SPAWN_DOCKER_CONTAINER - Static variable in class biolockj.util.DockerUtil
Name of the bash script function used to generate a new Docker container: "spawnDockerContainer"
SpecialPropertiesException - Exception in biolockj.exception
This type of exception is thrown if an error occurs while processing a special type of property such as "exe." properties or defaultProps.
SpecialPropertiesException(String) - Constructor for exception biolockj.exception.SpecialPropertiesException
 
SpecialPropertiesException(String, String) - Constructor for exception biolockj.exception.SpecialPropertiesException
 
SpecialPropertiesException(String, BioLockJException) - Constructor for exception biolockj.exception.SpecialPropertiesException
 
SPECIES - Static variable in class biolockj.Constants
Config option for "report.taxonomyLevels": "species"
SPECIES_DELIM - Static variable in class biolockj.node.OtuNodeImpl
Standard classifier output level delimiter for SPECIES
SRA_ACC_LIST - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
 
SRA_ACC_LIST_DESC - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
 
SraDownload - Class in biolockj.module.getData.sra
 
SraDownload() - Constructor for class biolockj.module.getData.sra.SraDownload
 
SraMetaData - Class in biolockj.module.getData.sra
 
SraMetaData() - Constructor for class biolockj.module.getData.sra.SraMetaData
 
SraMetaDB - Class in biolockj.module.getData.sra
 
SraMetaDB() - Constructor for class biolockj.module.getData.sra.SraMetaDB
 
SRP - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
 
SRP_DESC - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
 
SrpSrrConverter - Class in biolockj.module.getData.sra
 
SrpSrrConverter() - Constructor for class biolockj.module.getData.sra.SrpSrrConverter
 
stageRootConfig() - Static method in class biolockj.util.NextflowUtil
Before any AWS or Nextflow functionality can be used, the Docker root user $HOME directory must be updated with the EC2 user aws + Nextflow config.
STANDARD_CONFIG_PATH - Static variable in class biolockj.Constants
Default Config imported for all pipelines (if file exists)
startNextflow(List<BioModule>) - Static method in class biolockj.util.NextflowUtil
Call this method to build the Nextflow main.nf for the current pipeline.
startSpinner(String) - Static method in class biolockj.launch.ProgressUtil
 
STATUS_MARK_KEY - Static variable in class biolockj.Constants
Key used in standard err messages indicating that this line should be shown to the user.
STATUS_START_KEY - Static variable in class biolockj.Constants
Key used in standard err messages indicating that this line should be shown to the user.
statusStrings - Static variable in class biolockj.util.ValidationUtil
 
Step1 - Class in biolockj.module.hello_world
First set up a mostly-empty class.
Step1() - Constructor for class biolockj.module.hello_world.Step1
 
Step2 - Class in biolockj.module.hello_world
Start with the basic documentation.
Step2() - Constructor for class biolockj.module.hello_world.Step2
 
Step3 - Class in biolockj.module.hello_world
Even a very simple module probably uses at least one property.
Step3() - Constructor for class biolockj.module.hello_world.Step3
 
Step4 - Class in biolockj.module.hello_world
Specify the acceptable input data type for this module.
Step4() - Constructor for class biolockj.module.hello_world.Step4
 
Step5 - Class in biolockj.module.hello_world
 
Step5() - Constructor for class biolockj.module.hello_world.Step5
 
Stop - Class in biolockj.module
Stop a pipeline.
Stop() - Constructor for class biolockj.module.Stop
 
StopAfterPrecheck - Exception in biolockj.exception
When running in "precheck" mode, this is the mechanism that stops a pipeline from running.
StopAfterPrecheck(String) - Constructor for exception biolockj.exception.StopAfterPrecheck
 
StopAfterPrecheck() - Constructor for exception biolockj.exception.StopAfterPrecheck
 
StopModuleException - Exception in biolockj.exception
 
StopModuleException(Stop) - Constructor for exception biolockj.exception.StopModuleException
 
stopNextflow() - Static method in class biolockj.util.NextflowUtil
Stop Nextflow process (required since parent Java process that ran BioLockJ pipeline will not halt until this subprocess is finished.
STRING_TYPE - Static variable in class biolockj.Properties
 
subDirExists(BioModule, String) - Static method in class biolockj.util.ModuleUtil
Return TRUE if BioModule sub-directory exists
submitJob(String[], String) - Static method in class biolockj.Processor
Instantiates a new Processor.
String[] array used to control spacing between command/params.
As if executing on terminal args[0] args[1]...
submitQuery(String, String) - Static method in class biolockj.Processor
Run script that expects a single result
subProcAlive(Long) - Static method in class biolockj.Processor
Check if a specific process is alive
Subprocess(String[], String) - Constructor for class biolockj.Processor.Subprocess
Execute the command args in a separate thread and log output with label.
subProcsAlive() - Static method in class biolockj.Processor
Check if any Subprocess threads are still running.
SUMMARIZE_TAXA_SUPPRESS_BIOM - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
QIIME script "summarize_taxa.py" parameter used to suppress the output of biom files.
SUMMARY - Static variable in class biolockj.module.report.otu.CompileOtuCounts
Output file prefix: "summary"
SummaryUtil - Class in biolockj.util
This module builds an execution summary for the pipeline which is printed to the log file and is be sent to the user if the Email module is configured.
SummaryUtil() - Constructor for class biolockj.util.SummaryUtil
 
syncModuleLogs(ScriptModule) - Static method in class biolockj.util.LogUtil
Not used currently.
SYSTEM_OUT_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
Flag argument; if present, BioLockJ will print to System.out instead of Log for debugging early runtime errors.
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