- R_ADJ_PVALS_SCOPE - Static variable in class biolockj.module.report.r.R_CalculateStats
-
Config String property: "r_CalculateStats.pAdjustScope" defines R p.adjust( n ) parameter.
- R_CalculateStats - Class in biolockj.module.report.r
-
This BioModule is used to build the R script used to generate taxonomy statistics and plots.
- R_CalculateStats() - Constructor for class biolockj.module.report.r.R_CalculateStats
-
- R_COLOR_BASE - Static variable in class biolockj.Constants
-
- R_COLOR_FILE - Static variable in class biolockj.Constants
-
Config property "r.colorFile" gives the path to a tab-delimited file giving the color
to use for each value of each metadata filed plotted.
- R_COLOR_HIGHLIGHT - Static variable in class biolockj.Constants
-
Config property "r.colorHighlight" defines the highlight label color
- R_COLOR_PALETTE - Static variable in class biolockj.Constants
-
Config property "r.colorPalette" defines the color palette for PDF plots
- R_COLOR_POINT - Static variable in class biolockj.Constants
-
Config property "r.colorPoint" defines the pch point colors for PDF plots
- R_DEBUG - Static variable in class biolockj.Constants
-
Config boolean property "r.debug" sets the debug log function enabled
- R_EXCLUDE_FIELDS - Static variable in class biolockj.util.RMetaUtil
-
Config List property: "r.excludeFields"
R reports must contain at least one valid nominal or numeric metadata field.
- R_EXT - Static variable in class biolockj.Constants
-
File extension of BioLockJ generated R Scripts: ".R"
- R_FUNCTION_LIB - Static variable in class biolockj.Constants
-
This library script contains helper functions used in the R scripts: "BioLockJ_Lib.R"
- R_INTERNAL_RUN_HN2 - Static variable in class biolockj.Constants
-
Config Boolean property to signal R scripts to build HumanN2 reports
- R_MAIN_SCRIPT - Static variable in class biolockj.Constants
-
This main R script that sources helper libraries and calls modules main method function: "BioLockJ_MAIN.R"
- R_MDS_DISTANCE - Static variable in class biolockj.module.report.r.R_PlotMds
-
Config property: "r_PlotMds.distance" defines the distance index to use in the capscale
command.
- R_MDS_NUM_AXIS - Static variable in class biolockj.module.report.r.R_PlotMds
-
Config Integer property: "r_PlotMds.numAxis" defines the number of MDS axis to report
- R_MDS_REPORT_FIELDS - Static variable in class biolockj.module.report.r.R_PlotMds
-
Config List property: "r_PlotMds.reportFields"
List metadata fields to generate MDS ordination plots.
- R_MDS_REPORT_FIELDS - Static variable in class biolockj.util.RMetaUtil
-
Config List property: "r_PlotMds.reportFields"
Fields listed here must exist in the metadata file.
- R_Module - Class in biolockj.module.report.r
-
This BioModule is the superclass for R script generating modules.
- R_Module() - Constructor for class biolockj.module.report.r.R_Module
-
- R_NOMINAL_FIELDS - Static variable in class biolockj.util.RMetaUtil
-
Config List property: "r.nominalFields"
Override default property type by explicitly listing it as nominal.
- R_NUMERIC_FIELDS - Static variable in class biolockj.util.RMetaUtil
-
Config List property: "r.numericFields"
Override default property type by explicitly listing it as numeric.
- R_PCH - Static variable in class biolockj.Constants
-
Config property "r.pch" defines the plot point shape for PDF plots
- R_PlotEffectSize - Class in biolockj.module.report.r
-
This BioModule is used to run the R script used to generate OTU-metadata fold-change-barplots for each binary report
field.
- R_PlotEffectSize() - Constructor for class biolockj.module.report.r.R_PlotEffectSize
-
- R_PlotMds - Class in biolockj.module.report.r
-
This BioModule is used to build the R script used to generate MDS plots for each report field and each taxonomy level
configured.
- R_PlotMds() - Constructor for class biolockj.module.report.r.R_PlotMds
-
- R_PlotOtus - Class in biolockj.module.report.r
-
This BioModule is used to build the R script used to generate OTU-metadata box-plots and scatter-plots for each
report field and taxonomy level.
- R_PlotOtus() - Constructor for class biolockj.module.report.r.R_PlotOtus
-
- R_PlotPvalHistograms - Class in biolockj.module.report.r
-
This BioModule is used to build the R script used to generate p-value histograms for each report field and each
taxonomy level configured.
- R_PlotPvalHistograms() - Constructor for class biolockj.module.report.r.R_PlotPvalHistograms
-
- R_PVAL_ADJ_METHOD - Static variable in class biolockj.module.report.r.R_CalculateStats
-
Config String property: "r_CalculateStats.pAdjustMethod" defines p.adjust( method ) parameter.
- R_RARE_OTU_THRESHOLD - Static variable in class biolockj.Constants
-
Config Double property "r.rareOtuThreshold" defines number OTUs needed to includ in
reports
- R_REPORT_FIELDS - Static variable in class biolockj.util.RMetaUtil
-
Config List property: "r.reportFields"
R reports must contain at least one valid field.
- R_SAVE_R_DATA - Static variable in class biolockj.Constants
-
Config boolean property "r.saveRData" enables the .RData file to save.
- R_SQUARED_VALS - Static variable in class biolockj.module.report.r.R_CalculateStats
-
R^2 identifier: "rSquaredVals"
- R_TIMEOUT - Static variable in class biolockj.Constants
-
- R_USE_UINQUE_COLORS - Static variable in class biolockj.Constants
-
- rarefy(String, TreeMap<String, Long>, long) - Method in class biolockj.module.report.otu.RarefyOtuCounts
-
- rarefy(File) - Method in class biolockj.module.seq.RarefySeqs
-
Builds the rarefied file if too many seqs found, or adds files with too few samples to the list of bad samples.
- RarefyOtuCounts - Class in biolockj.module.report.otu
-
This BioModule applies a mean iterative post-OTU classification rarefication algorithm so that each output sample
will have approximately the same number of OTUs.
- RarefyOtuCounts() - Constructor for class biolockj.module.report.otu.RarefyOtuCounts
-
- RarefySeqs - Class in biolockj.module.seq
-
This BioModule imposes a minimum and/or maximum number of reads per sample.
- RarefySeqs() - Constructor for class biolockj.module.seq.RarefySeqs
-
- RDP_DB - Static variable in class biolockj.module.classifier.r16s.RdpClassifier
-
Config File property used to define an alternate RDP database file: "rdp.db"
- RDP_DOCKER_JAR - Static variable in class biolockj.module.classifier.r16s.RdpClassifier
-
Config File property for RDP java executable jar WHEN RUNNING IN DOCKER: "rdp.containerJar"
This is the path in the default docker container.
- RDP_JAR - Static variable in class biolockj.module.classifier.r16s.RdpClassifier
-
Config File property for RDP java executable JAR: "rdp.jar"
- RDP_PARAMS - Static variable in class biolockj.module.classifier.r16s.RdpClassifier
-
Config List property for RDP java executable JAR runtime params: "rdp.params"
- RDP_THRESHOLD_SCORE - Static variable in class biolockj.Constants
-
Config String property: "rdp.minThresholdScore"
RdpParser will ignore OTU assignments below the threshold score (0-100)
- RdpClassifier - Class in biolockj.module.classifier.r16s
-
This BioModule uses RDP to assign taxonomy to 16s sequences.
- RdpClassifier() - Constructor for class biolockj.module.classifier.r16s.RdpClassifier
-
- RdpHierParser - Class in biolockj.module.implicit.parser.r16s
-
- RdpHierParser() - Constructor for class biolockj.module.implicit.parser.r16s.RdpHierParser
-
- RdpNode - Class in biolockj.node.r16s
-
- RdpNode(String, String) - Constructor for class biolockj.node.r16s.RdpNode
-
Constructor called one line of RDP output.
- RdpParser - Class in biolockj.module.implicit.parser.r16s
-
This BioModule parses RDP output files to build standard OTU abundance tables.
- RdpParser() - Constructor for class biolockj.module.implicit.parser.r16s.RdpParser
-
- ReadCounter - Interface in biolockj.module
-
Identifies modules that can report the number of reads per file in the metadata.
- readProps(File, Properties) - Static method in class biolockj.Properties
-
Read the properties defined in the required propFile and defaultProps (if included) to build Config.
Properties in propFile will override the defaultProps.
- readTaxaTable(File) - Static method in class biolockj.util.TaxaUtil
-
Read a table of counts, formatted with samples as rows (ids in first column) and taxa as columns (ids in header).
- refreshCache() - Static method in class biolockj.util.MetaUtil
-
Refresh the metadata cache.
- refreshRCacheIfNeeded() - Static method in class biolockj.Pipeline
-
Refresh R cache if about to run the 1st R module.
- RegisterNumReads - Class in biolockj.module.implicit
-
This BioModule parses sequence file to count the number of reads per sample.
- RegisterNumReads() - Constructor for class biolockj.module.implicit.RegisterNumReads
-
- registerPairedReadStatus() - Static method in class biolockj.util.SeqUtil
-
Inspect the pipeline input files to determine if input includes paired reads.
- registerProp(String, String, String) - Static method in class biolockj.Properties
-
Allow utility classes to keep their props private but still register them with Properties for API.
- registerProps() - Static method in class biolockj.Constants
-
Register properties with the Properties class for API access.
- registerProps() - Static method in class biolockj.util.BashScriptBuilder
-
Register properties with the Properties class for API access.
- registerProps() - Static method in class biolockj.util.DemuxUtil
-
- registerProps() - Static method in class biolockj.util.DockerUtil
-
Register properties with the Properties class for API access.
- registerProps() - Static method in class biolockj.util.MetaUtil
-
- registerProps() - Static method in class biolockj.util.NextflowUtil
-
Register properties with the Properties class for API access.
- registerProps() - Static method in class biolockj.util.RMetaUtil
-
- registerProps() - Static method in class biolockj.util.ValidationUtil
-
- registerRuntimeParameters(String[]) - Static method in class biolockj.util.RuntimeParamUtil
-
TODO: runtime params should always store the string as given on the command line,
and that should be the host-file path, even when running in docker.
- REMOVE_LOW_ABUNDANT_SAMPLES - Static variable in class biolockj.module.report.otu.RarefyOtuCounts
-
Config Boolean property "rarefyOtuCounts.rmLowSamples" if TRUE, all samples below the
quantile sample are removed.
- removeBadFiles() - Method in class biolockj.module.seq.SeqFileValidator
-
Remove sequence files in which all reads failed validation checks, leaving only an empty file.
- removeColumn(String, File) - Static method in class biolockj.util.MetaUtil
-
Remove the metadata column from the metadata file
- removeIgnoredAndEmptyFiles(Collection<File>) - Static method in class biolockj.util.BioLockJUtil
-
Remove ignored and empty files from the input files.
- RemoveLowOtuCounts - Class in biolockj.module.report.otu
-
This BioModule set low OTU counts below a configured threshold to zero.
These low sample counts are assumed to be miscategorized or contaminents.
- RemoveLowOtuCounts() - Constructor for class biolockj.module.report.otu.RemoveLowOtuCounts
-
- removeLowOtuCounts(TreeMap<String, TreeMap<String, Long>>) - Method in class biolockj.module.report.otu.RemoveLowOtuCounts
-
- RemoveLowPathwayCounts - Class in biolockj.module.report.humann2
-
This BioModule set low Pathway counts below a configured threshold to zero.
These low sample counts are assumed to be miscategorized or genomic contamination.
- RemoveLowPathwayCounts() - Constructor for class biolockj.module.report.humann2.RemoveLowPathwayCounts
-
- removeLowPathwayCounts(File) - Method in class biolockj.module.report.humann2.RemoveLowPathwayCounts
-
- removeOuterQuotes(String) - Static method in class biolockj.util.BioLockJUtil
-
Remove the outer single or double quotes of the given value.
Quotes are only removed if quotes are found as very 1st and last characters.
- removeQuotes(String) - Static method in class biolockj.util.BioLockJUtil
-
Remove all single and double quotation marks found in value.
- RemoveScarceOtuCounts - Class in biolockj.module.report.otu
-
This BioModule removes scarce OTUs not found in enough samples.
The OTU must be found in a configurable percentage of samples.
- RemoveScarceOtuCounts() - Constructor for class biolockj.module.report.otu.RemoveScarceOtuCounts
-
- removeScarceOtuCounts(TreeMap<String, TreeMap<String, Long>>) - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts
-
Output OTU count files with the updatedOtuCounts
- RemoveScarcePathwayCounts - Class in biolockj.module.report.humann2
-
This BioModule removes scarce pathways not found in enough samples.
Each pathway must be found in a configurable percentage of samples to be retained.
- RemoveScarcePathwayCounts() - Constructor for class biolockj.module.report.humann2.RemoveScarcePathwayCounts
-
- removeScarcePathwayCounts(File, Set<String>) - Method in class biolockj.module.report.humann2.RemoveScarcePathwayCounts
-
- removeTempFiles() - Static method in class biolockj.BioLockJ
-
- REP_SET - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- replaceEnvVar(String) - Static method in class biolockj.Config
-
Interpret environment variable if included in the arg string, otherwise return the arg.
- replaceEnvVars(Properties) - Static method in class biolockj.Config
-
Interpret env variables defined in the Config file and runtime env - for example
These props are used in: $BLJ/resources/config/defult/docker.properties:
BLJ_ROOT=/mnt/efs
EFS_DB=${BLJ_ROOT}/db
humann2.protDB=${EFS_DB}/uniref
Therefore, getString( "humann2.protDB" ) returns "/mnt/efs/db/uniref"
If not found, check runtiem env (i.e., $HOME/bash_profile)
- report() - Method in class biolockj.node.JsonNode
-
Print node info.
- REPORT - Static variable in class biolockj.util.ValidationUtil
-
- REPORT_LOG_BASE - Static variable in class biolockj.Constants
-
Config String property: "report.logBase"
Required to be set to "e" or "10" to build log normalized reports.
- REPORT_MIN_COUNT - Static variable in class biolockj.Constants
-
Config Positive Integer property "report.minCount" defines the minimum table count
allowed, if a count less that this value is found, it is set to 0.
- REPORT_NUM_HITS - Static variable in class biolockj.Constants
-
Config Boolean property: "report.numHits"
If set to
"Y", NUM_OTUS will be added to metadata file by
ParserModuleImpl and included in R reports
- REPORT_NUM_READS - Static variable in class biolockj.Constants
-
Config Boolean property: "report.numReads"
If set to
"Y" and NUM_READS exists in metadata file, NUM_READS will be included in the R reports
- REPORT_ON - Static variable in class biolockj.util.ValidationUtil
-
Config property "validation.reportOn" giving the set of file metrics to use report.
- REPORT_SAMPLE_CUTOFF - Static variable in class biolockj.Constants
-
Config Positive Double property "report.scarceSampleCutoff" defines minimum percentage of
data columns must be non-zero to keep the sample.
- REPORT_SCARCE_CUTOFF - Static variable in class biolockj.Constants
-
Config Positive Double property "report.scarceCountCutoff" defines minimum percentage of
samples that must contain a count value for it to be kept.
- REPORT_TAXONOMY_LEVELS - Static variable in class biolockj.Constants
-
Config List property: "report.taxonomyLevels"
This property drives a lot of BioLockJ functionality and determines which taxonomy-levels are reported.
- REPORT_UNCLASSIFIED_TAXA - Static variable in class biolockj.Constants
-
Config Boolean property: "report.unclassifiedTaxa"
- reportFailure(Exception) - Static method in class biolockj.util.SummaryUtil
-
Report exception details in the summary
- reportMemoryUsage(String) - Static method in class biolockj.util.MemoryUtil
-
Print stats on memory usage: Max, Total, ∆Total, %Free, Free, ∆Free.
- reportSuccess(BioModule) - Static method in class biolockj.util.SummaryUtil
-
After each module completes, this method is called to track the execution summary.
If module is null, the pipeline is complete/successful.
- reportUnclassifiedTaxa() - Static method in class biolockj.node.OtuNodeImpl
-
- REQUIRE_EUQL_NUM_PAIRS - Static variable in class biolockj.module.seq.SeqFileValidator
-
Config Boolean property "seqFileValidator.requireEqualNumPairs" determines if module requires equal
number of forward and reverse reads (simple check).
- requireBoolean(BioModule, String) - Static method in class biolockj.Config
-
Required to return a valid boolean or
- REQUIRED - Static variable in class biolockj.Properties
-
Prefix for property types whose values cannot be null.
- requireDoubleVal(BioModule, String) - Static method in class biolockj.Config
-
Requires valid double value
- RequiredRPackageException - Exception in biolockj.exception
-
- RequiredRPackageException(String) - Constructor for exception biolockj.exception.RequiredRPackageException
-
Create exception based on which R package is missing.
- RequiredRPackageException(String, String) - Constructor for exception biolockj.exception.RequiredRPackageException
-
Create exception based on which R package is missing, and the URL to download it from.
- RequiredRPackageException(Set<String>, Map<String, String>) - Constructor for exception biolockj.exception.RequiredRPackageException
-
Create exception based on which R packages are missing, and the URLs of repos to download them from.
- requiredRPackages() - Method in class biolockj.module.report.r.R_CalculateStats
-
- requiredRPackages() - Method in class biolockj.module.report.r.R_Module
-
- requiredRPackages() - Method in class biolockj.module.report.r.R_PlotMds
-
- requireExistingDir(BioModule, String) - Static method in class biolockj.Config
-
Requires valid existing directory.
- requireExistingDirs(BioModule, String) - Static method in class biolockj.Config
-
Requires valid list of file directories
- requireExistingFile(BioModule, String) - Static method in class biolockj.Config
-
Require valid existing file
- requireInteger(BioModule, String) - Static method in class biolockj.Config
-
Requires valid integer value
- requireList(BioModule, String) - Static method in class biolockj.Config
-
Require valid list property
- requirePositiveDouble(BioModule, String) - Static method in class biolockj.Config
-
Require valid positive double value
- requirePositiveInteger(BioModule, String) - Static method in class biolockj.Config
-
Require valid positive integer value
- requireSet(BioModule, String) - Static method in class biolockj.Config
-
Require valid Set value
- requireString(BioModule, String) - Static method in class biolockj.Config
-
Require valid String value
- requireSubDir(BioModule, String) - Static method in class biolockj.util.ModuleUtil
-
Get BioModule subdirectory File object with given name.
- RES_DIR - Static variable in interface biolockj.module.BioModule
-
Name of the temporary sub-directory: "resources"
- Reset - Class in biolockj.launch
-
- Reset(String) - Constructor for class biolockj.launch.Reset
-
- resetModuleSummary(BioModule) - Static method in class biolockj.util.SummaryUtil
-
Modules can be forced to reset to incomplete status.
- resetPipeline(String) - Static method in class biolockj.launch.Reset
-
- resetUsedProps() - Static method in class biolockj.Config
-
Dump all of the properties stored for the current module into the allUsedProps set,
and clear out the module-used-props to start with a clean slate.
- RESOURCES - Static variable in class biolockj.module.diy.GenMod
-
Config property: "genMod.resources"
- RESOURCES - Static variable in class biolockj.module.diy.Rmarkdown
-
Config property: "rmarkdown.resources"
- RESTART_ARG - Static variable in class biolockj.launch.LaunchProcess
-
- RESTART_DIR - Static variable in class biolockj.util.RuntimeParamUtil
-
Restart pipeline runtime parameter switch: "-restartDir"
- restartDirHasStatusFlag() - Method in class biolockj.launch.LaunchProcess
-
- RETURN - Static variable in class biolockj.Constants
-
Return character: *backslash-n*
- RETURN - Static variable in exception biolockj.exception.BioLockJException
-
Return character constant *backslash-n*
- RETURN - Static variable in class biolockj.module.BioModuleImpl
-
Return character constant *backslash-n*
- RETURN - Static variable in class biolockj.util.BioLockJUtil
-
Return character constant *backslash-n*
- reverseComplement(String) - Static method in class biolockj.util.SeqUtil
-
Return the DNA reverse compliment for the input dna parameter.
- RM_TEMP_FILES - Static variable in class biolockj.Constants
-
Config property: "pipeline.deleteTempFiles"
- Rmarkdown - Class in biolockj.module.diy
-
- Rmarkdown() - Constructor for class biolockj.module.diy.Rmarkdown
-
- RMD_FILE - Static variable in class biolockj.module.diy.Rmarkdown
-
Config property: "rmarkdown.rmarkdown"
- RMetaUtil - Class in biolockj.util
-
This utility is used to validate the metadata to help ensure the format is valid R script input.
- ROOT_HOME - Static variable in class biolockj.util.DockerUtil
-
Docker container root user $HOME directory: /root
- RSCRIPT - Static variable in class biolockj.Constants
-
Rscript exe commmand.
- run() - Method in class biolockj.launch.JavaLaunchProcess.InterruptTimerTask
-
- run() - Method in class biolockj.launch.LabeledSpinner
-
- run() - Method in class biolockj.Processor.Subprocess
-
- runBioLockJ_CMD() - Method in class biolockj.module.JavaModuleImpl
-
Get the java command to launch a module directly.
- runCommand() - Method in class biolockj.launch.DockerLaunchProcess
-
- runCommand() - Method in class biolockj.launch.JavaLaunchProcess
-
- runCommand() - Method in class biolockj.launch.LaunchProcess
-
- runDirectModule(Integer) - Static method in class biolockj.Pipeline
-
If moduleName is null, run all modules, otherwise only run the specified module.
- runJob(String[], String, File, String[]) - Method in class biolockj.Processor
-
Execute the command args and log output with label.
- runJob(String[], String) - Method in class biolockj.Processor
-
- runJob(String[], String, File) - Method in class biolockj.Processor
-
- runModule() - Method in class biolockj.module.implicit.Demultiplexer
-
Module execution summary:
Execute
Demultiplexer.breakUpFiles() to split the multiplex file into smaller size for processing
Execute
Demultiplexer.getValidHeaders() to obtain list of valid headers matched to sample ID with the metadata
file and also verifies matching forward and reverse read headers if demuliplexing paired reads.
- runModule() - Method in class biolockj.module.implicit.parser.ParserModuleImpl
-
- runModule() - Method in class biolockj.module.implicit.parser.r16s.QiimeParser
-
- runModule() - Method in class biolockj.module.implicit.parser.r16s.RdpHierParser
-
- runModule() - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser
-
- runModule() - Method in class biolockj.module.implicit.RegisterNumReads
-
Register number of reads for each sample by parsing each file and counting number of lines.
- runModule() - Method in interface biolockj.module.JavaModule
-
This method executes the modules primary Java routine.
- runModule() - Method in class biolockj.module.JavaModuleImpl
-
- runModule() - Method in class biolockj.module.report.humann2.AddMetadataToPathwayTables
-
This method matches records from the Pathway Abundance table and the metadata file by matching the sample ID
value in the very 1st column (regardless of column title).
Set
- runModule() - Method in class biolockj.module.report.humann2.RemoveLowPathwayCounts
-
- runModule() - Method in class biolockj.module.report.humann2.RemoveScarcePathwayCounts
-
- runModule() - Method in class biolockj.module.report.JsonReport
-
Obtain parsed sample data, build root node, and create the jsonMap by passing both to buildMap().
- runModule() - Method in class biolockj.module.report.otu.CompileOtuCounts
-
- runModule() - Method in class biolockj.module.report.otu.RarefyOtuCounts
-
Apply the quantile Config to the number of OTUs per sample to calculate the maximum OTU count per sample.
- runModule() - Method in class biolockj.module.report.otu.RemoveLowOtuCounts
-
- runModule() - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts
-
- runModule() - Method in class biolockj.module.report.taxa.AddMetadataToTaxaTables
-
This method matches records from the OTU table and the metadata file by matching the sample ID value in the very
1st column.
- runModule() - Method in class biolockj.module.report.taxa.BuildTaxaTables
-
- runModule() - Method in class biolockj.module.report.taxa.TransformTaxaTables
-
- runModule() - Method in class biolockj.module.seq.Multiplexer
-
- runModule() - Method in class biolockj.module.seq.RarefySeqs
-
- runModule() - Method in class biolockj.module.seq.SeqFileValidator
-
Cache sampleIds to compare to validated sampleIds post-processing.
- runModule() - Method in class biolockj.module.seq.TrimPrimers
-
Trims primers from fasta or fastq files.
- runModuleMainScript(ScriptModule) - Static method in class biolockj.Processor
-
This method is called by script generating
ScriptModules to update the script
file-permissions to ensure they are executable by the program.
- runPipeline() - Static method in class biolockj.BioLockJ
-
- runPipeline() - Static method in class biolockj.Pipeline
-
This method initializes and executes the BioModules set in the BioLockJ configuration file.
- runSubprocess(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]...
- RuntimeParamException - Exception in biolockj.exception
-
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
- RuntimeParamException(String) - Constructor for exception biolockj.exception.RuntimeParamException
-
Print error message originating from
RuntimeParamUtil and print all runtime args.
- RuntimeParamException(String, String) - Constructor for exception biolockj.exception.RuntimeParamException
-
- RuntimeParamException(String, String, String) - Constructor for exception biolockj.exception.RuntimeParamException
-
- RuntimeParamUtil - Class in biolockj.util
-
This utility processes the application runtime parameters passed to BioLockJ.
- RuntimeParamUtil() - Constructor for class biolockj.util.RuntimeParamUtil
-