Uses of Class
fr.ens.biologie.genomique.aozan.aozan3.RunId
-
-
Uses of RunId in fr.ens.biologie.genomique.aozan.aozan3
Methods in fr.ens.biologie.genomique.aozan.aozan3 that return RunId Modifier and Type Method Description RunId
IlluminaRunIdWrapper. getRunId()
Get RunId.RunId
RunData. getRunId()
Get run Id.RunId
DefaultRunIdGenerator. newRunId(RunId runId, Map<String,String> constants)
RunId
RunIdGenerator. newRunId(RunId runId, Map<String,String> contants)
Create a new run id for the output of a processor.Methods in fr.ens.biologie.genomique.aozan.aozan3 with parameters of type RunId Modifier and Type Method Description String
SequencerNames. getIlluminaSequencerName(RunId runId)
Get the name of an Illumina sequencer from a runId.static SequencerSource
SequencerSourceFactory. newIlluminaSequencerSource(RunId illuminaRunId)
Create a new sequencer source from an Illumina runId.RunId
DefaultRunIdGenerator. newRunId(RunId runId, Map<String,String> constants)
RunData
RunData. newRunId(RunId runId)
Create a new RunData object from the current object with a new run Id.RunId
RunIdGenerator. newRunId(RunId runId, Map<String,String> contants)
Create a new run id for the output of a processor.Constructors in fr.ens.biologie.genomique.aozan.aozan3 with parameters of type RunId Constructor Description Aozan3Exception(RunId runId, String message)
Create a new Aozan3Exception with a message.Aozan3Exception(RunId runId, String message, Throwable cause)
Create a new Aozan3Exception with a message and a cause.Aozan3Exception(RunId runId, Throwable cause)
Create a new Aozan3Exception with a cause.IlluminaRunIdWrapper(RunId runId)
Constructor. -
Uses of RunId in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor
Methods in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor with parameters of type RunId Modifier and Type Method Description EmailMessage
DataProcessorTemplateEmailMessage. endDataProcessorEmail(String subject, RunId runId, Path outputDirectory, long startTime, long endTime, long outputSize, long diskFree, Map<String,String> variables)
Create an end of step message.String
ExternalTool. getToolVersion(RunId runId, String tmpDirPath, List<String> commandLine, boolean parseStdErr, Function<List<String>,String> parser)
Get the tool executable version.fr.ens.biologie.genomique.kenetre.util.process.SimpleProcess
ExternalTool. newSimpleProcess(RunId runId, boolean enableLogging)
Create a new process. -
Uses of RunId in fr.ens.biologie.genomique.aozan.aozan3.dataprovider
Method parameters in fr.ens.biologie.genomique.aozan.aozan3.dataprovider with type arguments of type RunId Modifier and Type Method Description List<RunData>
EmptyRunDataProvider. listCompletedRunData(Collection<RunId> excludedRuns)
List<RunData>
IlluminaProcessedRunDataProvider. listCompletedRunData(Collection<RunId> excludedRuns)
List<RunData>
IlluminaRawRunDataProvider. listCompletedRunData(Collection<RunId> excludedRuns)
List<RunData>
RunDataProvider. listCompletedRunData(Collection<RunId> excludedRuns)
List available runs in progress.List<RunData>
EmptyRunDataProvider. listInProgressRunData(Collection<RunId> excludedRuns)
List<RunData>
IlluminaProcessedRunDataProvider. listInProgressRunData(Collection<RunId> excludedRuns)
List<RunData>
IlluminaRawRunDataProvider. listInProgressRunData(Collection<RunId> excludedRuns)
List<RunData>
RunDataProvider. listInProgressRunData(Collection<RunId> excludedRuns)
List available runs in progress. -
Uses of RunId in fr.ens.biologie.genomique.aozan.aozan3.legacy
Methods in fr.ens.biologie.genomique.aozan.aozan3.legacy that return types with arguments of type RunId Modifier and Type Method Description Set<RunId>
RunIdStorage. load()
Load run ids.Methods in fr.ens.biologie.genomique.aozan.aozan3.legacy with parameters of type RunId Modifier and Type Method Description void
RunIdStorage. add(RunId runId)
Add a run id to the storage -
Uses of RunId in fr.ens.biologie.genomique.aozan.aozan3.log
Methods in fr.ens.biologie.genomique.aozan.aozan3.log with parameters of type RunId Modifier and Type Method Description void
Aozan3Logger. debug(RunId runId, String message)
Log a debug message.void
Aozan3Logger. error(RunId runId, String message)
Log an error message.void
Aozan3Logger. error(RunId runId, Throwable exception)
Log an error message.static void
Aozan3Logger. error(fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, RunId runId, String message)
Log an error message.static void
Aozan3Logger. error(fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, RunId runId, Throwable exception)
Log an error message.void
Aozan3Logger. info(RunId runId, String message)
Log an info message.static void
Aozan3Logger. info(fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, RunId runId, String message)
Log an info message.void
Aozan3Logger. warn(RunId runId, String message)
Log a warning message. -
Uses of RunId in fr.ens.biologie.genomique.aozan.aozan3.recipe
Methods in fr.ens.biologie.genomique.aozan.aozan3.recipe that return types with arguments of type RunId Modifier and Type Method Description Set<RunId>
Recipe. availableRuns()
Get available runs.Set<RunId>
Recipe. availableRuns(Collection<RunId> excludedRunIds)
Get available runs.Set<RunId>
Recipe. execute(List<String> runIds)
Execute a list of run Ids.Method parameters in fr.ens.biologie.genomique.aozan.aozan3.recipe with type arguments of type RunId Modifier and Type Method Description Set<RunId>
Recipe. availableRuns(Collection<RunId> excludedRunIds)
Get available runs.
-