Uses of Class
fr.ens.biologie.genomique.aozan.aozan3.Configuration
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Uses of Configuration in fr.ens.biologie.genomique.aozan.aozan3
Subclasses of Configuration in fr.ens.biologie.genomique.aozan.aozan3 Modifier and Type Class Description class
RunConfiguration
This class define a run configuration.Methods in fr.ens.biologie.genomique.aozan.aozan3 that return Configuration Modifier and Type Method Description Configuration
Main. getConfiguration()
Get the the startup configuration.Methods in fr.ens.biologie.genomique.aozan.aozan3 with parameters of type Configuration Modifier and Type Method Description void
SequencerNames. addSequencersFromConfiguration(Configuration conf)
Add sequencers in the aliases table from a configuration object.static EmailMessage
TemplateEmailMessage. errorMessage(Configuration conf, Throwable t)
void
Configuration. set(Configuration conf)
Add all the keys and value of a Configuration object in this one.void
Configuration. setFromOtherConf(Configuration conf, String key)
Set a value from the value of another configuration.void
Configuration. setFromOtherConf(Configuration conf, String key, String defaultValue)
Set a value from the value of another configuration.void
Configuration. setFromOtherConfIfExists(Configuration conf, String key)
Set a value from the value of another configuration.Constructors in fr.ens.biologie.genomique.aozan.aozan3 with parameters of type Configuration Constructor Description Configuration(Configuration conf)
Constructor.SendMail(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Public constructor.SequencerNames(Configuration conf)
Constructor.TemplateEmailMessage(Configuration conf)
Public constructor. -
Uses of Configuration in fr.ens.biologie.genomique.aozan.aozan3.action
Methods in fr.ens.biologie.genomique.aozan.aozan3.action with parameters of type Configuration Modifier and Type Method Description void
Action. action(Configuration conf, List<String> arguments, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Execute action.void
DoradoAction. action(Configuration conf, List<String> arguments, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
ExecAction. action(Configuration conf, List<String> arguments, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
GuppyAction. action(Configuration conf, List<String> arguments, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
LegacyAction. action(Configuration conf, List<String> arguments, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
ListAction. action(Configuration conf, List<String> arguments, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
SampleSheetConvertAction. action(Configuration conf, List<String> arguments, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
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Uses of Configuration in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor
Methods in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor with parameters of type Configuration Modifier and Type Method Description void
AbstractIlluminaDemuxDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
Aozan2QCDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
DataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Initialize the processor.void
DiscoverNewIlluminaRunDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
DoradoONTBasecallingDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
EndIlluminaRunDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
GuppyONTBasecallingDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
SyncDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Constructors in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor with parameters of type Configuration Constructor Description DataProcessorTemplateEmailMessage(Configuration conf, String templateKey, String defaultTemplateResource)
Public constructor. -
Uses of Configuration in fr.ens.biologie.genomique.aozan.aozan3.dataprovider
Methods in fr.ens.biologie.genomique.aozan.aozan3.dataprovider with parameters of type Configuration Modifier and Type Method Description void
EmptyRunDataProvider. init(DataStorage storage, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
IlluminaProcessedRunDataProvider. init(DataStorage storage, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
IlluminaRawRunDataProvider. init(DataStorage storage, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
RunDataProvider. init(DataStorage storage, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Initialize the provider. -
Uses of Configuration in fr.ens.biologie.genomique.aozan.aozan3.legacy
Constructors in fr.ens.biologie.genomique.aozan.aozan3.legacy with parameters of type Configuration Constructor Description LegacyRecipes(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, Path aozan2ConfFile)
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Uses of Configuration in fr.ens.biologie.genomique.aozan.aozan3.log
Methods in fr.ens.biologie.genomique.aozan.aozan3.log with parameters of type Configuration Modifier and Type Method Description static fr.ens.biologie.genomique.kenetre.log.GenericLogger
AozanLoggerFactory. newLogger(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger oldLogger)
Configure logger. -
Uses of Configuration in fr.ens.biologie.genomique.aozan.aozan3.recipe
Methods in fr.ens.biologie.genomique.aozan.aozan3.recipe that return Configuration Modifier and Type Method Description Configuration
Recipe. getConfiguration()
Get the configuration.protected Configuration
ConfigurationXMLParser. parse(NodeList nList, String source)
Methods in fr.ens.biologie.genomique.aozan.aozan3.recipe with parameters of type Configuration Modifier and Type Method Description void
Recipe. addDataProvider(String providerName, String storageName, boolean inProgress, Configuration conf)
Add a data provider.Constructors in fr.ens.biologie.genomique.aozan.aozan3.recipe with parameters of type Configuration Constructor Description ConfigurationXMLParser(String rootTagName, String sectionName, Configuration parentConfiguration, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Constructor.Recipe(String recipeName, String description, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Public constructor.RecipeXMLParser(Configuration conf, Configuration cliConf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Public constructor.RecipeXMLParser(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Public constructor.Step(Recipe recipe, String stepName, String processorName, String sinkName, Configuration conf, RunConfigurationProvider runConfProvider, RunIdGenerator runIdGenerator)
Constructor. -
Uses of Configuration in fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider
Methods in fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider with parameters of type Configuration Modifier and Type Method Description void
EmptyRunConfigurationProvider. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
IlluminaSamplesheetRunConfigurationProvider. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
RunConfigurationProvider. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Initialize the run configurator provider.
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