Serialized Form (Eoulsan 2.6.1 API)

Package fr.ens.biologie.genomique.eoulsan
- Class fr.ens.biologie.genomique.eoulsan.EoulsanError extends Error implements Serializable
  
  serialVersionUID:
  
  -8816286109335295387L
- Class fr.ens.biologie.genomique.eoulsan.EoulsanException extends Exception implements Serializable
  
  serialVersionUID:
  
  7021095498629981700L
- Class fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException extends EoulsanRuntimeException implements Serializable
  
  serialVersionUID:
  
  -1897738767737351557L
- Class fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  4568739390687951448L
- Class fr.ens.biologie.genomique.eoulsan.Settings extends Object implements Serializable
  
  serialVersionUID:
  
  -7897805708866950402L
  - Serialized Fields
    - properties
      
      Properties properties
Package fr.ens.biologie.genomique.eoulsan.checkers
- Class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker extends Object implements Serializable
  
  serialVersionUID:
  
  -7079642248159153890L
Package fr.ens.biologie.genomique.eoulsan.core
- Class fr.ens.biologie.genomique.eoulsan.core.AbstractPort extends Object implements Serializable
  
  serialVersionUID:
  
  1773398938012180465L
  - Serialized Fields
    - format
      
      DataFormat format
    - list
      
      boolean list
    - name
      
      String name
- Class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts extends Object implements Serializable
  
  serialVersionUID:
  
  -5116830881426447140L
  - Serialized Fields
    - ports
      
      Map<String,E extends Port> ports
- Class fr.ens.biologie.genomique.eoulsan.core.FileNamingParsingRuntimeException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  7857462649825953398L
- Class fr.ens.biologie.genomique.eoulsan.core.Parameter extends Object implements Serializable
  
  serialVersionUID:
  
  -3788321419921821433L
  - Serialized Fields
    - name
      
      String name
    - value
      
      String value
- Class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort extends AbstractPort implements Serializable
  
  serialVersionUID:
  
  4663590179211976634L
  - Serialized Fields
    - compressionsAccepted
      
      EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> compressionsAccepted
    - requiredInWorkingDirectory
      
      boolean requiredInWorkingDirectory
- Class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPorts extends AbstractPorts<InputPort> implements Serializable
  
  serialVersionUID:
  
  -6661589274392547355L
- Class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort extends AbstractPort implements Serializable
  
  serialVersionUID:
  
  3565485272173523695L
  - Serialized Fields
    - compression
      
      fr.ens.biologie.genomique.kenetre.io.CompressionType compression
- Class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPorts extends AbstractPorts<OutputPort> implements Serializable
  
  serialVersionUID:
  
  -1607044916452828888L
Package fr.ens.biologie.genomique.eoulsan.core.workflow
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep extends Object implements Serializable
  
  serialVersionUID:
  
  2040628014465126384L
  - Serialized Fields
    - checker
      
      Checker checker
    - createLogFiles
      
      boolean createLogFiles
    - dataProduct
      
      fr.ens.biologie.genomique.eoulsan.core.workflow.DataProduct dataProduct
    - dataProductConfiguration
      
      String dataProductConfiguration
    - discardOutput
      
      Step.DiscardOutput discardOutput
    - id
      
      String id
    - inputPorts
      
      fr.ens.biologie.genomique.eoulsan.core.workflow.StepInputPorts inputPorts
    - inputPortsParameter
      
      InputPorts inputPortsParameter
    - mode
      
      ExecutionMode mode
    - moduleName
      
      String moduleName
    - number
      
      int number
    - outputDir
      
      DataFile outputDir
    - outputPorts
      
      fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPorts outputPorts
    - outputPortsParameter
      
      OutputPorts outputPortsParameter
    - parallelizationMode
      
      ParallelizationMode parallelizationMode
    - parameters
      
      Set<Parameter> parameters
    - requiredMemory
      
      int requiredMemory
    - requiredProcessors
      
      int requiredProcessors
    - skip
      
      boolean skip
    - stepStateDependencies
      
      StepStateDependencies stepStateDependencies
    - terminalStep
      
      boolean terminalStep
    - type
      
      Step.StepType type
    - version
      
      String version
    - workflow
      
      AbstractWorkflow workflow
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow extends Object implements Serializable
  
  serialVersionUID:
  
  4865597995432347155L
  - Serialization Methods
    - writeObject
      
      private void writeObject(ObjectOutputStream s) throws IOException
      
      Throws:
      
      IOException
  - Serialized Fields
    - checkerStep
      
      AbstractStep checkerStep
    - dataDir
      
      DataFile dataDir
    - deleteOnExitFiles
      
      Set<DataFile> deleteOnExitFiles
    - design
      
      Design design
    - designStep
      
      AbstractStep designStep
    - firstStep
      
      AbstractStep firstStep
    - hadoopWorkingDir
      
      DataFile hadoopWorkingDir
    - jobDir
      
      DataFile jobDir
    - localWorkingDir
      
      DataFile localWorkingDir
    - outputDir
      
      DataFile outputDir
    - rootStep
      
      AbstractStep rootStep
    - shutdownNow
      
      boolean shutdownNow
    - states
      
      com.google.common.collect.Multimap<Step.StepState,AbstractStep> states
    - stepIds
      
      Set<String> stepIds
    - steps
      
      Map<AbstractStep,Step.StepState> steps
    - stopwatch
      
      SerializableStopwatch stopwatch
    - taskDir
      
      DataFile taskDir
    - tmpDir
      
      DataFile tmpDir
    - workflowContext
      
      WorkflowContext workflowContext
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep extends AbstractStep implements Serializable
  
  serialVersionUID:
  
  -1736197317540226070L
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflow extends AbstractWorkflow implements Serializable
  
  serialVersionUID:
  
  4132064673361068654L
  - Serialized Fields
    - steps
      
      List<CommandStep> steps
    - stepsIds
      
      Set<String> stepsIds
    - workflowCommand
      
      CommandWorkflowModel workflowCommand
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel extends Object implements Serializable
  
  serialVersionUID:
  
  -5182569666862886788L
  - Serialized Fields
    - author
      
      String author
    - description
      
      String description
    - globalParameters
      
      Set<Parameter> globalParameters
    - moduleNames
      
      Map<String,String> moduleNames
    - name
      
      String name
    - stepDataProduct
      
      Map<String,String> stepDataProduct
    - stepDiscardOutput
      
      Map<String,Step.DiscardOutput> stepDiscardOutput
    - stepIdList
      
      List<String> stepIdList
    - stepInputs
      
      Map<String,Map<String,fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel.StepPort>> stepInputs
    - stepParameters
      
      Map<String,Set<Parameter>> stepParameters
    - stepRequiredMemory
      
      Map<String,Integer> stepRequiredMemory
    - stepRequiredProcessors
      
      Map<String,Integer> stepRequiredProcessors
    - stepSkipped
      
      Map<String,Boolean> stepSkipped
    - stepVersions
      
      Map<String,String> stepVersions
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList extends fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractData implements Serializable
  
  serialVersionUID:
  
  -2933515018143805029L
  - Serialized Fields
    - design
      
      Design design
    - list
      
      List<Data> list
    - port
      
      fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch extends Object implements Serializable
  
  serialVersionUID:
  
  75544289032075405L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream s) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeObject
      
      private void writeObject(ObjectOutputStream s) throws IOException
      
      Throws:
      
      IOException
  - Serialized Fields
    - stopWatch
      
      fr.ens.biologie.genomique.eoulsan.core.workflow.Stopwatch stopWatch
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies extends Object implements Serializable
  
  serialVersionUID:
  
  3290646225243643382L
  - Serialized Fields
    - dependenciesDone
      
      Map<Integer,Boolean> dependenciesDone
    - noInput
      
      boolean noInput
    - requiredSteps
      
      Set<AbstractStep> requiredSteps
    - step
      
      AbstractStep step
    - stepState
      
      Step.StepState stepState
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl extends Object implements Serializable
  
  serialVersionUID:
  
  8288158811122533646L
  - Serialized Fields
    - contextName
      
      String contextName
    - id
      
      int id
    - inputData
      
      Map<String,Data> inputData
    - outputData
      
      Map<String,fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractData> outputData
    - step
      
      AbstractStep step
    - workflowContext
      
      WorkflowContext workflowContext
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -1698693204391020077L
  - Serialized Fields
    - context
      
      TaskContextImpl context
    - counters
      
      Map<String,Long> counters
    - duration
      
      long duration
    - endTime
      
      Date endTime
    - errorMessage
      
      String errorMessage
    - exception
      
      Throwable exception
    - startTime
      
      Date startTime
    - success
      
      boolean success
    - taskCommandLine
      
      String taskCommandLine
    - taskDescription
      
      String taskDescription
    - taskMessage
      
      String taskMessage
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData extends Object implements Serializable
  
  serialVersionUID:
  
  -7754468478398255288L
  - Serialized Fields
    - data
      
      Data data
- Class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext extends Object implements Serializable
  
  serialVersionUID:
  
  -260344001954382358L
  - Serialized Fields
    - commandAuthor
      
      String commandAuthor
    - commandDescription
      
      String commandDescription
    - commandName
      
      String commandName
    - contextCreationTime
      
      long contextCreationTime
    - designFile
      
      DataFile designFile
    - host
      
      String host
    - jarFile
      
      DataFile jarFile
    - jobDescription
      
      String jobDescription
    - jobEnvironment
      
      String jobEnvironment
    - jobId
      
      String jobId
    - jobUUID
      
      String jobUUID
    - workflow
      
      AbstractWorkflow workflow
    - workflowFile
      
      DataFile workflowFile
Package fr.ens.biologie.genomique.eoulsan.data
- Class fr.ens.biologie.genomique.eoulsan.data.DataFile extends Object implements Serializable
  
  serialVersionUID:
  
  -3280343485491150872L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Deserialize the object.
      
      Throws:
      
      IOException - if an error occurs while deserializing the object
      
      ClassNotFoundException
    - writeObject
      
      private void writeObject(ObjectOutputStream out) throws IOException
      
      Serialize the object.
      
      Throws:
      
      IOException - if an error occurs while serializing the object
  - Serialized Fields
    - md
      
      DataFileMetadata md
    - name
      
      String name
    - protocol
      
      DataProtocol protocol
    - protocolPrefixInSource
      
      String protocolPrefixInSource
    - src
      
      String src
    - unknownProtocolName
      
      String unknownProtocolName
- Class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat extends fr.ens.biologie.genomique.eoulsan.data.AbstractDataFormat implements Serializable
  
  serialVersionUID:
  
  -943794645213547885L
  - Serialized Fields
    - formatName
      
      String formatName
    - mapperName
      
      String mapperName
    - prefix
      
      String prefix
- Class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat extends fr.ens.biologie.genomique.eoulsan.data.AbstractDataFormat implements Serializable
  
  serialVersionUID:
  
  -6926659317643003910L
  - Serialized Fields
    - alias
      
      String alias
    - checkerClassName
      
      String checkerClassName
    - contentType
      
      String contentType
    - dataFormatFromDesignFile
      
      boolean dataFormatFromDesignFile
    - description
      
      String description
    - designMetadataKeyName
      
      String designMetadataKeyName
    - extensions
      
      List<String> extensions
    - galaxyFormatNames
      
      List<String> galaxyFormatNames
    - generatorClassName
      
      String generatorClassName
    - generatorParameters
      
      Set<Parameter> generatorParameters
    - maxFilesCount
      
      int maxFilesCount
    - mergerClassName
      
      String mergerClassName
    - name
      
      String name
    - oneFilePerAnalysis
      
      boolean oneFilePerAnalysis
    - prefix
      
      String prefix
    - sampleMetadataKeyName
      
      String sampleMetadataKeyName
    - splitterClassName
      
      String splitterClassName
Package fr.ens.biologie.genomique.eoulsan.design
- Class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata extends Object implements Serializable
  
  serialVersionUID:
  
  5756414666624839231L
  - Serialized Fields
    - metadata
      
      Map<String,String> metadata
- Class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl extends AbstractMetadata implements Serializable
  
  serialVersionUID:
  
  -2481571646937449716L
- Class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -2644491674956956116L
  - Serialized Fields
    - design
      
      Design design
    - experimentId
      
      String experimentId
    - experimentName
      
      String experimentName
    - experimentNumber
      
      int experimentNumber
    - metadata
      
      fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadataImpl metadata
    - sampleNames
      
      Set<String> sampleNames
    - samples
      
      List<ExperimentSample> samples
- Class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -3180171254543892681L
  - Serialized Fields
    - metadata
      
      ExperimentSampleMetadataImpl metadata
    - sample
      
      Sample sample
- Class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl extends AbstractMetadata implements Serializable
  
  serialVersionUID:
  
  4079804296437126108L
- Class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment extends Object implements Serializable
  
  serialVersionUID:
  
  2564230655661740901L
  - Serialized Fields
    - experiment
      
      Experiment experiment
- Class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata extends Object implements Serializable
  
  serialVersionUID:
  
  -426306838693570333L
  - Serialized Fields
    - md
      
      ExperimentMetadata md
- Class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata extends Object implements Serializable
  
  serialVersionUID:
  
  2441285392336371023L
  - Serialized Fields
    - md
      
      ExperimentSampleMetadata md
Package fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop
- Class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp.DuplicationException extends IOException implements Serializable
  
  serialVersionUID:
  
  1L
Package fr.ens.biologie.genomique.eoulsan.util
- Class fr.ens.biologie.genomique.eoulsan.util.EnhancedBloomFilter extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - addedNumberOfElements
      
      int addedNumberOfElements
    - bf
      
      com.google.common.hash.BloomFilter<String> bf
    - expectedNumberOfElements
      
      int expectedNumberOfElements
    - falsePositiveProbability
      
      double falsePositiveProbability
Package fr.ens.biologie.genomique.eoulsan.util.locker
- Class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket extends Object implements Serializable
  
  serialVersionUID:
  
  -7934169474677708526L
  - Serialized Fields
    - creationTime
      
      long creationTime
    - description
      
      String description
    - lastActiveTime
      
      long lastActiveTime
    - nanoCreationTime
      
      long nanoCreationTime
    - pid
      
      int pid
    - threadId
      
      long threadId
    - working
      
      boolean working

Serialized Form

Package fr.ens.biologie.genomique.eoulsan

Class fr.ens.biologie.genomique.eoulsan.EoulsanError extends Error implements Serializable

Class fr.ens.biologie.genomique.eoulsan.EoulsanException extends Exception implements Serializable

Class fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException extends EoulsanRuntimeException implements Serializable

Class fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException extends RuntimeException implements Serializable

Class fr.ens.biologie.genomique.eoulsan.Settings extends Object implements Serializable

Serialized Fields

properties

Package fr.ens.biologie.genomique.eoulsan.checkers

Class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker extends Object implements Serializable

Package fr.ens.biologie.genomique.eoulsan.core

Class fr.ens.biologie.genomique.eoulsan.core.AbstractPort extends Object implements Serializable

Serialized Fields

format

list

name

Class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts extends Object implements Serializable

Serialized Fields

ports

Class fr.ens.biologie.genomique.eoulsan.core.FileNamingParsingRuntimeException extends RuntimeException implements Serializable

Class fr.ens.biologie.genomique.eoulsan.core.Parameter extends Object implements Serializable

Serialized Fields

name

value

Class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort extends AbstractPort implements Serializable

Serialized Fields

compressionsAccepted

requiredInWorkingDirectory

Class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPorts extends AbstractPorts<InputPort> implements Serializable

Class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort extends AbstractPort implements Serializable

Serialized Fields

compression

Class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPorts extends AbstractPorts<OutputPort> implements Serializable

Package fr.ens.biologie.genomique.eoulsan.core.workflow

Class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep extends Object implements Serializable

Serialized Fields

checker

createLogFiles

dataProduct

dataProductConfiguration

discardOutput

id

inputPorts

inputPortsParameter

mode

moduleName

number

outputDir

outputPorts

outputPortsParameter

parallelizationMode

parameters

requiredMemory

requiredProcessors

skip

stepStateDependencies

terminalStep

type

version

workflow

Class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow extends Object implements Serializable

Serialization Methods

writeObject

Serialized Fields

checkerStep

dataDir

deleteOnExitFiles

design

designStep

firstStep

hadoopWorkingDir

jobDir

localWorkingDir

outputDir

rootStep

shutdownNow

states

stepIds

steps