Package fr.ens.biologie.genomique.aozan.aozan3.dataprocessor

Class SyncDataProcessor

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SyncDataProcessor

All Implemented Interfaces:

DataProcessor

Direct Known Subclasses:

IlluminaSyncDataProcessor

public abstract class SyncDataProcessor
extends Object
implements DataProcessor

This class define an Illumina synchronization data processor.

Since:

3.0

Author:

Laurent Jourdren

Nested Class Summary

Nested classes/interfaces inherited from interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor

DataProcessor.ProcessResult

Constructor Summary

Constructors

Constructor	Description
SyncDataProcessor()

Method Summary

Modifier and Type	Method	Description
void	init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Initialize the processor.
protected abstract void	partialSync(Path inputPath, Path outputPath)
DataProcessor.ProcessResult	process(InputData input, RunConfiguration runConf)	Process data.
protected abstract void	sync(Path inputPath, Path outputPath)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor

getInputRequirements, getName

Constructor Detail

SyncDataProcessor

public SyncDataProcessor()

Method Detail

init

public void init(Configuration conf,
                 fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
          throws Aozan3Exception

Description copied from interface: DataProcessor

Initialize the processor.

Specified by:

init in interface DataProcessor

Parameters:

conf - the configuration of the processor

logger - the logger to use

Throws:

Aozan3Exception - if an error occurs while initialize the processor

process

public DataProcessor.ProcessResult process(InputData input,
                                           RunConfiguration runConf)
                                    throws Aozan3Exception

Description copied from interface: DataProcessor

Process data.

Specified by:

process in interface DataProcessor

Parameters:

input - input run data

runConf - run configuration

Returns:

a ProcessResult object

Throws:

Aozan3Exception - if an error occurs while processing the data

sync

protected abstract void sync(Path inputPath,
                             Path outputPath)
                      throws IOException

Throws:

IOException

partialSync

protected abstract void partialSync(Path inputPath,
                                    Path outputPath)
                             throws IOException

Throws:

IOException