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

Class IlluminaRawRunDataProvider

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider

All Implemented Interfaces:

RunDataProvider

public class IlluminaRawRunDataProvider
extends Object
implements RunDataProvider

This class define a processed data provider for Illumina runs.

Since:

3.0

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static String	PROVIDER_NAME

Constructor Summary

Constructors

Constructor	Description
IlluminaRawRunDataProvider()

Method Summary

Modifier and Type	Method	Description
boolean	canProvideRunData()	Test if provider can provide RunData
DataStorage	getDataStorage()	Get the data storage of used by the provider.
String	getName()	Get the name of the provider.
void	init(DataStorage storage, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Initialize the provider.
List<RunData>	listCompletedRunData(Collection<RunId> excludedRuns)	List available runs in progress.
List<RunData>	listInProgressRunData(Collection<RunId> excludedRuns)	List available runs in progress.
static boolean	runCompleted(Path runDirectory)	Test if a run is completed.

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.dataprovider.RunDataProvider

listCompletedRunData, listInProgressRunData

Field Detail

PROVIDER_NAME

public static final String PROVIDER_NAME

See Also:

Constant Field Values

Constructor Detail

IlluminaRawRunDataProvider

public IlluminaRawRunDataProvider()

Method Detail

getName

public String getName()

Description copied from interface: RunDataProvider

Get the name of the provider.

Specified by:

getName in interface RunDataProvider

Returns:

the name of the provider

init

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

Description copied from interface: RunDataProvider

Initialize the provider.

Specified by:

init in interface RunDataProvider

Parameters:

storage - used for the source

conf - the configuration of the provider

logger - the logger to use

Throws:

Aozan3Exception - if an error occurs while initialize the provider

getDataStorage

public DataStorage getDataStorage()

Description copied from interface: RunDataProvider

Get the data storage of used by the provider.

Specified by:

getDataStorage in interface RunDataProvider

Returns:

the DataStorage used by the provider

canProvideRunData

public boolean canProvideRunData()

Description copied from interface: RunDataProvider

Test if provider can provide RunData

Specified by:

canProvideRunData in interface RunDataProvider

Returns:

true if provider can provide RunData

listInProgressRunData

public List<RunData> listInProgressRunData(Collection<RunId> excludedRuns)

Description copied from interface: RunDataProvider

List available runs in progress.

Specified by:

listInProgressRunData in interface RunDataProvider

Parameters:

excludedRuns - runs to exclude

Returns:

a list of RunData

listCompletedRunData

public List<RunData> listCompletedRunData(Collection<RunId> excludedRuns)

Description copied from interface: RunDataProvider

List available runs in progress.

Specified by:

listCompletedRunData in interface RunDataProvider

Parameters:

excludedRuns - runs to exclude

Returns:

a list of RunData

runCompleted

public static boolean runCompleted(Path runDirectory)

Test if a run is completed.

Parameters:

runDirectory - the path to the run directory

Returns:

true if the run is completed