Package net.sf.basedb.util.export.spotdata

Class SerialBaseFileExporter

java.lang.Object

net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

net.sf.basedb.util.export.spotdata.BaseFileExporter

net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

public class SerialBaseFileExporter
extends BaseFileExporter

Exporter implementation that exports bioassay set data as a serial BASEfile.

Version:

2.12

Author:

Nicklas

Last modified

$Date: 2011-08-11 11:09:06 +0200 (to, 11 aug 2011) $

Field Summary

Fields

Modifier and Type	Field	Description
private List<BioAssay>	bioAssays
private DynamicSpotQuery	countQuery
private int	nextBioAssay
private BaseFileWriter	out
private long	spotCount
private DynamicSpotQuery	spotQuery
static final String	SUBTYPE

Constructor Summary

Constructors

Constructor	Description
SerialBaseFileExporter()	Create a new serial BASEfile exporter.

Method Summary

Modifier and Type	Method	Description
protected void	beginExport()	Prepare the export by pre-loading some information and configure the queries that we are going to use.
protected void	endExport(RuntimeException e)	End the export and clean up/close all aquired resources.
protected void	exportSectionData()	Exports data for the current bioassay in a 'spots' section.
protected boolean	exportSectionFooter()	Ends the current 'spots' section.
protected void	exportSectionHeader()	Exports headers for a 'spots' section, and make preparations for the current data section (one section per bioassay).

Methods inherited from class net.sf.basedb.util.export.spotdata.BaseFileExporter

addAssayField, addAssayFields, addReporterField, addReporterFields, addSpotField, addSpotFields, exportAssaysSectionData, exportAssaysSectionHeaders, exportGlobalHeader, exportSettingsSection, exportSpotSectionData, exportSpotSectionHeaders, getAssayFields, getAverageOnReporter, getBaseFileWriter, getCountQuery, getParameter, getReporterFields, getSpotFields, setAutoCloseWriters, setAverageOnReporter, setParameter, setWriter

Methods inherited from class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

addExperimentalFactorsAsAssayFields, cacheReporterData, copyReporterFields, doExport, exportGlobalFooter, getAssayIndex, getBioAssays, getDbControl, getProgressReporter, getReporterQuery, getSnapshotManager, getSource, getSpotQuery, prepareAssayIndexMap, setDbControl, setProgress, setProgressReporter, setSnapshotManager, setSource, validate

Methods inherited from class java.lang.Object

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

Field Details

SUBTYPE

public static final String SUBTYPE

See Also:

• Constant Field Values

bioAssays

private List<BioAssay> bioAssays

nextBioAssay

private int nextBioAssay

out

private BaseFileWriter out

spotQuery

private DynamicSpotQuery spotQuery

countQuery

private DynamicSpotQuery countQuery

spotCount

private long spotCount

Constructor Details

SerialBaseFileExporter

public SerialBaseFileExporter()

Create a new serial BASEfile exporter.

Method Details

beginExport

protected void beginExport()

Prepare the export by pre-loading some information and configure the queries that we are going to use.

Overrides:

beginExport in class BaseFileExporter

exportSectionHeader

protected void exportSectionHeader()

Exports headers for a 'spots' section, and make preparations for the current data section (one section per bioassay).

Overrides:

exportSectionHeader in class AbstractBioAssaySetExporter

exportSectionData

protected void exportSectionData()

Exports data for the current bioassay in a 'spots' section.

Overrides:

exportSectionData in class AbstractBioAssaySetExporter

exportSectionFooter

protected boolean exportSectionFooter()

Ends the current 'spots' section.

Overrides:

exportSectionFooter in class AbstractBioAssaySetExporter

Returns:

Always FALSE if this was the last bioassay, or TRUE if there are more bioassays to export

endExport

protected void endExport(RuntimeException e)

Description copied from class: AbstractBioAssaySetExporter

End the export and clean up/close all aquired resources. This method is always called last. In the case of an error the exception parameter has a non-null value. The default implementation clears up values that has been cached so it is recommended that subclasses always call this method as part of their own cleanup. If the subclass implementation wants to throw a different exception it is recommended that the given exception is chained to allow developers to debug problems.

Overrides:

endExport in class BaseFileExporter