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

Class MatrixBaseFileExporter

java.lang.Object

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

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

net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

public class MatrixBaseFileExporter
extends BaseFileExporter

Exporter implementation that exports bioassay set data as a matrix 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 BaseFileWriter	out
private ChainedProgressReporter	progress
private long	spotCount
private DynamicSpotQuery	spotQuery
static final String	SUBTYPE

Constructor Summary

Constructors

Constructor	Description
MatrixBaseFileExporter()	Create a new matrix 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 all bioassays in a single 'spots' section.
protected boolean	exportSectionFooter()	Ends the 'spots' section.
protected void	exportSectionHeader()	Exports headers for a single 'spots' section.

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

out

private BaseFileWriter out

bioAssays

private List<BioAssay> bioAssays

spotQuery

private DynamicSpotQuery spotQuery

countQuery

private DynamicSpotQuery countQuery

progress

private ChainedProgressReporter progress

spotCount

private long spotCount

Constructor Details

MatrixBaseFileExporter

public MatrixBaseFileExporter()

Create a new matrix 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 single 'spots' section.

Overrides:

exportSectionHeader in class AbstractBioAssaySetExporter

exportSectionData

protected void exportSectionData()

Exports data for all bioassays in a single 'spots' section.

Overrides:

exportSectionData in class AbstractBioAssaySetExporter

exportSectionFooter

protected boolean exportSectionFooter()

Ends the 'spots' section.

Overrides:

exportSectionFooter in class AbstractBioAssaySetExporter

Returns:

Always FALSE, since there are no more spot sections

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