Class MatrixBaseFileExporter
- java.lang.Object
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- net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
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- net.sf.basedb.util.export.spotdata.BaseFileExporter
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- net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
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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) $
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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 String
SUBTYPE
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Constructor Summary
Constructors Constructor Description MatrixBaseFileExporter()
Create a new matrix BASEfile exporter.
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Method Summary
All Methods Instance Methods Concrete Methods 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
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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
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Field Detail
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SUBTYPE
public static final String SUBTYPE
- See Also:
- Constant Field Values
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out
private BaseFileWriter out
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spotQuery
private DynamicSpotQuery spotQuery
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countQuery
private DynamicSpotQuery countQuery
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progress
private ChainedProgressReporter progress
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spotCount
private long spotCount
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Method Detail
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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 classBaseFileExporter
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exportSectionHeader
protected void exportSectionHeader()
Exports headers for a single 'spots' section.- Overrides:
exportSectionHeader
in classAbstractBioAssaySetExporter
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exportSectionData
protected void exportSectionData()
Exports data for all bioassays in a single 'spots' section.- Overrides:
exportSectionData
in classAbstractBioAssaySetExporter
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exportSectionFooter
protected boolean exportSectionFooter()
Ends the 'spots' section.- Overrides:
exportSectionFooter
in classAbstractBioAssaySetExporter
- Returns:
- Always FALSE, since there are no more spot sections
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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 classBaseFileExporter
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