Class SerialBfsExporter
- java.lang.Object
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- net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
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- net.sf.basedb.util.export.spotdata.BfsExporter
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- net.sf.basedb.util.export.spotdata.SerialBfsExporter
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public class SerialBfsExporter extends BfsExporter
BFS exporter implementation that exports spot data in serial format. This format creates one file per assay in the bioassay set. Each data file contains columns for the registered spot fields. For example, the 'sdata1' file contains channel 1 and 2 intensity for the first assay, and 'sdata2' contains the same data for the second assay, etc.- Version:
- 2.15
- Author:
- Nicklas
- Last modified
- $Date: 2010-04-20 10:02:16 +0200 (ti, 20 apr 2010) $
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Constructor Summary
Constructors Constructor Description SerialBfsExporter()
Create a new serial BFS exporter.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
arrangeData(int position, short column, Object[][] data, Object[] spotData)
The column number is used to find the assay index.protected List<DataWriter>
createDataWriters()
Create one data writer for each assay in the bioassay set.String
getBFSSubtype()
Get the BFS subtype.-
Methods inherited from class net.sf.basedb.util.export.spotdata.BfsExporter
addAssayField, addAssayFields, addExtraFile, addReporterField, addReporterFields, addSpotField, addSpotFields, beginExport, createDataWriter, endExport, exportAssayAnnotations, exportGlobalFooter, exportGlobalHeader, exportMetadata, exportReporterAnnotations, exportSectionData, exportSpotData, getAssayAnnotationsWriter, getAssayFields, getDataWriterFactory, getMetadataWriter, getParameter, getReporterAnnotationsWriter, getReporterFields, getSpotFields, setAssayAnnotationsWriter, setAutoCloseWriters, setDataWriterFactory, setMetadataWriter, setParameter, setReporterAnnotationsWriter, validate
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Methods inherited from class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
addExperimentalFactorsAsAssayFields, cacheReporterData, copyReporterFields, doExport, exportSectionFooter, exportSectionHeader, getAssayIndex, getAverageOnReporter, getBioAssays, getDbControl, getProgressReporter, getReporterQuery, getSnapshotManager, getSource, getSpotQuery, prepareAssayIndexMap, setAverageOnReporter, setDbControl, setProgress, setProgressReporter, setSnapshotManager, setSource
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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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Method Detail
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getBFSSubtype
public String getBFSSubtype()
Description copied from class:BfsExporter
Get the BFS subtype. This method may be overridden by subclasses. The default implementation returns null. The subtype is written to the metadata file:MetadataWriter.setSubtype(String)
.- Overrides:
getBFSSubtype
in classBfsExporter
- Returns:
- "serial"
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createDataWriters
protected List<DataWriter> createDataWriters() throws IOException
Create one data writer for each assay in the bioassay set. Each data writer is configured with one column per spot field.- Specified by:
createDataWriters
in classBfsExporter
- Returns:
- A list with data writers
- Throws:
IOException
- If there is a problem with creating the writers
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arrangeData
protected void arrangeData(int position, short column, Object[][] data, Object[] spotData)
The column number is used to find the assay index. Then, the spot data is copied to the correct data writer.- Specified by:
arrangeData
in classBfsExporter
- Parameters:
position
- The current position of the spot datacolumn
- The current column of the spot datadata
- The data array to copy the data tospotData
- The current row of spot data, in the same order asBfsExporter.getSpotFields()
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