Class MatrixBfsExporter
java.lang.Object
net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
net.sf.basedb.util.export.spotdata.BfsExporter
net.sf.basedb.util.export.spotdata.MatrixBfsExporter
BFS exporter implementation that exports spot data in matrix format. This
format creates one file per spot data field. Each data file contains
data columns for all assays in the bioassay set. For example, the 'sdata1'
file contains channel 1 intensity and 'sdata2' contains channel 2 intensity.
- Version:
- 2.15
- Author:
- Nicklas
- Last modified
- $Date: 2010-04-20 10:02:16 +0200 (ti, 20 apr 2010) $
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Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionprotected void
arrangeData
(int position, short column, Object[][] data, Object[] spotData) The column number is used to find the assay index.protected List<DataWriter>
Create one data writer for each registered spot field.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
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 Details
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SUBTYPE
- See Also:
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Constructor Details
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MatrixBfsExporter
public MatrixBfsExporter()Create a new matrix BFS exporter.
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Method Details
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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:
- "matrix"
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createDataWriters
Create one data writer for each registered spot field. Each data writer is configured with one column per assay in the bioassay set.- 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
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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