net.sf.basedb.util.export.spotdata
Class SerialBfsExporter
java.lang.Object
net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
net.sf.basedb.util.export.spotdata.BfsExporter
net.sf.basedb.util.export.spotdata.SerialBfsExporter
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 (Tue, 20 Apr 2010) $
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, checkInterrupted, copyReporterFields, doExport, exportSectionFooter, exportSectionHeader, getAssayIndex, getAverageOnReporter, getBioAssays, getDbControl, getProgressReporter, getReporterQuery, getSnapshotManager, getSource, getSpotQuery, prepareAssayIndexMap, setAverageOnReporter, setDbControl, setProgress, setProgressReporter, setSnapshotManager, setSource |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SUBTYPE
public static final String SUBTYPE
- See Also:
- Constant Field Values
SerialBfsExporter
public SerialBfsExporter()
- Create a new serial BFS exporter.
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 class BfsExporter
- Returns:
- "serial"
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 class BfsExporter
- Returns:
- A list with data writers
- Throws:
IOException
- If there is a problem with creating the writers
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 class BfsExporter
- 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
as BfsExporter.getSpotFields()