2.17.2: 2011-06-17

Class MatrixBfsExporter

  extended by net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
      extended by net.sf.basedb.util.export.spotdata.BfsExporter
          extended by net.sf.basedb.util.export.spotdata.MatrixBfsExporter

public class MatrixBfsExporter
extends BfsExporter

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.

Last modified
$Date: 2010-04-20 10:02:16 +0200 (Tue, 20 Apr 2010) $

Field Summary
static String SUBTYPE
Constructor Summary
          Create a new matrix BFS exporter.
Method Summary
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 registered spot field.
 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
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

Field Detail


public static final String SUBTYPE
See Also:
Constant Field Values
Constructor Detail


public MatrixBfsExporter()
Create a new matrix BFS exporter.

Method Detail


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).

getBFSSubtype in class BfsExporter


protected List<DataWriter> createDataWriters()
                                      throws IOException
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 class BfsExporter
A list with data writers
IOException - If there is a problem with creating the writers


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
position - The current position of the spot data
column - The current column of the spot data
data - The data array to copy the data to
spotData - The current row of spot data, in the same order as BfsExporter.getSpotFields()

2.17.2: 2011-06-17