net.sf.basedb.util.export.spotdata
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
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.
- 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
MatrixBfsExporter
public MatrixBfsExporter()
- Create a new matrix 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:
- "matrix"
createDataWriters
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
- 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()