Package 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 (ti, 20 apr 2010) $

Field Summary

Fields

Modifier and Type	Field	Description
static final String	SUBTYPE

Constructor Summary

Constructors

Constructor	Description
MatrixBfsExporter()	Create a new matrix BFS exporter.

Method Summary

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 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, 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 Details

SUBTYPE

public static final String SUBTYPE

See Also:

• Constant Field Values

Constructor Details

MatrixBfsExporter

public MatrixBfsExporter()

Create a new matrix BFS exporter.

Method Details

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 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()