2.17.2: 2011-06-17

net.sf.basedb.util.export.spotdata
Class MatrixBaseFileExporter

java.lang.Object
  extended by net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
      extended by net.sf.basedb.util.export.spotdata.BaseFileExporter
          extended by net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

public class MatrixBaseFileExporter
extends BaseFileExporter

Exporter implementation that exports bioassay set data as a matrix BASEfile.

Version:
2.12
Author:
Nicklas
Last modified
$Date: 2010-08-03 11:11:54 +0200 (Tue, 03 Aug 2010) $

Field Summary
private  List<BioAssay> bioAssays
           
private  DynamicSpotQuery countQuery
           
private  BaseFileWriter out
           
private  ChainedProgressReporter progress
           
private  long spotCount
           
private  DynamicSpotQuery spotQuery
           
static String SUBTYPE
           
 
Constructor Summary
MatrixBaseFileExporter()
          Create a new matrix BASEfile exporter.
 
Method Summary
protected  void beginExport()
          Prepare the export by pre-loading some information and configure the queries that we are going to use.
protected  void endExport(RuntimeException e)
          End the export and clean up/close all aquired resources.
protected  void exportSectionData()
          Exports data for all bioassays in a single 'spots' section.
protected  boolean exportSectionFooter()
          Ends the 'spots' section.
protected  void exportSectionHeader()
          Exports headers for a single 'spots' section.
 
Methods inherited from class net.sf.basedb.util.export.spotdata.BaseFileExporter
addAssayField, addAssayFields, addReporterField, addReporterFields, addSpotField, addSpotFields, exportAssaysSectionData, exportAssaysSectionHeaders, exportGlobalHeader, exportSettingsSection, exportSpotSectionData, exportSpotSectionHeaders, getAssayFields, getAverageOnReporter, getBaseFileWriter, getCountQuery, getParameter, getReporterFields, getSpotFields, setAverageOnReporter, setParameter, setWriter
 
Methods inherited from class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
addExperimentalFactorsAsAssayFields, cacheReporterData, checkInterrupted, copyReporterFields, doExport, exportGlobalFooter, getAssayIndex, getBioAssays, getDbControl, getProgressReporter, getReporterQuery, getSnapshotManager, getSource, getSpotQuery, prepareAssayIndexMap, setDbControl, setProgress, setProgressReporter, setSnapshotManager, setSource, validate
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

SUBTYPE

public static final String SUBTYPE
See Also:
Constant Field Values

out

private BaseFileWriter out

bioAssays

private List<BioAssay> bioAssays

spotQuery

private DynamicSpotQuery spotQuery

countQuery

private DynamicSpotQuery countQuery

progress

private ChainedProgressReporter progress

spotCount

private long spotCount
Constructor Detail

MatrixBaseFileExporter

public MatrixBaseFileExporter()
Create a new matrix BASEfile exporter.

Method Detail

beginExport

protected void beginExport()
Prepare the export by pre-loading some information and configure the queries that we are going to use.

Overrides:
beginExport in class BaseFileExporter

exportSectionHeader

protected void exportSectionHeader()
Exports headers for a single 'spots' section.

Overrides:
exportSectionHeader in class AbstractBioAssaySetExporter

exportSectionData

protected void exportSectionData()
Exports data for all bioassays in a single 'spots' section.

Overrides:
exportSectionData in class AbstractBioAssaySetExporter

exportSectionFooter

protected boolean exportSectionFooter()
Ends the 'spots' section.

Overrides:
exportSectionFooter in class AbstractBioAssaySetExporter
Returns:
Always FALSE, since there are no more spot sections

endExport

protected void endExport(RuntimeException e)
Description copied from class: AbstractBioAssaySetExporter
End the export and clean up/close all aquired resources. This method is always called last. In the case of an error the exception parameter has a non-null value. The default implementation clears up values that has been cached so it is recommended that subclasses always call this method as part of their own cleanup. If the subclass implementation wants to throw a different exception it is recommended that the given exception is chained to allow developers to debug problems.

Overrides:
endExport in class AbstractBioAssaySetExporter

2.17.2: 2011-06-17