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

java.lang.Object
  net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Direct Known Subclasses:

BaseFileExporter, BfsExporter

public abstract class AbstractBioAssaySetExporter
extends Object

An abstract superclass for all exporters that exports spot data from a bioassay set. The purpose of this class is to collect some minimal configurations options (such as the source bioassay set and a DbControl) and to outline a generic export procedure. This class also has a lot of support functionality for subclass that wants to specify exactly which information that should be exported (spot data, reporter annotations, assay annotations, etc.), query generation, progress reporting, thread interruption controls, etc.

The exporter has been designed to export three types of information associated with a bioassay set.

• Spot data: intensity values, extra values, raw data values
• Reporter data: reporter annotations, position extra values
• Bioassay data: annotations

Subclass implementors can override doExport() if they wish. A better option is to override the other methods that are called from this method in this order:

1. beginExport(): One time only
2. exportGlobalHeader(): One time only. If false is returned, the export skips to the last step
3. exportSectionHeader(): One or more times
4. exportSectionData(): One or more times
5. exportSectionFooter(): One or more times. If true is returned, the steps 3-5 are repeated.
6. endExport(RuntimeException): Always called last. If the parameter is not null an error has occurred

Version:

2.12

Author:

Nicklas

Last modified

$Date: 2010-09-10 13:09:05 +0200 (Fri, 10 Sep 2010) $

Field Summary

private List<AssayField>	assayFields
private Map<Short,Integer>	assayIndexMap
private boolean	averageOnReporter
private List<BioAssay>	bioAssays
private DbControl	dc
private ProgressReporter	progress
private Map<Integer,Object[]>	reporterCache
private List<DynamicField>	reporterFields
private SnapshotManager	snapshotManager
private BioAssaySet	source
private List<DynamicField>	spotFields

Constructor Summary

protected

AbstractBioAssaySetExporter()

Method Summary

protected void	addAssayField(AssayField field) Add information about an assay field that should be exported.
protected void	addExperimentalFactorsAsAssayFields() Adds all experimental factors from the experiment that the source bioassay set belongs to as assay fields.
protected void	addReporterField(DynamicField field) Add information about a reporter field that should be exported.
protected void	addSpotField(DynamicField field) Add information about a spot field that should be exported.
protected void	beginExport() Make preparations for the export.
protected int	cacheReporterData() Loads and caches reporter data in an internal structure for quick access.
protected void	checkInterrupted() Deprecated. In 2.16, use ThreadSignalHandler.checkInterrupted() instead
protected void	copyReporterFields(int key, Object[] data, int startIndex) Copy cached reporter data into a data array.
void	doExport() Run the export.
protected void	endExport(RuntimeException e) End the export and clean up/close all aquired resources.
protected void	exportGlobalFooter() Export global footer or other data that only appears once in the end of the exported file.
protected boolean	exportGlobalHeader() Export global headers or other data that only appear once in the beginning of the exported file.
protected void	exportSectionData() Export section data.
protected boolean	exportSectionFooter() End the section by exporting a footer.
protected void	exportSectionHeader() Start a new section in the export by exporting section headers.
protected List<AssayField>	getAssayFields() Get the list of registered assay fields, in the order they were registered.
protected int	getAssayIndex(short column) Get the cached index value for an assay when you know the assay's column number.
protected boolean	getAverageOnReporter()
protected List<BioAssay>	getBioAssays() Get a list with all bioassays in the source bioassay set.
DbControl	getDbControl() Get the current DbControl.
ProgressReporter	getProgressReporter() Get the progress reporter
protected List<DynamicField>	getReporterFields() Get the list of registered reporter fields, in the order they were registered.
protected DynamicPositionQuery	getReporterQuery() Get a configured query for position data that returns all fields that has been registered with addReporterField(DynamicField).
SnapshotManager	getSnapshotManager() Get the current snapshot manager.
BioAssaySet	getSource() Get the source bioassay set.
protected List<DynamicField>	getSpotFields() Get the list of registered spot fields, in the order they were registered.
protected DynamicSpotQuery	getSpotQuery(boolean bioAssayRestriction) Get a configured query for spot data that returns all fields that has been registered with addSpotField(DynamicField).
protected void	prepareAssayIndexMap(List<BioAssay> assays, int firstIndex, int columnsPerAssay) Prepare a cache that maps the bioassay column (BioAssay.getDataCubeColumnNo()) value to an index in the 'data' array this is generated.
protected void	setAverageOnReporter(boolean averageOnReporter) Specify if the exported data should be averaged on reporter or not.
void	setDbControl(DbControl dc) Set's the DbControl that should be used to get data from the database.
protected void	setProgress(int percent, String message) Update the progress of the export.
void	setProgressReporter(ProgressReporter progress) Set the progress reporter that is used to report progress.
void	setSnapshotManager(SnapshotManager snapshotManager) Set's the snapshot manager that should be used to load annotation values.
void	setSource(BioAssaySet source) Set the bioassay set that is used as a source for the spot data.
protected void	validate() Validate that all required options has been set and that other options have sensible values.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

source

private BioAssaySet source

dc

private DbControl dc

snapshotManager

private SnapshotManager snapshotManager

progress

private ProgressReporter progress

assayFields

private List<AssayField> assayFields

reporterFields

private List<DynamicField> reporterFields

spotFields

private List<DynamicField> spotFields

averageOnReporter

private boolean averageOnReporter

bioAssays

private List<BioAssay> bioAssays

reporterCache

private Map<Integer,Object[]> reporterCache

assayIndexMap

private Map<Short,Integer> assayIndexMap

Constructor Detail

AbstractBioAssaySetExporter

protected AbstractBioAssaySetExporter()

Method Detail

setDbControl

public void setDbControl(DbControl dc)

Set's the DbControl that should be used to get data from the database.

getDbControl

public DbControl getDbControl()

Get the current DbControl.

setSnapshotManager

public void setSnapshotManager(SnapshotManager snapshotManager)

Set's the snapshot manager that should be used to load annotation values. If no snapshot manager is provided an internal, temporary one is used.

Since:

2.14

getSnapshotManager

public SnapshotManager getSnapshotManager()

Get the current snapshot manager.

Since:

2.14

setProgressReporter

public void setProgressReporter(ProgressReporter progress)

Set the progress reporter that is used to report progress. Subclasses can call setProgress(int, String) to update the current status.

getProgressReporter

public ProgressReporter getProgressReporter()

Get the progress reporter

setSource

public void setSource(BioAssaySet source)

Set the bioassay set that is used as a source for the spot data.

getSource

public BioAssaySet getSource()

Get the source bioassay set.

addSpotField

protected void addSpotField(DynamicField field)

Add information about a spot field that should be exported.

Parameters:

field - The spot field (null is ignored)

getSpotFields

protected List<DynamicField> getSpotFields()

Get the list of registered spot fields, in the order they were registered.

addReporterField

protected void addReporterField(DynamicField field)

Add information about a reporter field that should be exported.

Parameters:

field - The reporter field (null is ignored)

getReporterFields

protected List<DynamicField> getReporterFields()

Get the list of registered reporter fields, in the order they were registered.

addAssayField

protected void addAssayField(AssayField field)

Add information about an assay field that should be exported.

Parameters:

field - The assay field (null is ignored)

getAssayFields

protected List<AssayField> getAssayFields()

Get the list of registered assay fields, in the order they were registered.

setAverageOnReporter

protected void setAverageOnReporter(boolean averageOnReporter)

Specify if the exported data should be averaged on reporter or not.

getAverageOnReporter

protected boolean getAverageOnReporter()

doExport

public void doExport()

Run the export.

validate

protected void validate()

Validate that all required options has been set and that other options have sensible values. Subclasses that override this method should call super.validate(). The default implementation will at least validate that a DbControl and a source bioassay set has been set.

Since:

2.15

beginExport

protected void beginExport()

Make preparations for the export. Subclasses that need to initialise things should override this method. This is the first method that is called from doExport() and is only called once. The default implementation does nothing.

exportGlobalHeader

protected boolean exportGlobalHeader()

Export global headers or other data that only appear once in the beginning of the exported file. This method is called after beginExport() and is only called once. The return value can be used to indicate if the export should continue with sections or with global footers. The default implementation does nothing and returns TRUE.

Returns:

TRUE to continue with a section exportSectionHeader(), FALSE to continue with global footers exportGlobalFooter()

exportSectionHeader

protected void exportSectionHeader()

Start a new section in the export by exporting section headers. This method is called after exportGlobalHeader() and may be called multiple times as determined by the return value of exportSectionFooter(). The default implementation does nothing.

exportSectionData

protected void exportSectionData()

Export section data. This method is called after exportSectionHeader() and may be called multiple times as determined by the return value of exportSectionFooter(). The default implementation does nothing.

exportSectionFooter

protected boolean exportSectionFooter()

End the section by exporting a footer. This method is called after exportSectionData(). The return value is used to determine if the export should be repeated with a new section or if it should move on to global footers. The default implementation returns false.

Returns:

TRUE to continue with another section exportSectionHeader(), FALSE to continue with global footers exportGlobalFooter()

exportGlobalFooter

protected void exportGlobalFooter()

Export global footer or other data that only appears once in the end of the exported file. This method is called after FALSE has been returned from either exportGlobalHeader() or exportSectionFooter(). The default implementation does nothing.

endExport

protected void endExport(RuntimeException e)

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.

getBioAssays

protected List<BioAssay> getBioAssays()

Get a list with all bioassays in the source bioassay set. The list is sorted by assay name and id. The list is cached internally and if this method is called several times, the same list is returned.

addExperimentalFactorsAsAssayFields

protected void addExperimentalFactorsAsAssayFields()

Adds all experimental factors from the experiment that the source bioassay set belongs to as assay fields. The experimental factors are ordered by name.

getSpotQuery

protected DynamicSpotQuery getSpotQuery(boolean bioAssayRestriction)

Get a configured query for spot data that returns all fields that has been registered with addSpotField(DynamicField). The fields are selected in the order they were registered. This method also adds the position and column of the spot as the last two fields. Note! If the setAverageOnReporter(boolean) option has been enabled there is no unique position so the query returns the reporter id instead of the position in this case.

Parameters:

bioAssayRestriction - If TRUE a restriction is added to the query to make it return data for a single bioassay only. Use query.setParameter("bioAssayColumn", (int)bioAssay.getDataCubeColumnNo(), Type.INT) to set the value for the restriction

Returns:

A prepared query

getReporterQuery

protected DynamicPositionQuery getReporterQuery()

Get a configured query for position data that returns all fields that has been registered with addReporterField(DynamicField). The fields are selected in the order they were registered. This method also adds the position of the spot as the last field.

Note 1! If the setAverageOnReporter(boolean) option has been enabled there is no unique position so the query returns the reporter id instead of the position in this case.

Note 2! If the setAverageOnReporter(boolean) option has been enabled the query may return the same reporter information multiple times.

Note 3! A subclass may override this method, but it should at least still select the same number of fields as is expected from the default implementation.

Returns:

A prepared query

cacheReporterData

protected int cacheReporterData()

Loads and caches reporter data in an internal structure for quick access. This method will execute the query returned by getReporterQuery() and read all data into a memory structure. The data is indexed by position number or by reporter id (if average on reporters is enabled).

prepareAssayIndexMap

protected void prepareAssayIndexMap(List<BioAssay> assays,
                                    int firstIndex,
                                    int columnsPerAssay)

Prepare a cache that maps the bioassay column (BioAssay.getDataCubeColumnNo()) value to an index in the 'data' array this is generated. The map is generated as follows:

• first assay -> firstIndex
• second assay -> firstIndex + columnsPerAssay
• third assay -> firtsIndex + 2 * columnsPerAssay
• ... and so on

Use getAssayIndex(short) to get the indexed values.

Parameters:

assays - The assays that should be mapped

firstIndex - The index of the first assay

columnsPerAssay - Number of columns for each assay

getAssayIndex

protected int getAssayIndex(short column)

Get the cached index value for an assay when you know the assay's column number.

Parameters:

column - The column number (BioAssay.getDataCubeColumnNo())

Returns:

The index of the first position in the 'data' array that data for the assay should be written to.

See Also:

prepareAssayIndexMap(List, int, int)

copyReporterFields

protected void copyReporterFields(int key,
                                  Object[] data,
                                  int startIndex)

Copy cached reporter data into a data array.

Parameters:

key - The cache key (=position or reporter id)

data - The data array to copy to

startIndex - The start index in the data array for the first reporter field

checkInterrupted

@Deprecated
protected void checkInterrupted()

Deprecated. In 2.16, use ThreadSignalHandler.checkInterrupted() instead

Checks if the currently executing thread has been interrupted and throws a SignalException if it has.

setProgress

protected void setProgress(int percent,
                           String message)

Update the progress of the export.

See Also:

ProgressReporter