Deprecated Methods |
net.sf.basedb.core.AnnotationSet.autoInherit(DbControl, AnnotationType, boolean)
In 2.15, use AnnotationSet.autoInherit(DbControl, Collection, SnapshotManager, boolean)
instead since it has better performance |
net.sf.basedb.core.query.Annotations.between(AnnotationType, Object, Object, boolean)
Use Annotations.between(String, AnnotationType, Object, Object, boolean)
instead with alias=null |
net.sf.basedb.core.VirtualColumn.channel(int)
In 2.12. Use VirtualColumn.channelIntensity(int) or
VirtualColumn.channelRaw(int) instead. This method is forwarded
to VirtualColumn.channelIntensity(int) for maximum backwards
compatibility. |
net.sf.basedb.core.plugin.AbstractPlugin.checkInterrupted()
In 2.16, use ThreadSignalHandler.checkInterrupted() instead |
net.sf.basedb.util.basefile.BaseFileParser.checkInterrupted()
In 2.16, use ThreadSignalHandler.checkInterrupted() instead |
net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter.checkInterrupted()
In 2.16, use ThreadSignalHandler.checkInterrupted() instead |
net.sf.basedb.util.importer.spotdata.BaseFileImporter.checkInterrupted()
In 2.16, use ThreadSignalHandler.checkInterrupted() instead |
net.sf.basedb.util.importer.spotdata.BfsImporter.checkInterrupted()
In 2.16, use ThreadSignalHandler.checkInterrupted() instead |
net.sf.basedb.core.ItemContext.configureQuery(EntityQuery, boolean)
Use ItemContext.configureQuery(DbControl, EntityQuery, boolean) instead |
net.sf.basedb.core.hibernate.SessionWrapper.connection()
|
net.sf.basedb.util.BioAssaySetUtil.createJepExpression(DbControl, BioAssaySet, String, boolean)
In 2.15, use BioAssaySetUtil.createJepExpression(DbControl, String, DynamicQuery)
instead. The 'allowRawIfMultipleMappings' parameter is replaced with an
option on the spot query: DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean)
(it has no meaning on other queries) |
net.sf.basedb.util.BioAssaySetUtil.createJepRestriction(DbControl, BioAssaySet, String, boolean)
In 2.15, use BioAssaySetUtil.createJepRestriction(DbControl, String, DynamicQuery)
instead. The 'allowRawIfMultipleMappings' parameter is replaced with an
option on the spot query: DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean)
(it has no meaning on other queries) |
net.sf.basedb.core.AnyToAny.deleteStrayLinks()
Use AnyToAny.deleteStrayLinks(ProgressReporter) instead. |
net.sf.basedb.core.ProjectKey.deleteUnusedKeys()
Use ProjectKey.deleteUnusedProjectKeys() instead which returns the number of
deleted keys |
net.sf.basedb.core.ItemKey.deleteUnusedKeys()
Use ItemKey.deleteUnusedItemKeys() instead which returns the number of
deleted keys |
net.sf.basedb.ws.client.BioAssaySetClient.downloadBioAssaySet(int, String, String[], String[], boolean)
In 2.12.
See BioAssaySetService.downloadBioAssaySet(String, int, String, String[], String[], Boolean)
for more information. Use BioAssaySetClient.downloadDataFile(int, String) instead. |
net.sf.basedb.ws.server.BioAssaySetService.downloadBioAssaySet(String, int, String, String[], String[], Boolean)
In 2.12. Spot data should not be exported dynamically. Instead,
plug-ins should be used and attach the result to the bioassay set and
the files can then be downloaded when needed. Use
BioAssaySetService.downloadDataFile(String, int, String) instead. |
net.sf.basedb.core.query.Annotations.eq(AnnotationType, Object, boolean)
Use Annotations.eq(String, AnnotationType, Object, boolean) instead with alias=null |
net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileMatrix(BioAssaySet, File, Map, List, List, Boolean)
In 2.11 and 2.12, use MatrixBaseFileExporter instead |
net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileMatrix(BioAssaySet, File, Map, List, List, Boolean, ProgressReporter)
In 2.12, use MatrixBaseFileExporter instead |
net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileMatrix(BioAssaySet, OutputStream, Map, List, List, boolean)
In 2.11 and 2.12, use MatrixBaseFileExporter instead. |
net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileMatrix(BioAssaySet, OutputStream, Map, List, List, boolean, ProgressReporter)
In 2.11 and 2.12, use MatrixBaseFileExporter instead. |
net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileSerial(BioAssaySet, File, Map, List, List, Boolean)
In 2.11 and 2.12, use SerialBaseFileExporter instead. |
net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileSerial(BioAssaySet, File, Map, List, List, Boolean, ProgressReporter)
In 2.12, use SerialBaseFileExporter instead. |
net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileSerial(BioAssaySet, OutputStream, Map, List, List, boolean)
In 2.11 and 2.12, use SerialBaseFileExporter instead. |
net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileSerial(BioAssaySet, OutputStream, Map, List, List, boolean, ProgressReporter)
In 2.12, use SerialBaseFileExporter instead. |
net.sf.basedb.plugins.GalExporter.exportGal(DbControl, ArrayDesign, PrintWriter, ProgressReporter)
Use
GalExporter.exportGal(DbControl, ArrayDesign, Integer, PrintWriter, ProgressReporter)
instead |
net.sf.basedb.plugins.BioAssaySetExporter.exportMeV(BioAssaySet, OutputStream, ProgressReporter)
In 2.12, use extension package found at
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev instead |
net.sf.basedb.plugins.BioAssaySetExporter.exportPlainMatrix(BioAssaySet, OutputStream, ProgressReporter)
In 2.12, no direct replacement, write a subclass of
AbstractBioAssaySetExporter instead |
net.sf.basedb.core.AnnotationSet.findAnnotation(AnnotationType)
Use AnnotationSet.findAnnotations(DbControl, AnnotationType, Boolean) instead |
net.sf.basedb.util.AutoDetectFileFormat.findPlugins(DbControl, GuiContext, File, PluginDefinition)
|
net.sf.basedb.util.Values.formatDate(Date)
Use a Formatter for dates instead |
net.sf.basedb.util.Values.formatDateTime(Date)
Use a Formatter for dates instead |
net.sf.basedb.util.Values.formatTime(Date)
Use a Formatter for dates instead |
net.sf.basedb.core.hibernate.SessionWrapper.get(Class, Serializable, LockMode)
|
net.sf.basedb.core.hibernate.SessionWrapper.get(String, Serializable, LockMode)
|
net.sf.basedb.clients.web.ExperimentExplorer.getAnnotationTypeId()
In 2.14, use ExperimentExplorer.getAnnotationTypeIds() instead |
net.sf.basedb.util.BioAssaySetUtil.getAnnotationValues(DbControl, BioAssay, AnnotationType)
In BASE 2.14 due to performance problems, use
BioAssaySetUtil.getAnnotationValues(DbControl, SnapshotManager, BioAssay, AnnotationType)
instead |
net.sf.basedb.core.Affymetrix.getCdfFile(ArrayDesign)
Use FileStoreUtil.getDataFile(DbControl, FileStoreEnabled, String)
with a data file type of DataFileType.AFFYMETRIX_CDF
instead |
net.sf.basedb.core.Affymetrix.getCelFile(RawBioAssay)
|
net.sf.basedb.plugins.AbstractFlatFileImporter.getCharsetParameter(String, String, String)
USe Parameters.charsetParameter(String, String, String) |
net.sf.basedb.clients.web.Base.getConfiguredQuery(ItemContext, boolean, ItemQuery, ModeInfo)
Use Base.getConfiguredQuery(DbControl, ItemContext, boolean, ItemQuery, ModeInfo)
instead |
net.sf.basedb.util.Values.getDate(String)
Use a Formatter for dates instead |
net.sf.basedb.util.Values.getDate(String[])
Use a Formatter for dates instead |
net.sf.basedb.util.Values.getDate(String, Date)
Use a Formatter for dates instead |
net.sf.basedb.plugins.AbstractFlatFileImporter.getDecimalSeparatorParameter(String, String, String)
Use Parameters.decimalSeparatorParameter(String, String, String) |
net.sf.basedb.clients.web.Base.getEncodedName(Nameable, boolean, String)
Use Base.getLinkedName(String, Nameable, boolean, boolean) instead |
net.sf.basedb.ws.client.BioAssaySetClient.getExportFormats()
In 2.12. Use BioAssaySetClient.getDataFileTypes(int, QueryOptions) instead. |
net.sf.basedb.ws.server.BioAssaySetService.getExportFormats(String)
In 2.12. Use BioAssaySetService.getDataFileTypes(String, int, QueryOptions)
instead |
net.sf.basedb.core.ArrayDesign.getFeatureBatcher()
Use ArrayDesign.getFeatureBatcher(FeatureIdentificationMethod, Job) instead |
net.sf.basedb.core.Type.getHibernateType()
In 2.16. The NullableType class was deprecated in Hibernate 3.5.2.
It will be removed in Hibernate 3.6. Since BASE probably will switch to newer
Hibernate versions in the future this method will also be removed. The
Type.getTypeWrapper() is intended to replace this method, but it may
not provide the same information that a NullableType can. Problems are solved
on a case-by-case basis. Please ask on the BASE developers mailing list if
you have any issues related to this. |
net.sf.basedb.core.Project.getItems(Item, int, int, Permission)
Use Project.getItems(Item, int, int, Permission, Set) instead |
net.sf.basedb.core.User.getItems(Set- , int, int, Permission)
In 2.15, use User.getItems(Set, int, int, Permission, Restriction) instead |
net.sf.basedb.core.Project.getItems(Set- , int, int, Permission, Set)
In 2.15, use Project.getItems(Set, int, int, Permission, Set, Restriction)
instead |
net.sf.basedb.util.jobagent.JobAgentInfo.getJobs()
Use JobAgentInfo.getJobInfo() instead |
net.sf.basedb.core.ArrayDesign.getNew(DbControl, boolean)
Use ArrayDesign.getNew(DbControl, Platform) instead |
net.sf.basedb.core.BioPlate.getNew(DbControl, PlateGeometry)
In 2.16, use BioPlate.getNew(DbControl, PlateGeometry, BioPlateType) instead
Will try to find a bioplate type that is not locked to a specific biomaterial
type. If not found an exception is thrown. |
net.sf.basedb.core.Job.getNew(DbControl, PluginDefinition, PluginConfiguration)
Use Job.getNew(DbControl, PluginDefinition, PluginConfiguration, Experiment)
instead |
net.sf.basedb.core.RawBioAssay.getNew(DbControl, RawDataType)
Use RawBioAssay.getNew(DbControl, Platform, RawDataType) or
RawBioAssay.getNew(DbControl, PlatformVariant, RawDataType) instead.
This method will set the platform to Platform.GENERIC . |
net.sf.basedb.core.ArrayDesign.getNumFeatures(DbControl)
Use ArrayDesign.getNumDbFeatures() and/or ArrayDesign.getNumFileFeatures()
instead |
net.sf.basedb.clients.web.ExperimentExplorer.getNumPositions(DbControl, ReporterData)
In 2.11 for performance reasons, use ExperimentExplorer.getNumPositions(DbControl, int)
instead |
net.sf.basedb.util.overview.ExperimentOverview.getOverview(Experiment, Project)
(In 2.10) Use OverviewUtil.getNewOrCurrentOverview(DbControl, BasicItem, Project) instead |
net.sf.basedb.util.BioAssaySetUtil.getParentProperties(DbControl, BioAssay, String)
In 2.15, use BioAssaySetUtil.getParentProperties(DbControl, BioAssay, Metadata.PropertyPath) instead |
net.sf.basedb.clients.web.ExperimentExplorer.getPosition(DbControl, ReporterData, int)
In 2.11 for performance reasons, use ExperimentExplorer.getPosition(DbControl, int, int)
instead |
net.sf.basedb.plugins.AbstractFlatFileImporter.getPrimaryLocationFilter()
In 2.16. Since files can now be references to external URL:s
this filter no longer makes sense. Plug-ins should not use the location
to filter files. |
net.sf.basedb.core.Metadata.getPropertyValue(BasicItem, String)
In 2.15, use Metadata.getPropertyPath(String, boolean) instead |
net.sf.basedb.core.Metadata.getPropertyValue(DbControl, C, String)
In 2.15, use Metadata.getPropertyPath(String, boolean) instead |
net.sf.basedb.core.RawBioAssay.getRawDataBatcher()
Use RawBioAssay.getRawDataBatcher(FeatureIdentificationMethod, Job) instead |
net.sf.basedb.core.RawBioAssay.getRawDataBatcher(FeatureIdentificationMethod)
Use RawBioAssay.getRawDataBatcher(FeatureIdentificationMethod, Job)
instead. |
net.sf.basedb.clients.web.ExperimentExplorer.getReporterIndex(DbControl, ReporterData)
This method is a helper for other deprecated methods.
Do not use it in non-deprecated methods. |
net.sf.basedb.core.PropertyFilter.getRestriction()
Use PropertyFilter.getRestriction(DbControl, EntityQuery) instead |
net.sf.basedb.core.PropertyFilter.getRestriction(DbControl)
Use PropertyFilter.getRestriction(DbControl, EntityQuery) instead |
net.sf.basedb.util.importer.spotdata.BaseFileImporter.getSourceFile()
In 2.16, use BaseFileImporter.getSourceFileWrapper() instead |
net.sf.basedb.clients.web.ExperimentExplorer.getSpotQuery(DbControl, ReporterData, int, List)
In 2.11. For performance reasons, use ExperimentExplorer.getSpotQuery(DbControl, int, int, List) instead |
net.sf.basedb.core.RawBioAssay.getSpots()
Use RawBioAssay.getNumDbSpots() or RawBioAssay.getNumFileSpots()
instead. This method first checks the database and if not 0, it
returns that value, otherwise it returns the number of file spots |
net.sf.basedb.core.VirtualColumn.getType()
In 2.16. The NullableType class was deprecated in Hibernate 3.5.2.
It will be removed in Hibernate 3.6. Since BASE probably will switch to newer
Hibernate versions in the future this method will also be removed. The
VirtualColumn.getTypeWrapper() is intended to replace this method, but it may
not provide the same information that a NullableType can. Problems are solved
on a case-by-case basis. Please ask on the BASE developers mailing list if
you have any issues related to this. |
net.sf.basedb.util.XMLUtil.getValidatedXML(InputStream, URL)
Use XMLUtil.getValidatedXML(InputStream, URL, String) instead |
net.sf.basedb.util.overview.ExperimentOverview.getValidationPresets(SessionControl)
(In 2.10) Use OverviewUtil.getValidationPresets(SessionControl) instead |
net.sf.basedb.util.overview.ExperimentOverview.getValidators()
(In 2.10) Use OverviewUtil.getValidators() instead |
net.sf.basedb.core.query.Annotations.gt(AnnotationType, Object, boolean)
Use Annotations.gt(String, AnnotationType, Object, boolean) instead with alias=null |
net.sf.basedb.core.query.Annotations.gteq(AnnotationType, Object, boolean)
Use Annotations.gteq(String, AnnotationType, Object, boolean) instead with alias=null |
net.sf.basedb.core.query.Annotations.in(AnnotationType, boolean, Object...)
Use Annotations.in(String, AnnotationType, boolean, Object[])
instead with alias=null |
net.sf.basedb.core.RawDataBatcher.insert(RawData, String)
Use RawDataBatcher.insert(RawData, String, String) instead |
net.sf.basedb.plugins.HelpImporter.installHelpTexts(Client, boolean, InputStream)
Use HelpImporter.installHelpTexts(Client, boolean, InputStream, String) instead |
net.sf.basedb.core.ArrayDesign.isAffyChip()
Use ArrayDesign.isPlatform(String) instead with
Platform.AFFYMETRIX as the parameter |
net.sf.basedb.core.data.ArrayDesignData.isAffyChip()
Has been replaced by platform |
net.sf.basedb.core.RawDataType.isAffymetrix()
Use RawDataType.getPlatform(DbControl) and compare
the external ID with Platform.AFFYMETRIX |
net.sf.basedb.util.export.spotdata.ExportableFieldFactory.jep(String, String, Formula.AverageMethod, Formatter>)
In 2.15, use ExportableFieldFactory.jep(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter)
instead |
net.sf.basedb.core.query.Annotations.like(AnnotationType, Object, boolean)
Use Annotations.like(String, AnnotationType, Object, boolean) instead with alias=null |
net.sf.basedb.core.hibernate.SessionWrapper.load(Class, Serializable, LockMode)
|
net.sf.basedb.core.hibernate.SessionWrapper.load(String, Serializable, LockMode)
|
net.sf.basedb.core.Affymetrix.loadCdfFile(File)
Use AffymetrixFileHandler.loadCdfFile(File) instead |
net.sf.basedb.core.Affymetrix.loadCelFile(File)
Use AffymetrixFileHandler.loadCdfFile(File) instead |
net.sf.basedb.core.hibernate.SessionWrapper.lock(Object, LockMode)
|
net.sf.basedb.core.hibernate.SessionWrapper.lock(String, Object, LockMode)
|
net.sf.basedb.core.query.Annotations.lt(AnnotationType, Object, boolean)
Use Annotations.lt(String, AnnotationType, Object, boolean) instead with alias=null |
net.sf.basedb.core.query.Annotations.lteq(AnnotationType, Object, boolean)
Use Annotations.lteq(String, AnnotationType, Object, boolean) instead with alias=null |
net.sf.basedb.core.query.Annotations.neq(AnnotationType, Object, boolean)
Use Annotations.neq(String, AnnotationType, Object, boolean) instead with alias=null |
net.sf.basedb.core.PluginConfiguration.newJob()
Use PluginConfiguration.newJob(Experiment) instead |
net.sf.basedb.core.Scan.newRawBioAssay(RawDataType)
Use RawBioAssay.getNew(DbControl, Platform, RawDataType)
or RawBioAssay.getNew(DbControl, PlatformVariant, RawDataType) instead |
net.sf.basedb.core.Type.parseString(String, NumberFormat)
Use Type.parseString(String, NumberFormat, boolean) instead |
net.sf.basedb.core.ExtendedProperty.parseString(String, NumberFormat)
Use ExtendedProperty.parseString(String, NumberFormat, boolean) instead |
net.sf.basedb.util.export.spotdata.ExportableFieldFactory.rawData(String, String, Formula.AverageMethod, Formatter>)
In 2.15, use ExportableFieldFactory.rawData(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter)
instead |
net.sf.basedb.core.DbControl.reattachItem(BasicItem)
Use DbControl.reattachItem(BasicItem, boolean) instead |
net.sf.basedb.core.hibernate.SessionWrapper.reconnect()
|
net.sf.basedb.core.hibernate.SessionWrapper.refresh(Object, LockMode)
|
net.sf.basedb.util.export.spotdata.ExportableFieldFactory.reporter(String, String, Formula.AverageMethod, Formatter>)
In 2.15, use ExportableFieldFactory.reporter(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter)
instead |
net.sf.basedb.core.Job.retry(boolean)
Use Job.retry(boolean, boolean) instead |
net.sf.basedb.util.overview.ExperimentOverview.saveValidationPresets(SessionControl)
In 2.10, use OverviewUtil.saveValidationPresets(SessionControl) instead |
net.sf.basedb.core.signal.AbstractSignalReceiver.sendToAll(Signal)
In 2.16, use AbstractSignalReceiver.sendToAll(SignalSender) instead |
net.sf.basedb.core.signal.SignalReceiver.sendToAll(Signal)
In 2.16, use SignalReceiver.sendToAll(SignalSender) instead |
net.sf.basedb.clients.web.util.SimpleSignalProgressReporter.sendToAll(Signal)
|
net.sf.basedb.core.data.ArrayDesignData.setAffyChip(boolean)
Has been replaced by platform |
net.sf.basedb.clients.web.ExperimentExplorer.setAnnotationTypeId(int)
In 2.14, use ExperimentExplorer.setAnnotationTypeIds(Collection) instead |
net.sf.basedb.clients.web.ExperimentExplorer.setCacheSize(int)
In 2.11. For performance reasons the full reporter set
is always cached. |
net.sf.basedb.core.Affymetrix.setCdfFile(ArrayDesign, File)
Use FileStoreUtil.setDataFile(DbControl, FileStoreEnabled, String, File)
instead with DataFileType.AFFYMETRIX_CDF as the file
type |
net.sf.basedb.core.Affymetrix.setCelFile(RawBioAssay, File)
Use FileStoreUtil.setDataFile(DbControl, FileStoreEnabled, String, File)
instead with DataFileType.AFFYMETRIX_CEL as the file
type |
net.sf.basedb.util.parser.FlatFileParser.setInputStream(InputStream)
Use FlatFileParser.setInputStream(InputStream, String) instead |
net.sf.basedb.core.ShareableUtil.setItemKey(ShareableData, ItemKey)
Use ShareableUtil.setItemKey(DbControl, ShareableData, ItemKey) instead |
net.sf.basedb.core.Job.setPrepared(String)
Use Job.setPrepared(String, JobAgent) instead |
net.sf.basedb.core.RawBioAssay.setRawDataType(RawDataType)
Use RawBioAssay.setPlatform(Platform, RawDataType) or
RawBioAssay.setVariant(PlatformVariant, RawDataType) instead |
net.sf.basedb.util.importer.spotdata.BaseFileImporter.setSourceFile(File)
In 2.16, use BaseFileImporter.setSourceFileWrapper(FileWrapper) instead |
net.sf.basedb.util.export.spotdata.ExportableFieldFactory.simple(Expression, String, Formula.AverageMethod, Formatter>)
In 2.15, use ExportableFieldFactory.simple(Expression, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter)
instead |
net.sf.basedb.core.Job.start(String, String)
Use Job.start(String, String, JobAgent) instead |
net.sf.basedb.core.RawBioAssay.updateArrayDesign(ArrayDesign, ProgressReporter)
Use RawBioAssay.updateArrayDesign(ArrayDesign, FeatureIdentificationMethod, ProgressReporter)
instead |
net.sf.basedb.core.ArrayDesign.xgetFeatureBatcher(FeatureIdentificationMethod)
Use ArrayDesign.getFeatureBatcher(FeatureIdentificationMethod, Job)
instead |
net.sf.basedb.core.Formula.xgetQuery(Formula.Type, RawDataType)
In 2.12. Use Formula.getQuery(Type, RawDataType, IntensityTransform) instead |