|
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.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.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 |