2.14.2: 2010-02-22

Deprecated API


Contents
Deprecated Classes
net.sf.basedb.plugins.BioAssaySetExporter
          In 2.12. Use: SerialBaseFileExporter or MatrixBaseFileExporter for BASEfile export and the extension package at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev for MeV export 
net.sf.basedb.util.overview.ExperimentOverview
          (In 2.10) Use GenericOverview instead 
 

Deprecated Fields
net.sf.basedb.core.Affymetrix.CDF_LINK_NAME
          See DataFileType.AFFYMETRIX_CDF 
net.sf.basedb.core.Affymetrix.CEL_LINK_NAME
          See DataFileType.AFFYMETRIX_CEL 
net.sf.basedb.plugins.AbstractFlatFileImporter.CHARSET
          Use Parameters.CHARSET_PARAMETER 
net.sf.basedb.plugins.AbstractFlatFileImporter.charsetType
          Use Parameters.charsetParameter(String, String, String) 
net.sf.basedb.core.Affymetrix.CHP_LINK_NAME
          See DataFileType 
net.sf.basedb.plugins.AbstractFlatFileImporter.DECIMAL_SEPARATOR
          Use Parameters.DECIMAL_SEPARATOR_PARAMETER 
net.sf.basedb.plugins.AbstractFlatFileImporter.decimalSeparatorType
          Use Parameters.decimalSeparatorParameter(String, String, String) 
net.sf.basedb.clients.web.ExperimentExplorer.DEFAULT_CACHE_SIZE
          In 2.11, for performance reasons the cache always contains the full set of reporters 
 

Deprecated Methods
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.ItemContext.configureQuery(EntityQuery, boolean)
          Use ItemContext.configureQuery(DbControl, EntityQuery, boolean) instead 
net.sf.basedb.core.AnyToAny.deleteStrayLinks()
          Use AnyToAny.deleteStrayLinks(ProgressReporter) instead. 
net.sf.basedb.core.ItemKey.deleteUnusedKeys()
          Use ItemKey.deleteUnusedItemKeys() instead which returns the number of deleted keys 
net.sf.basedb.core.ProjectKey.deleteUnusedKeys()
          Use ProjectKey.deleteUnusedProjectKeys() 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.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.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.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.clients.web.ExperimentExplorer.getPosition(DbControl, ReporterData, int)
          In 2.11 for performance reasons, use ExperimentExplorer.getPosition(DbControl, int, int) 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.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.core.query.Annotations.like(AnnotationType, Object, boolean)
          Use Annotations.like(String, AnnotationType, Object, boolean) instead with alias=null 
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.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.ExtendedProperty.parseString(String, NumberFormat)
          Use ExtendedProperty.parseString(String, NumberFormat, boolean) instead 
net.sf.basedb.core.Type.parseString(String, NumberFormat)
          Use Type.parseString(String, NumberFormat, boolean) instead 
net.sf.basedb.core.DbControl.reattachItem(BasicItem)
          Use DbControl.reattachItem(BasicItem, boolean) 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.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.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 
 

Deprecated Constructors
net.sf.basedb.core.AnnotationBetweenRestriction(AnnotationType, Object, Object, boolean)
          Use AnnotationBetweenRestriction.AnnotationBetweenRestriction(String, AnnotationType, Object, Object, boolean) instead with alias=null 
net.sf.basedb.core.AnnotationInRestriction(AnnotationType, boolean, Object...)
          Use AnnotationInRestriction.AnnotationInRestriction(String, AnnotationType, boolean, Object[]) instead with alias=null 
net.sf.basedb.core.AnnotationSimpleRestriction(AnnotationType, Operator, Object, boolean)
          Use AnnotationSimpleRestriction.AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, boolean) instead with alias=null 
net.sf.basedb.core.AnnotationSimpleRestriction(int, Type, Operator, Object, boolean)
          Use AnnotationSimpleRestriction.AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean) instead with alias=null 
net.sf.basedb.util.jep.ChannelFunction(int[])
          In 2.12. Use ChannelFunction.ChannelFunction(int[], IntensityTransform) instead. Using this constructor will disable the untransformation of transformed values when JEP dynamic evalution is used. 
net.sf.basedb.util.parser.ColumnMapper(int, String, NumberFormat)
          Use ColumnMapper.ColumnMapper(int, String, NumberFormat, boolean) 
net.sf.basedb.util.parser.CompoundMapper(List, NumberFormat)
          Use CompoundMapper.CompoundMapper(List, NumberFormat, boolean) 
net.sf.basedb.util.parser.ConstantMapper(String, NumberFormat)
          Use ConstantMapper.ConstantMapper(String, NumberFormat, boolean) 
net.sf.basedb.clients.web.taglib.table.TableColumn(String, String, String, Type, String, String)
            
 


2.14.2: 2010-02-22