2.9.1: 2008-12-18

Deprecated API


Contents
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) 
 

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.ItemContext.configureQuery(EntityQuery, boolean)
          Use ItemContext.configureQuery(DbControl, EntityQuery, boolean) 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.GalExporter.exportGal(DbControl, ArrayDesign, PrintWriter, ProgressReporter)
          Use GalExporter.exportGal(DbControl, ArrayDesign, Integer, PrintWriter, ProgressReporter) 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.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.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.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.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.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.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.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.core.Job.retry(boolean)
          Use Job.retry(boolean, boolean) instead 
net.sf.basedb.core.data.ArrayDesignData.setAffyChip(boolean)
          Has been replaced by platform 
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 
 

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.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)
            
 


2.9.1: 2008-12-18