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.util.overview.ExperimentOverview.getOverview(Experiment, Project)
(In 2.10) Use OverviewUtil.getNewOrCurrentOverview(DbControl, BasicItem, Project) 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.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.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.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.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 |