Hierarchy For All Packages

Package Hierarchies:

• ubic.gemma.web.assets,
• ubic.gemma.web.context,
• ubic.gemma.web.controller.analysis.expression.coexpression,
• ubic.gemma.web.controller.analysis.expression.coexpression.links,
• ubic.gemma.web.controller.analysis.expression.diff,
• ubic.gemma.web.controller.analysis.preprocess,
• ubic.gemma.web.controller.analysis.report,
• ubic.gemma.web.controller.analysis.sequence,
• ubic.gemma.web.controller.common,
• ubic.gemma.web.controller.common.auditAndSecurity,
• ubic.gemma.web.controller.common.auditAndSecurity.recaptcha,
• ubic.gemma.web.controller.common.description,
• ubic.gemma.web.controller.common.description.bibref,
• ubic.gemma.web.controller.common.rss,
• ubic.gemma.web.controller.dwr,
• ubic.gemma.web.controller.expression.arrayDesign,
• ubic.gemma.web.controller.expression.bioAssay,
• ubic.gemma.web.controller.expression.biomaterial,
• ubic.gemma.web.controller.expression.designElement,
• ubic.gemma.web.controller.expression.experiment,
• ubic.gemma.web.controller.genome,
• ubic.gemma.web.controller.genome.gene,
• ubic.gemma.web.controller.job,
• ubic.gemma.web.controller.monitoring,
• ubic.gemma.web.controller.ontology,
• ubic.gemma.web.controller.persistence,
• ubic.gemma.web.controller.search,
• ubic.gemma.web.controller.util,
• ubic.gemma.web.controller.util.upload,
• ubic.gemma.web.controller.util.view,
• ubic.gemma.web.controller.visualization,
• ubic.gemma.web.listener,
• ubic.gemma.web.metrics,
• ubic.gemma.web.metrics.binder.servlet,
• ubic.gemma.web.service,
• ubic.gemma.web.service.expression.experiment,
• ubic.gemma.web.taglib,
• ubic.gemma.web.taglib.arrayDesign,
• ubic.gemma.web.taglib.common.auditAndSecurity,
• ubic.gemma.web.taglib.expression.experiment,
• ubic.gemma.web.util

Class Hierarchy

• java.lang.Object
  • org.springframework.web.servlet.handler.AbstractHandlerExceptionResolver (implements org.springframework.web.servlet.HandlerExceptionResolver, org.springframework.core.Ordered)
    • ubic.gemma.web.controller.util.ClientAbortExceptionResolver
  • ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer (implements org.springframework.beans.factory.InitializingBean)
    • ubic.gemma.web.metrics.MeterRegistryWebConfigurer
  • ubic.gemma.web.controller.persistence.AbstractSetListContainer (implements java.io.Serializable)
    • ubic.gemma.web.controller.persistence.ExperimentSetListContainer
    • ubic.gemma.web.controller.persistence.GeneSetListContainer
  • ubic.gemma.web.controller.expression.experiment.AnnotationController
  • org.springframework.context.support.ApplicationObjectSupport (implements org.springframework.context.ApplicationContextAware)
    • org.springframework.web.context.support.WebApplicationObjectSupport (implements org.springframework.web.context.ServletContextAware)
      • org.springframework.web.servlet.view.AbstractView (implements org.springframework.beans.factory.BeanNameAware, org.springframework.web.servlet.View)
        • org.springframework.web.servlet.view.feed.AbstractFeedView<T>
          • org.springframework.web.servlet.view.feed.AbstractRssFeedView
            • ubic.gemma.web.controller.common.rss.CustomRssViewer
        • ubic.gemma.web.controller.util.view.TextView
      • org.springframework.web.servlet.support.WebContentGenerator
        • org.springframework.web.servlet.mvc.AbstractController (implements org.springframework.web.servlet.mvc.Controller)
          • org.springframework.web.servlet.mvc.AbstractUrlViewController
            • ubic.gemma.web.controller.common.auditAndSecurity.SystemStatsController
          • org.springframework.web.servlet.mvc.BaseCommandController
            • org.springframework.web.servlet.mvc.AbstractFormController
              • org.springframework.web.servlet.mvc.SimpleFormController
                • ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
          • ubic.gemma.web.controller.genome.BlatResultTrackController
          • ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController
  • ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
  • ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
  • ubic.gemma.web.taglib.arrayDesign.ArrayDesignHtmlUtil
  • ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignProbeMapperController
  • ubic.gemma.web.controller.analysis.sequence.ArrayDesignRepeatScanController
  • ubic.gemma.web.controller.common.auditAndSecurity.AuditController
  • org.directwebremoting.convert.BaseV20Converter (implements org.directwebremoting.extend.Converter)
    • org.directwebremoting.convert.BasicObjectConverter (implements org.directwebremoting.extend.NamedConverter)
      • org.directwebremoting.convert.BeanConverter (implements org.directwebremoting.extend.Converter)
        • ubic.gemma.web.controller.dwr.CharacteristicConverter
        • ubic.gemma.web.controller.dwr.DoublePointConverter
    • org.directwebremoting.convert.StringConverter (implements org.directwebremoting.extend.Converter)
      • ubic.gemma.web.controller.dwr.ClassConverter
      • ubic.gemma.web.controller.dwr.DirectionConverter
      • ubic.gemma.web.controller.dwr.GOEvidenceCodeConverter
      • ubic.gemma.web.controller.dwr.ScaleTypeConverter
      • ubic.gemma.web.controller.dwr.StandardQuantitationTypeConverter
  • ubic.gemma.web.controller.analysis.preprocess.BatchInfoFetchController
  • ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController (implements org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.web.controller.expression.bioAssay.BioAssayController
  • ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
  • ubic.gemma.web.controller.monitoring.CacheMonitorImpl (implements ubic.gemma.web.controller.monitoring.CacheMonitor, org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.web.controller.common.description.CharacteristicBrowserController
  • ubic.gemma.web.controller.analysis.expression.coexpression.CoexpressionSearchController
  • ubic.gemma.web.controller.util.upload.CommonsMultipartFile (implements org.springframework.web.multipart.MultipartFile, java.io.Serializable)
  • ubic.gemma.web.controller.util.upload.CommonsMultipartMonitoredResolver (implements org.springframework.web.multipart.MultipartResolver, org.springframework.web.context.ServletContextAware)
  • ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
  • ubic.gemma.web.util.Constants
  • org.springframework.web.context.ContextLoader
    • org.springframework.web.context.ContextLoaderListener (implements javax.servlet.ServletContextListener)
      • ubic.gemma.web.listener.StartupListener
  • ubic.gemma.web.controller.util.ControllerUtils
  • ubic.gemma.web.controller.expression.experiment.DEDVController
  • ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject (implements java.io.Serializable)
  • ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalysisController
  • ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalyzerInfo
  • ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionSearchController
  • ubic.gemma.web.controller.analysis.expression.diff.DiffExMetaAnalyzerController
  • ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand (implements java.io.Serializable)
  • org.apache.commons.fileupload.disk.DiskFileItem (implements org.apache.commons.fileupload.FileItem)
    • ubic.gemma.web.controller.util.upload.MonitoredDiskFileItem
  • org.apache.commons.fileupload.disk.DiskFileItemFactory (implements org.apache.commons.fileupload.FileItemFactory)
    • ubic.gemma.web.controller.util.upload.MonitoredDiskFileItemFactory
  • ubic.gemma.web.controller.util.DownloadUtil
  • ubic.gemma.web.controller.util.EntityDelegator<T>
  • ubic.gemma.persistence.util.EntityUrlBuilder
    • ubic.gemma.web.util.WebEntityUrlBuilder
  • ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
  • ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
  • ubic.gemma.web.service.expression.experiment.ExpressionExperimentControllerHelperService
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
  • ubic.gemma.web.controller.analysis.report.ExpressionExperimentReportGenerationController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse (implements java.io.Serializable)
  • ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand (implements java.io.Serializable)
  • ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
  • ubic.gemma.web.assets.ExternalStaticAssetServer (implements ubic.gemma.web.assets.StaticAssetServer)
  • ubic.gemma.web.controller.visualization.FactorProfile
  • ubic.gemma.web.controller.common.auditAndSecurity.FileUpload (implements java.io.Serializable)
  • ubic.gemma.web.controller.util.upload.FileUploadUtil
  • ubic.gemma.web.controller.genome.gene.GeneController
  • ubic.gemma.web.controller.visualization.GeneExpressionProfile
  • ubic.gemma.web.controller.genome.gene.GenePickerController
  • ubic.gemma.web.controller.search.GeneralSearchController
  • ubic.gemma.web.controller.search.GeneralSearchController.SearchResultValueObject<T>
  • org.springframework.web.filter.GenericFilterBean (implements org.springframework.beans.factory.BeanNameAware, org.springframework.beans.factory.DisposableBean, org.springframework.context.EnvironmentAware, javax.servlet.Filter, org.springframework.beans.factory.InitializingBean, org.springframework.web.context.ServletContextAware)
    • org.springframework.web.filter.OncePerRequestFilter
      • ubic.gemma.web.metrics.binder.servlet.ServletMetricsFilter
  • ubic.gemma.web.controller.genome.gene.GeneSetController
  • ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController
  • org.springframework.web.servlet.handler.HandlerExceptionResolverComposite (implements org.springframework.web.servlet.HandlerExceptionResolver, org.springframework.core.Ordered)
    • ubic.gemma.web.controller.util.DefaultHandlerExceptionResolver (implements org.springframework.web.servlet.HandlerExceptionResolver)
  • ubic.gemma.web.controller.monitoring.HibernateMonitorImpl (implements ubic.gemma.web.controller.monitoring.HibernateMonitor)
  • ubic.gemma.web.controller.common.HomePageController
  • ubic.gemma.model.common.IdentifiableValueObject<O> (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject<C>
      • ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject (implements ubic.gemma.model.common.description.Versioned)
        • ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
      • ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject (implements ubic.gemma.model.expression.experiment.BioAssaySetValueObject)
        • ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
          • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
    • ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
      • ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject
  • ubic.gemma.web.controller.common.IndexController
  • ubic.gemma.web.context.InitializeContext (implements org.springframework.context.ApplicationContextInitializer<C>)
  • ubic.gemma.web.assets.InternalStaticAssetServer (implements org.springframework.context.SmartLifecycle, ubic.gemma.web.assets.StaticAssetServer)
  • ubic.gemma.web.controller.common.JavascriptLogger
  • ubic.gemma.web.controller.util.view.JsonReaderResponse<T>
  • ubic.gemma.web.controller.util.JsonUtil
  • ubic.gemma.web.controller.util.view.JSONView (implements org.springframework.web.servlet.View)
  • ubic.gemma.web.controller.analysis.expression.coexpression.links.LinkAnalysisController
  • ubic.gemma.web.controller.util.ListBatchCommand
  • ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
  • ubic.gemma.web.controller.util.MessageUtil
  • ubic.gemma.web.controller.expression.experiment.MetaFile
  • ubic.gemma.web.controller.ontology.OntologyController
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • ubic.gemma.web.controller.util.upload.MonitoredOutputStream
  • ubic.gemma.web.controller.analysis.preprocess.PreprocessController
  • ubic.gemma.web.controller.job.ProgressStatusController
  • ubic.gemma.web.controller.common.description.bibref.PubMedQueryController (implements org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.web.controller.common.description.bibref.PubMedSearchCommand
  • ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
  • ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaResponse
  • ubic.gemma.web.controller.common.rss.RssFeedController
  • ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
  • ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
  • javax.servlet.ServletRequestWrapper (implements javax.servlet.ServletRequest)
    • javax.servlet.http.HttpServletRequestWrapper (implements javax.servlet.http.HttpServletRequest)
      • org.springframework.web.multipart.support.AbstractMultipartHttpServletRequest (implements org.springframework.web.multipart.MultipartHttpServletRequest)
        • ubic.gemma.web.controller.util.upload.FailedMultipartHttpServletRequest
  • ubic.gemma.web.assets.ServletStaticAssetServer (implements ubic.gemma.web.assets.StaticAssetServer)
  • ubic.gemma.web.controller.persistence.SessionListManagerImpl (implements ubic.gemma.web.controller.persistence.SessionListManager)
  • ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.web.controller.common.auditAndSecurity.SignupController (implements org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation (implements java.io.Serializable)
  • ubic.gemma.web.assets.StaticAssetResolver (implements org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.web.assets.StaticAssetServerConfig
  • ubic.gemma.web.controller.job.SubmittedTaskValueObject (implements java.io.Serializable)
  • ubic.gemma.web.controller.analysis.preprocess.SvdController
  • ubic.gemma.web.controller.monitoring.SystemMonitorController
  • javax.servlet.jsp.tagext.TagExtraInfo
    • ubic.gemma.web.taglib.ConstantsTei
  • javax.servlet.jsp.tagext.TagSupport (implements javax.servlet.jsp.tagext.IterationTag, java.io.Serializable)
    • ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
    • ubic.gemma.web.taglib.ConstantsTag
    • ubic.gemma.web.taglib.DatabaseEntryTag
    • org.springframework.web.servlet.tags.RequestContextAwareTag (implements javax.servlet.jsp.tagext.TryCatchFinally)
      • ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
      • org.springframework.web.servlet.tags.HtmlEscapingAwareTag
        • ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag<T> (implements javax.servlet.jsp.tagext.DynamicAttributes)
          • ubic.gemma.web.taglib.expression.experiment.ExpressionDataHeatmapTag
          • ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
        • ubic.gemma.web.taglib.AbstractStaticAssetTag
          • ubic.gemma.web.taglib.ImageTag (implements javax.servlet.jsp.tagext.DynamicAttributes)
          • ubic.gemma.web.taglib.ScriptTag (implements javax.servlet.jsp.tagext.DynamicAttributes)
          • ubic.gemma.web.taglib.StyleTag (implements javax.servlet.jsp.tagext.DynamicAttributes)
        • ubic.gemma.web.taglib.expression.experiment.AssayViewTag
        • ubic.gemma.web.taglib.CharacteristicTag
        • ubic.gemma.web.taglib.EntityLinkTag (implements javax.servlet.jsp.tagext.DynamicAttributes)
        • ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag (implements javax.servlet.jsp.tagext.DynamicAttributes)
        • ubic.gemma.web.taglib.FactorValueTag
    • ubic.gemma.web.taglib.ShortBibliographicReferenceTag
  • ubic.gemma.web.taglib.TagWriterUtils
  • ubic.gemma.core.job.TaskCommand (implements java.io.Serializable)
    • ubic.gemma.web.controller.analysis.expression.coexpression.CoexSearchTaskCommand
    • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
    • ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
  • ubic.gemma.web.controller.job.TaskCompletionController
  • ubic.gemma.web.controller.expression.experiment.TaxonController
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • ubic.gemma.web.controller.util.EntityNotFoundException
        • ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException
        • ubic.gemma.web.controller.util.ServiceUnavailableException
  • ubic.gemma.web.controller.analysis.preprocess.TwoChannelMissingValueController
  • ubic.gemma.web.controller.util.UnhandledExceptionResolver (implements org.springframework.web.servlet.HandlerExceptionResolver)
  • ubic.gemma.web.controller.util.upload.UploadInfo (implements java.io.Serializable)
  • ubic.gemma.web.controller.util.upload.UploadListener (implements ubic.gemma.web.controller.util.upload.OutputStreamListener)
  • ubic.gemma.web.listener.UserCounterListener (implements javax.servlet.http.HttpSessionListener, javax.servlet.ServletContextListener)
  • ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController
  • ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
  • ubic.gemma.web.controller.common.auditAndSecurity.UserListController
  • ubic.gemma.web.listener.UserTracker
  • ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
  • ubic.gemma.web.controller.visualization.VisualizationValueObject
  • ubic.gemma.web.controller.analysis.report.WhatsNewController

Interface Hierarchy

• ubic.gemma.web.controller.monitoring.CacheMonitor
• ubic.gemma.web.controller.monitoring.HibernateMonitor
• ubic.gemma.web.controller.util.upload.OutputStreamListener
• ubic.gemma.web.controller.persistence.SessionListManager
• ubic.gemma.web.assets.StaticAssetServer