Hierarchy For All Packages

Package Hierarchies:

• ubic.gemma.web.controller,
• ubic.gemma.web.controller.analysis.expression.coexpression.links,
• ubic.gemma.web.controller.analysis.preprocess,
• ubic.gemma.web.controller.analysis.sequence,
• ubic.gemma.web.controller.coexpressionSearch,
• ubic.gemma.web.controller.common,
• ubic.gemma.web.controller.common.auditAndSecurity,
• ubic.gemma.web.controller.common.auditAndSecurity.recaptcha,
• ubic.gemma.web.controller.common.description.bibref,
• ubic.gemma.web.controller.common.rss,
• ubic.gemma.web.controller.diff,
• 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.monitoring,
• ubic.gemma.web.controller.visualization,
• ubic.gemma.web.feed,
• ubic.gemma.web.job.progress,
• ubic.gemma.web.listener,
• ubic.gemma.web.logging,
• ubic.gemma.web.metrics,
• ubic.gemma.web.metrics.binder.servlet,
• ubic.gemma.web.persistence,
• ubic.gemma.web.propertyeditor,
• ubic.gemma.web.remote,
• ubic.gemma.web.scheduler,
• ubic.gemma.web.services,
• ubic.gemma.web.taglib,
• ubic.gemma.web.taglib.arrayDesign,
• ubic.gemma.web.taglib.common.auditAndSecurity,
• ubic.gemma.web.taglib.expression.experiment,
• ubic.gemma.web.tasks.analysis.sequence,
• ubic.gemma.web.util,
• ubic.gemma.web.util.upload,
• ubic.gemma.web.view

Class Hierarchy

• java.lang.Object
  • ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer (implements org.springframework.beans.factory.InitializingBean)
    • ubic.gemma.web.metrics.MeterRegistryWebConfigurer
  • ubic.gemma.web.persistence.AbstractSetListContainer (implements java.io.Serializable)
    • ubic.gemma.web.persistence.ExperimentSetListContainer
    • ubic.gemma.web.persistence.GeneSetListContainer
  • ubic.gemma.core.tasks.AbstractTask<C> (implements ubic.gemma.core.tasks.Task<C>)
    • ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskImpl (implements ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTask)
  • ubic.gemma.web.util.AnchorTagUtil
  • ubic.gemma.web.controller.expression.experiment.AnnotationController
  • org.apache.log4j.AppenderSkeleton (implements org.apache.log4j.Appender, org.apache.log4j.spi.OptionHandler)
    • ubic.gemma.web.logging.SlackAppender (implements org.apache.log4j.Appender)
  • org.springframework.context.support.ApplicationObjectSupport (implements org.springframework.context.ApplicationContextAware)
    • ubic.gemma.web.util.MessageUtilImpl (implements ubic.gemma.web.util.MessageUtil)
    • 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.view.TextView
        • ubic.gemma.web.view.XmlView
      • 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.BaseFormController
                  • ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
                  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
                  • ubic.gemma.web.controller.GeneralSearchControllerImpl (implements ubic.gemma.web.controller.GeneralSearchController)
          • 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.ArrayDesignControllerImpl (implements 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.remote.AuditController
  • ubic.gemma.web.controller.BaseController
    • ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl (implements ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController)
    • ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
    • ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
    • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
    • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
    • ubic.gemma.web.controller.genome.gene.GeneController
    • ubic.gemma.web.controller.PhenotypeController
    • ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerImpl (implements ubic.gemma.web.controller.common.description.bibref.PubMedQueryController)
    • ubic.gemma.web.controller.common.auditAndSecurity.SignupController (implements org.springframework.beans.factory.InitializingBean)
    • ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController
  • 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.remote.CharacteristicConverter
        • ubic.gemma.web.remote.DoublePointConverter
    • org.directwebremoting.convert.StringConverter (implements org.directwebremoting.extend.Converter)
      • ubic.gemma.web.remote.ClassConverter
      • ubic.gemma.web.remote.DirectionConverter
      • ubic.gemma.web.remote.GOEvidenceCodeConverter
      • ubic.gemma.web.remote.ScaleTypeConverter
      • ubic.gemma.web.remote.StandardQuantitationTypeConverter
  • ubic.gemma.web.controller.analysis.preprocess.BatchInfoFetchController
  • ubic.gemma.web.controller.expression.bioAssay.BioAssayController
  • ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
  • ubic.gemma.web.util.CacheMonitorImpl (implements ubic.gemma.web.util.CacheMonitor, org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.web.controller.common.CharacteristicBrowserController
  • ubic.gemma.web.util.ClientAbortExceptionResolver (implements org.springframework.web.servlet.HandlerExceptionResolver)
  • ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController
  • ubic.gemma.web.util.upload.CommonsMultipartFile (implements org.springframework.web.multipart.MultipartFile, java.io.Serializable)
  • ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver (implements org.springframework.web.multipart.MultipartResolver, org.springframework.web.context.ServletContextAware)
  • 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.ControllerUtils
  • javax.servlet.http.Cookie (implements java.lang.Cloneable, java.io.Serializable)
    • ubic.gemma.web.util.ConfigurationCookie
  • ubic.gemma.web.controller.expression.experiment.DEDVController
  • ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject (implements java.io.Serializable)
  • ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject.Factory
  • ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController
  • ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo
  • ubic.gemma.web.controller.diff.DifferentialExpressionSearchController
  • ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
  • ubic.gemma.web.controller.diff.DiffExpressionSearchCommand (implements java.io.Serializable)
  • org.apache.commons.fileupload.disk.DiskFileItem (implements org.apache.commons.fileupload.FileItem)
    • ubic.gemma.web.util.upload.MonitoredDiskFileItem
  • org.apache.commons.fileupload.disk.DiskFileItemFactory (implements org.apache.commons.fileupload.FileItemFactory)
    • ubic.gemma.web.util.upload.MonitoredDiskFileItemFactory
  • ubic.gemma.web.controller.EmptyController
  • ubic.gemma.web.remote.EntityDelegator<T>
  • ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils
  • ubic.gemma.web.controller.ExpressionExperimentReportGenerationController
  • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
  • ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand (implements java.io.Serializable)
  • ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
  • ubic.gemma.web.controller.visualization.FactorProfile
  • ubic.gemma.web.feed.FeedReader (implements org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.web.controller.common.auditAndSecurity.FileUpload (implements java.io.Serializable)
  • ubic.gemma.web.util.upload.FileUploadUtil
  • ubic.gemma.web.controller.common.GemmaClassicHomePageController
  • ubic.gemma.web.controller.visualization.GeneExpressionProfile
  • ubic.gemma.web.controller.genome.gene.GenePickerController
  • ubic.gemma.web.controller.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.util.GeneSymbolComparator (implements java.util.Comparator<T>)
  • ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController
  • ubic.gemma.web.util.HibernateMonitorImpl (implements ubic.gemma.web.util.HibernateMonitor)
  • ubic.gemma.web.controller.common.HomePageController
  • ubic.gemma.model.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 gemma.gsec.model.SecureValueObject)
        • 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.IndexController
  • ubic.gemma.web.util.JavascriptLogger
  • ubic.gemma.web.remote.JsonReaderResponse<T>
  • ubic.gemma.web.view.JSONTableRenderer
  • ubic.gemma.web.util.JsonUtil
  • ubic.gemma.web.view.JSONView (implements org.springframework.web.servlet.View)
  • javax.servlet.jsp.JspContext
    • javax.servlet.jsp.PageContext
      • ubic.gemma.web.taglib.SimplePageContext
  • ubic.gemma.web.util.LabelValue (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.web.controller.analysis.expression.coexpression.links.LinkAnalysisController
  • ubic.gemma.web.remote.ListBatchCommand
  • ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
  • ubic.gemma.web.controller.expression.experiment.MetaFile
  • org.springframework.util.MethodInvoker
    • org.springframework.beans.support.ArgumentConvertingMethodInvoker
      • org.springframework.scheduling.quartz.MethodInvokingJobDetailFactoryBean (implements org.springframework.beans.factory.BeanClassLoaderAware, org.springframework.beans.factory.BeanFactoryAware, org.springframework.beans.factory.BeanNameAware, org.springframework.beans.factory.FactoryBean<T>, org.springframework.beans.factory.InitializingBean)
        • ubic.gemma.web.scheduler.SecureMethodInvokingJobDetailFactoryBean
  • ubic.gemma.web.util.MinifierPostProcessor (implements net.jawr.web.resource.bundle.postprocess.ResourceBundlePostProcessor)
  • ubic.gemma.web.feed.NewsItem
  • ubic.gemma.web.controller.OntologyController
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • ubic.gemma.web.util.upload.MonitoredOutputStream
  • ubic.gemma.web.controller.analysis.preprocess.PreprocessController
  • ubic.gemma.web.job.progress.ProgressStatusServiceImpl (implements ubic.gemma.web.job.progress.ProgressStatusService)
  • java.beans.PropertyEditorSupport (implements java.beans.PropertyEditor)
    • ubic.gemma.web.propertyeditor.ArrayDesignPropertyEditor
    • ubic.gemma.web.propertyeditor.QuantitationTypePropertyEditor
    • ubic.gemma.web.propertyeditor.SequenceTypePropertyEditor
    • ubic.gemma.web.propertyeditor.TaxonPropertyEditor
  • 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.util.RequestUtil
  • ubic.gemma.web.controller.common.rss.RssFeedController
  • ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl (implements 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.util.upload.FailedMultipartHttpServletRequest
  • ubic.gemma.web.persistence.SessionListManagerImpl (implements ubic.gemma.web.persistence.SessionListManager)
  • ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
  • ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.SimpleHttp
  • ubic.gemma.web.remote.StringPoint
  • 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.expression.experiment.AssayViewTag
    • ubic.gemma.web.taglib.ConstantsTag
    • ubic.gemma.web.taglib.DatabaseEntryTag
    • ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
    • ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
    • ubic.gemma.web.taglib.ShortBibliographicReferenceTag
  • ubic.gemma.core.job.TaskCommand (implements java.io.Serializable)
    • ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
    • ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand
    • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
    • ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
      • ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
  • ubic.gemma.web.controller.TaskCompletionController
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • ubic.gemma.web.util.EntityNotFoundException
        • ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException
        • ubic.gemma.web.util.ServiceUnavailableException
  • org.springframework.xml.transform.TransformerObjectSupport
    • org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint (implements org.springframework.ws.server.endpoint.PayloadEndpoint)
      • ubic.gemma.web.services.AbstractGemmaEndpoint
        • ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint
        • ubic.gemma.web.services.ArrayDesignUsedEndpoint
        • ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint
        • ubic.gemma.web.services.DEDVRankEndpoint
        • ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint
        • ubic.gemma.web.services.ExperimentAnnotationEndpoint
        • ubic.gemma.web.services.ExperimentDEDVEndpoint
        • ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint
        • ubic.gemma.web.services.ExperimentIdEndpoint
        • ubic.gemma.web.services.ExperimentNameEndpoint
        • ubic.gemma.web.services.ExperimentNumSamplesEndpoint
        • ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint
        • ubic.gemma.web.services.Gene2GOdescriptionEndpoint
        • ubic.gemma.web.services.Gene2GoTermEndpoint
        • ubic.gemma.web.services.Gene2ProbeEndpoint
        • ubic.gemma.web.services.GeneByNCBIIdEndpoint
        • ubic.gemma.web.services.GeneCoexpressionEndpoint
        • ubic.gemma.web.services.GeneCoexpressionSearchEndpoint
        • ubic.gemma.web.services.GeneDetailsByGeneIDEndpoint
        • ubic.gemma.web.services.GeneIDbyTaxonEndpoint
        • ubic.gemma.web.services.GeneIdEndpoint
        • ubic.gemma.web.services.GeneNameEndpoint
        • ubic.gemma.web.services.GeneOverlapEndpoint
        • ubic.gemma.web.services.GoTerm2GeneEndpoint
        • ubic.gemma.web.services.Probe2GeneEndpoint
  • ubic.gemma.web.controller.analysis.preprocess.TwoChannelMissingValueController
  • ubic.gemma.web.util.UnhandledExceptionResolver (implements org.springframework.web.servlet.HandlerExceptionResolver)
  • ubic.gemma.web.util.upload.UploadInfo (implements java.io.Serializable)
  • ubic.gemma.web.util.upload.UploadListener (implements ubic.gemma.web.util.upload.OutputStreamListener)
  • ubic.gemma.web.listener.UserCounterListener (implements javax.servlet.http.HttpSessionListener, javax.servlet.ServletContextListener)
  • ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
  • ubic.gemma.web.controller.common.auditAndSecurity.UserListControllerImpl (implements ubic.gemma.web.controller.common.auditAndSecurity.UserListController)
  • ubic.gemma.web.listener.UserTracker
  • ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
  • ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
  • ubic.gemma.web.controller.visualization.VisualizationValueObject
  • ubic.gemma.web.controller.WebConstants
  • ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController

Interface Hierarchy

• ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
• ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
• ubic.gemma.web.util.CacheMonitor
• java.util.concurrent.Callable<V>
  • ubic.gemma.core.tasks.Task<C>
    • ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTask
• ubic.gemma.web.controller.GeneralSearchController
• ubic.gemma.web.util.HibernateMonitor
• ubic.gemma.web.util.MessageUtil
• ubic.gemma.web.util.upload.OutputStreamListener
• ubic.gemma.web.job.progress.ProgressStatusService
• ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
• ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
• ubic.gemma.web.persistence.SessionListManager
• ubic.gemma.web.controller.common.auditAndSecurity.UserListController