Hierarchy For All Packages

Package Hierarchies:

• org.intermine.bio.web,
• org.intermine.bio.web.biojava,
• org.intermine.bio.web.displayer,
• org.intermine.bio.web.export,
• org.intermine.bio.web.logic,
• org.intermine.bio.web.model,
• org.intermine.bio.web.struts,
• org.intermine.bio.web.widget,
• org.intermine.bio.webservice,
• org.intermine.webservice.server.complexes,
• org.intermine.webservice.server.jbrowse.genomic

Class Hierarchy

• java.lang.Object
  • org.biojava.nbio.core.sequence.template.AbstractSequence<C> (implements org.biojava.nbio.core.sequence.template.Sequence<C>)
    • org.intermine.bio.web.biojava.BioSequence
  • org.apache.struts.action.Action
    • org.intermine.bio.web.struts.GenomicRegionSearchAjaxAction
    • org.intermine.web.struts.InterMineAction
      • org.intermine.bio.web.struts.GalaxyExportAction
      • org.intermine.bio.web.struts.GenomicRegionSearchAction
      • org.intermine.bio.web.struts.SequenceExportAction
    • org.apache.struts.tiles.actions.TilesAction
      • org.intermine.bio.web.AttributeLinksController
      • org.intermine.bio.web.EsynListDisplayer
      • org.intermine.bio.web.FriendlyMineLinkController
      • org.intermine.bio.web.struts.GalaxyExportOptionsController
      • org.intermine.bio.web.struts.GenomicRegionSearchOptionsController
      • org.intermine.bio.web.OtherMinesLinkController
      • org.intermine.bio.web.struts.SequenceExportOptionsController
      • org.intermine.bio.web.struts.SequenceFeatureExportOptionsController
  • org.apache.struts.action.ActionForm (implements java.io.Serializable)
    • org.apache.struts.action.DynaActionForm (implements org.apache.commons.beanutils.DynaBean)
      • org.intermine.bio.web.struts.GenomicRegionSearchForm
    • org.intermine.web.struts.TableExportForm
      • org.intermine.bio.web.struts.BEDExportForm
      • org.intermine.bio.web.struts.GalaxyExportForm
      • org.intermine.bio.web.struts.GFF3ExportForm
      • org.intermine.bio.web.struts.SequenceExportForm
  • org.intermine.web.logic.bag.BagConverter
    • org.intermine.bio.web.logic.OrthologueConverter
  • org.intermine.bio.web.export.BEDExporter (implements org.intermine.web.logic.export.Exporter)
  • org.intermine.bio.web.biojava.BioSequenceFactory
  • org.intermine.bio.web.widget.BioWidgetUtil (implements org.intermine.web.logic.widget.WidgetHelper)
  • org.intermine.bio.web.model.ChromosomeInfo
  • org.intermine.webservice.server.jbrowse.CommandRunner
    • org.intermine.webservice.server.jbrowse.genomic.Engine
  • org.intermine.webservice.server.complexes.ExportService.FeatureHolder
  • org.intermine.bio.web.displayer.FriendlyMineLinkGenerator (implements org.intermine.web.displayer.InterMineLinkGenerator)
  • org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions
  • org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByPValueComparator (implements java.util.Comparator<T>)
  • org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByTStatisticComparator (implements java.util.Comparator<T>)
  • org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.CaseInsensitiveComparator (implements java.util.Comparator<T>)
  • org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ExpressionList
  • org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions
  • org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByPValueComparator (implements java.util.Comparator<T>)
  • org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByTStatisticComparator (implements java.util.Comparator<T>)
  • org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.CaseInsensitiveComparator (implements java.util.Comparator<T>)
  • org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ExpressionList
  • org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient (implements org.intermine.web.logic.widget.CorrectionCoefficient)
  • org.intermine.bio.web.model.GeneModel
  • org.intermine.bio.web.model.GeneModelCache
  • org.intermine.bio.web.model.GeneModelSettings
  • javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
    • javax.servlet.http.HttpServlet
      • org.intermine.bio.webservice.ExternalLinksServlet
      • org.intermine.webservice.server.core.WebServiceServlet
        • org.intermine.bio.webservice.BioExportServlet
          • org.intermine.bio.webservice.BEDQueryServlet
          • org.intermine.bio.webservice.FastaListServlet
          • org.intermine.bio.webservice.FastaQueryServlet
          • org.intermine.bio.webservice.GenomicRegionBedServlet
          • org.intermine.bio.webservice.GenomicRegionFastaServlet
          • org.intermine.bio.webservice.GenomicRegionGFF3Servlet
          • org.intermine.bio.webservice.GenomicRegionSearchServlet
          • org.intermine.bio.webservice.GFF3ListServlet
          • org.intermine.bio.webservice.GFF3QueryServlet
  • org.intermine.bio.web.model.GenomicRegion (implements java.lang.Comparable<T>)
  • org.intermine.bio.web.model.GenomicRegionSearchConstraint
  • org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
  • org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner (implements java.lang.Runnable)
  • org.intermine.bio.web.logic.GenomicRegionSearchService
  • org.intermine.bio.web.logic.GenomicRegionSearchUtil
  • org.intermine.bio.web.export.GenomicRegionSequenceExporter
  • org.intermine.bio.web.export.GFF3Exporter (implements org.intermine.web.logic.export.Exporter)
  • org.intermine.web.logic.export.http.HttpExporterBase
    • org.intermine.bio.web.export.BEDHttpExporter (implements org.intermine.web.logic.export.http.TableHttpExporter)
    • org.intermine.bio.web.export.GFF3HttpExporter (implements org.intermine.web.logic.export.http.TableHttpExporter)
    • org.intermine.bio.web.export.SequenceHttpExporter (implements org.intermine.web.logic.export.http.TableHttpExporter)
  • org.intermine.bio.web.logic.LiftOverService
  • org.intermine.api.LinkRedirectManager
    • org.intermine.bio.web.BioLinkRedirectManager
  • org.intermine.webservice.server.lists.ListInput
    • org.intermine.bio.webservice.GenomicRegionSearchListInput
  • org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
  • org.intermine.bio.web.logic.OrganismGenomeBuildLookup
  • org.intermine.bio.web.model.OrganismInfo
  • org.intermine.bio.web.model.ProteinAtlasExpressions
  • org.intermine.bio.web.model.ProteinAtlasExpressions.ByCellCountComparator (implements java.util.Comparator<T>)
  • org.intermine.bio.web.model.ProteinAtlasExpressions.ByOverallLevelComparator (implements java.util.Comparator<T>)
  • org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList
  • org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList.StainingLevel
  • org.intermine.bio.web.model.ProteinAtlasExpressions.StainingLevelEvaluator
    • org.intermine.bio.web.model.ProteinAtlasExpressions.ByLevelComparator (implements java.util.Comparator<T>)
  • org.intermine.web.displayer.ReportDisplayer
    • org.intermine.bio.web.displayer.ComplexDisplayer
    • org.intermine.bio.web.displayer.CuratedProteinsDisplayer
    • org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer
    • org.intermine.bio.web.displayer.DiseaseDisplayer
    • org.intermine.bio.web.displayer.EsynDisplayer
    • org.intermine.bio.web.displayer.FlyBaseExpressionDisplayer
    • org.intermine.bio.web.displayer.GBrowseDisplayer
    • org.intermine.bio.web.displayer.GeneExpressionAtlasDiseasesDisplayer
    • org.intermine.bio.web.displayer.GeneExpressionAtlasTissuesDisplayer
    • org.intermine.bio.web.displayer.GeneIdentifiersDisplayer
    • org.intermine.bio.web.displayer.GeneOntologyDisplayer
    • org.intermine.bio.web.displayer.GeneStructureDisplayer
    • org.intermine.bio.web.displayer.HomologueDisplayer
    • org.intermine.bio.web.displayer.JBrowseDisplayer
    • org.intermine.bio.web.displayer.JMOLDisplayer
    • org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer
    • org.intermine.bio.web.displayer.MinePathwaysDisplayer
    • org.intermine.bio.web.displayer.MouseAllelesDisplayer
    • org.intermine.bio.web.displayer.OverlappingFeaturesDisplayer
    • org.intermine.bio.web.displayer.PathwayDescriptionDisplayer
    • org.intermine.bio.web.displayer.PathwaysDisplayer
    • org.intermine.bio.web.displayer.ProteinAtlasDisplayer
    • org.intermine.bio.web.displayer.ProteinSequenceDisplayer
    • org.intermine.bio.web.displayer.ProteinStructureATMDisplayer
    • org.intermine.bio.web.displayer.PublicationAnnotationsDisplayer
    • org.intermine.bio.web.displayer.PublicationCountsDisplayer
    • org.intermine.bio.web.displayer.RegulatoryRegionsDisplayer
    • org.intermine.bio.web.displayer.ReportWidgetDisplayer
    • org.intermine.bio.web.displayer.SequenceFeatureDisplayer
    • org.intermine.bio.web.displayer.SnpToGeneDisplayer
    • org.intermine.bio.web.displayer.UniProtCommentsDisplayer
  • org.intermine.bio.web.export.ResidueFieldExporter (implements org.intermine.web.logic.export.FieldExporter)
  • org.intermine.bio.web.export.SequenceExporter (implements org.intermine.web.logic.export.Exporter)
  • org.intermine.bio.web.logic.SequenceFeatureExportUtil
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.intermine.bio.web.logic.RegionParseException
      • java.lang.RuntimeException
        • org.intermine.bio.web.logic.SequenceFeatureExportUtil.InvalidQueryException
  • org.intermine.webservice.server.WebService
    • org.intermine.webservice.server.query.AbstractQueryService
      • org.intermine.bio.webservice.BioQueryService
        • org.intermine.bio.webservice.BEDQueryService
        • org.intermine.bio.webservice.FastaQueryService
          • org.intermine.bio.webservice.FastaListService
        • org.intermine.bio.webservice.GFFQueryService
          • org.intermine.bio.webservice.GFF3ListService
    • org.intermine.webservice.server.core.JSONService
      • org.intermine.webservice.server.lists.AbstractListService
        • org.intermine.webservice.server.lists.AuthenticatedListService
          • org.intermine.webservice.server.lists.ListMakerService
            • org.intermine.bio.webservice.GenomicRegionSearchService
              • org.intermine.bio.webservice.AbstractRegionExportService
                • org.intermine.bio.webservice.GenomicRegionBedService
                • org.intermine.bio.webservice.GenomicRegionFastaService
                • org.intermine.bio.webservice.GenomicRegionGFF3Service
      • org.intermine.webservice.server.complexes.ExportService
      • org.intermine.bio.webservice.ExternalLinksService
  • org.intermine.bio.web.XRef

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.intermine.bio.web.biojava.BioSequenceFactory.SequenceType