Hierarchy For All Packages

Package Hierarchies:

• org.jbei.auth,
• org.jbei.auth.hmac,
• org.jbei.ice,
• org.jbei.ice.lib.access,
• org.jbei.ice.lib.account,
• org.jbei.ice.lib.account.authentication,
• org.jbei.ice.lib.bulkupload,
• org.jbei.ice.lib.common.logging,
• org.jbei.ice.lib.config,
• org.jbei.ice.lib.dto,
• org.jbei.ice.lib.dto.access,
• org.jbei.ice.lib.dto.bulkupload,
• org.jbei.ice.lib.dto.comment,
• org.jbei.ice.lib.dto.common,
• org.jbei.ice.lib.dto.entry,
• org.jbei.ice.lib.dto.folder,
• org.jbei.ice.lib.dto.group,
• org.jbei.ice.lib.dto.message,
• org.jbei.ice.lib.dto.sample,
• org.jbei.ice.lib.dto.search,
• org.jbei.ice.lib.dto.user,
• org.jbei.ice.lib.dto.web,
• org.jbei.ice.lib.email,
• org.jbei.ice.lib.entry,
• org.jbei.ice.lib.entry.attachment,
• org.jbei.ice.lib.entry.sample,
• org.jbei.ice.lib.entry.sequence,
• org.jbei.ice.lib.entry.sequence.annotation,
• org.jbei.ice.lib.entry.sequence.composers,
• org.jbei.ice.lib.entry.sequence.composers.formatters,
• org.jbei.ice.lib.entry.sequence.composers.pigeon,
• org.jbei.ice.lib.executor,
• org.jbei.ice.lib.experiment,
• org.jbei.ice.lib.folder,
• org.jbei.ice.lib.folder.collection,
• org.jbei.ice.lib.group,
• org.jbei.ice.lib.manuscript,
• org.jbei.ice.lib.message,
• org.jbei.ice.lib.net,
• org.jbei.ice.lib.parsers,
• org.jbei.ice.lib.parsers.abi,
• org.jbei.ice.lib.parsers.bl2seq,
• org.jbei.ice.lib.parsers.fasta,
• org.jbei.ice.lib.parsers.genbank,
• org.jbei.ice.lib.parsers.sbol,
• org.jbei.ice.lib.search,
• org.jbei.ice.lib.search.blast,
• org.jbei.ice.lib.search.filter,
• org.jbei.ice.lib.shared,
• org.jbei.ice.lib.utils,
• org.jbei.ice.services.rest,
• org.jbei.ice.services.rest.multipart,
• org.jbei.ice.servlet,
• org.jbei.ice.servlet.filter,
• org.jbei.ice.storage,
• org.jbei.ice.storage.hibernate,
• org.jbei.ice.storage.hibernate.bridge,
• org.jbei.ice.storage.hibernate.dao,
• org.jbei.ice.storage.hibernate.filter,
• org.jbei.ice.storage.hibernate.search,
• org.jbei.ice.storage.model

Class Hierarchy

• java.lang.Object
  • org.jbei.ice.lib.parsers.ABIParser
  • org.jbei.ice.lib.parsers.abi.ABITrace
  • org.jbei.ice.lib.folder.AbstractFolder (implements java.lang.Comparable<T>, org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.bulkupload.BulkUploadInfo
    • org.jbei.ice.lib.dto.folder.FolderDetails
  • org.jbei.ice.lib.entry.sequence.composers.formatters.AbstractFormatter (implements org.jbei.ice.lib.entry.sequence.composers.formatters.IFormatter)
    • org.jbei.ice.lib.entry.sequence.composers.formatters.FastaFormatter
    • org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
    • org.jbei.ice.lib.entry.sequence.composers.formatters.SBOL2Formatter
    • org.jbei.ice.lib.entry.sequence.composers.formatters.SBOLFormatter
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • org.jbei.auth.MemoryKeyTable (implements org.jbei.auth.KeyTable)
  • org.jbei.ice.lib.dto.access.AccessKey (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.access.AccessPermission (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.access.RemoteAccessPermission
  • org.jbei.ice.lib.access.AccessTokens
  • org.jbei.ice.storage.model.Account (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.account.AccountController
  • org.jbei.ice.storage.model.AccountPreferences (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.dto.AccountResults (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.account.Accounts
  • org.jbei.ice.lib.account.AccountTransfer (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.account.AccountUtils
  • org.jbei.ice.storage.model.AnnotationLocation (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.entry.sequence.annotation.Annotations
  • org.jbei.ice.storage.model.ApiKey (implements org.jbei.ice.storage.DataModel)
  • javax.ws.rs.core.Application
    • org.jbei.ice.services.rest.multipart.IceApplication
  • org.jbei.ice.ApplicationInitialize
  • org.jbei.ice.lib.dto.entry.ArabidopsisSeedData (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.services.rest.ArrayDataJSONHandler (implements javax.ws.rs.ext.MessageBodyReader<T>, javax.ws.rs.ext.MessageBodyWriter<T>)
  • org.jbei.ice.storage.model.Attachment (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.dto.entry.AttachmentInfo (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.entry.attachment.Attachments
  • org.jbei.ice.storage.model.Audit (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.services.rest.AuthenticationInterceptor (implements javax.ws.rs.container.ContainerRequestFilter, javax.ws.rs.ext.ReaderInterceptor)
  • org.jbei.ice.lib.access.Authorization<T>
    • org.jbei.ice.lib.bulkupload.BulkUploadAuthorization
    • org.jbei.ice.lib.entry.EntryAuthorization
    • org.jbei.ice.lib.dto.folder.FolderAuthorization
    • org.jbei.ice.lib.entry.sample.SampleAuthorization
  • org.jbei.ice.lib.dto.entry.AutoCompleteFieldValues
  • org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
  • org.jbei.ice.lib.search.blast.BlastPlus
  • org.jbei.ice.lib.dto.search.BlastQuery (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.bulkupload.BulkCSVUpload
    • org.jbei.ice.lib.bulkupload.BulkZipUpload
  • org.jbei.ice.lib.bulkupload.BulkCSVUploadHeaders
  • org.jbei.ice.lib.bulkupload.BulkEntryCreator
  • org.jbei.ice.lib.bulkupload.BulkFileSBOLUpload
  • org.jbei.ice.storage.model.BulkUpload (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.bulkupload.BulkUploadController
  • org.jbei.ice.lib.bulkupload.BulkUploadValidation
  • org.jbei.ice.lib.entry.sequence.ByteArrayWrapper
  • org.jbei.ice.lib.folder.collection.Collection
  • org.jbei.ice.lib.folder.CollectionCounts (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.folder.collection.CollectionEntries
  • org.jbei.ice.lib.folder.collection.Collections
  • org.jbei.ice.storage.model.Comment (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.storage.model.Configuration (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.config.ConfigurationController
  • org.jbei.ice.lib.dto.Curation (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.entry.CustomField (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.entry.CustomFields
  • org.jbei.ice.storage.DAOFactory
  • org.jbei.auth.hmac.DefaultHmacSignature (implements org.jbei.auth.hmac.HmacSignature)
  • org.jbei.ice.lib.dto.DNAFeature (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.bulkupload.DNAFeatureComparator (implements java.util.Comparator<T>)
  • org.jbei.ice.lib.dto.DNAFeatureLocation (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.DNAFeatureNote (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.DNAFeatures (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.DNASequence (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.FeaturedDNASequence
  • org.jbei.ice.lib.email.Email
    • org.jbei.ice.lib.email.CustomEmail
    • org.jbei.ice.lib.email.GMail
  • org.jbei.ice.lib.email.EmailFactory
  • org.jbei.ice.lib.entry.EntriesAsCSV
  • org.jbei.ice.storage.model.Entry (implements org.jbei.ice.storage.DataModel)
    • org.jbei.ice.storage.model.ArabidopsisSeed
    • org.jbei.ice.storage.model.Part
    • org.jbei.ice.storage.model.Plasmid
    • org.jbei.ice.storage.model.Strain
  • org.jbei.ice.storage.hibernate.bridge.EntryBooleanPropertiesBridge (implements org.hibernate.search.bridge.FieldBridge, org.hibernate.search.bridge.ParameterizedBridge)
  • org.jbei.ice.lib.entry.EntryFactory
  • org.jbei.ice.lib.entry.EntryFields
  • org.jbei.ice.storage.hibernate.filter.EntryHasFilterFactory
  • org.jbei.ice.lib.bulkupload.EntryHeaderValue (implements org.jbei.ice.lib.bulkupload.HeaderValue)
  • org.jbei.ice.lib.entry.EntryHistory
  • org.jbei.ice.storage.hibernate.filter.EntrySecurityFilterFactory
  • org.jbei.ice.lib.entry.EntrySelection (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.entry.EntryUtil
  • org.jbei.ice.services.rest.ErrorResponse (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.storage.model.Experiment (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.services.rest.ExtensionToMimeType
  • org.jbei.ice.storage.model.Feature (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.storage.model.FeatureCurationModel (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.dto.search.FieldFilter (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.bulkupload.FileBulkUpload
  • org.jbei.ice.storage.model.Folder (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.folder.FolderContents
  • org.jbei.ice.lib.folder.FolderController
  • org.jbei.ice.lib.folder.FolderPermissions
  • org.jbei.ice.lib.folder.Folders
  • org.jbei.ice.lib.parsers.genbank.GenbankLocation
  • org.jbei.ice.lib.parsers.GeneralParser
  • javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
    • javax.servlet.http.HttpServlet
      • org.jbei.ice.servlet.SBOLVisualDownloadServlet
  • org.jbei.ice.storage.model.Group (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.group.GroupController
  • org.jbei.ice.lib.group.Groups
  • org.jbei.ice.lib.entry.HasEntry
    • org.jbei.ice.lib.parsers.AbstractParser
      • org.jbei.ice.lib.parsers.fasta.FastaParser
      • org.jbei.ice.lib.parsers.genbank.GenBankParser
      • org.jbei.ice.lib.parsers.PlainParser
      • org.jbei.ice.lib.parsers.sbol.SBOLParser
    • org.jbei.ice.lib.entry.Entries
    • org.jbei.ice.lib.entry.EntryController
    • org.jbei.ice.lib.entry.EntryCreator
    • org.jbei.ice.lib.entry.EntryFolders
    • org.jbei.ice.lib.entry.EntryLinks
    • org.jbei.ice.lib.experiment.Experiments
    • org.jbei.ice.lib.entry.sequence.PartSequence
    • org.jbei.ice.lib.access.Permissions
      • org.jbei.ice.lib.entry.EntryPermissions
    • org.jbei.ice.lib.entry.sample.SampleService
    • org.jbei.ice.lib.entry.sequence.SequenceController
  • org.jbei.ice.lib.dto.entry.HasEntryData (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.search.SearchResult
  • org.jbei.ice.services.rest.Headers
  • org.jbei.ice.storage.hibernate.HibernateRepository<T> (implements org.jbei.ice.storage.IRepository<T>)
    • org.jbei.ice.storage.hibernate.dao.AccountDAO
    • org.jbei.ice.storage.hibernate.dao.ApiKeyDAO
    • org.jbei.ice.storage.hibernate.dao.AttachmentDAO
    • org.jbei.ice.storage.hibernate.dao.AuditDAO
    • org.jbei.ice.storage.hibernate.dao.BulkUploadDAO
    • org.jbei.ice.storage.hibernate.dao.CommentDAO
    • org.jbei.ice.storage.hibernate.dao.ConfigurationDAO
    • org.jbei.ice.storage.hibernate.dao.EntryDAO
    • org.jbei.ice.storage.hibernate.dao.ExperimentDAO
    • org.jbei.ice.storage.hibernate.dao.FeatureCurationModelDAO
    • org.jbei.ice.storage.hibernate.dao.FeatureDAO
    • org.jbei.ice.storage.hibernate.dao.FolderDAO
    • org.jbei.ice.storage.hibernate.dao.GroupDAO
    • org.jbei.ice.storage.hibernate.dao.ManuscriptModelDAO
    • org.jbei.ice.storage.hibernate.dao.MessageDAO
    • org.jbei.ice.storage.hibernate.dao.ParameterDAO
    • org.jbei.ice.storage.hibernate.dao.PermissionDAO
    • org.jbei.ice.storage.hibernate.dao.PreferencesDAO
    • org.jbei.ice.storage.hibernate.dao.RemoteAccessModelDAO
    • org.jbei.ice.storage.hibernate.dao.RemoteClientModelDAO
    • org.jbei.ice.storage.hibernate.dao.RemotePartnerDAO
    • org.jbei.ice.storage.hibernate.dao.RemoteShareModelDAO
    • org.jbei.ice.storage.hibernate.dao.RequestDAO
    • org.jbei.ice.storage.hibernate.dao.SampleDAO
    • org.jbei.ice.storage.hibernate.dao.SelectionMarkerDAO
    • org.jbei.ice.storage.hibernate.dao.SequenceDAO
    • org.jbei.ice.storage.hibernate.dao.SequenceFeatureDAO
    • org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
    • org.jbei.ice.storage.hibernate.dao.StorageDAO
    • org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO
  • org.jbei.ice.storage.hibernate.search.HibernateSearch
  • org.jbei.ice.storage.hibernate.HibernateUtil
  • org.jbei.ice.lib.dto.History (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.auth.hmac.HmacAuthorizor
  • org.jbei.auth.hmac.HmacSignatureFactory
  • org.jbei.ice.services.rest.ICEExceptionMapper (implements javax.ws.rs.ext.ExceptionMapper<E>)
  • org.jbei.ice.lib.executor.IceExecutorService
  • org.jbei.ice.servlet.filter.IceFilter (implements javax.servlet.Filter)
  • org.jbei.ice.services.rest.IceRequestFilter (implements javax.ws.rs.container.ContainerRequestFilter)
  • org.jbei.ice.services.rest.IceResponseFilter (implements javax.ws.rs.container.ContainerResponseFilter)
  • org.jbei.ice.lib.entry.sequence.composers.formatters.IceSequenceOntology
  • org.jbei.ice.servlet.IceServletContextListener (implements javax.servlet.ServletContextListener)
  • org.jbei.ice.lib.search.IndexBuildStatus (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.search.IndexerProgressMonitor (implements org.hibernate.search.batchindexing.MassIndexerProgressMonitor)
  • org.jbei.ice.servlet.InfoToModelFactory
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • org.jbei.auth.hmac.HmacInputStream
  • org.jbei.ice.lib.account.authentication.LblLdapAuthentication (implements org.jbei.ice.lib.account.authentication.IAuthentication)
  • org.jbei.ice.storage.model.Link (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.account.authentication.LocalAuthentication (implements org.jbei.ice.lib.account.authentication.IAuthentication)
  • org.jbei.ice.lib.common.logging.Logger
  • org.jbei.ice.lib.manuscript.Manuscript (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.storage.model.ManuscriptModel (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.manuscript.Manuscripts
  • org.jbei.ice.storage.model.Message (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.dto.message.MessageInfo (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.message.Messages
  • org.jbei.ice.storage.ModelToInfoFactory
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • java.io.FilterOutputStream
      • org.jbei.auth.hmac.HmacOutputStream
  • org.jbei.ice.lib.entry.OwnerEntries
  • org.jbei.ice.lib.utils.PackageAssembler
  • org.jbei.ice.lib.dto.common.PageParameters
  • org.jbei.ice.storage.model.Parameter (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.dto.entry.ParsedEntryId (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.entry.PartData (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.services.rest.PartDataJSONHandler (implements javax.ws.rs.ext.MessageBodyReader<T>, javax.ws.rs.ext.MessageBodyWriter<T>)
  • org.jbei.ice.lib.entry.PartDataUtil
  • org.jbei.ice.lib.entry.PartDefaults
  • org.jbei.ice.lib.dto.entry.PartInformation (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.web.PartnerEntries (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.sample.PartSample (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.entry.PartStatistics (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.bulkupload.PartWithSample
  • org.jbei.ice.storage.model.Permission (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.access.PermissionEntryBridge (implements org.hibernate.search.bridge.FieldBridge)
  • org.jbei.ice.lib.access.PermissionsController
  • org.jbei.ice.lib.entry.sequence.composers.pigeon.PigeonSBOLv
  • org.jbei.ice.lib.dto.entry.PlasmidData (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.storage.model.Preference (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.dto.bulkupload.PreferenceInfo (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.account.PreferencesController
  • org.jbei.ice.lib.bulkupload.ProcessedBulkUpload (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.web.RegistryPartner (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.access.RemoteAccess
  • org.jbei.ice.storage.model.RemoteAccessModel (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.storage.model.RemoteClientModel (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.net.RemoteContact
  • org.jbei.ice.lib.net.RemoteEntries
  • org.jbei.ice.lib.net.RemoteEntriesAsCSV
  • org.jbei.ice.lib.net.RemoteEntry
  • org.jbei.ice.lib.net.RemoteFolder
  • org.jbei.ice.lib.net.RemoteFolders
  • org.jbei.ice.storage.model.RemotePartner (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.net.RemoteSequence
  • org.jbei.ice.storage.model.RemoteShareModel (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.net.RemoteTransfer
  • org.jbei.ice.lib.dto.web.RemoteUser (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.web.RemoteUsers
  • org.jbei.ice.storage.model.Request (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.entry.sample.RequestRetriever
  • org.jbei.ice.services.rest.RestClient
    • org.jbei.ice.services.rest.IceRestClient
  • org.jbei.ice.services.rest.RestResource
    • org.jbei.ice.services.rest.AccessTokenResource
    • org.jbei.ice.services.rest.AnnotationResource
    • org.jbei.ice.services.rest.ApiKeyResource
    • org.jbei.ice.services.rest.BulkUploadResource
    • org.jbei.ice.services.rest.CollectionResource
    • org.jbei.ice.services.rest.ConfigResource
    • org.jbei.ice.services.rest.CustomFieldResource
    • org.jbei.ice.services.rest.FileResource
    • org.jbei.ice.services.rest.FolderResource
    • org.jbei.ice.services.rest.GroupResource
    • org.jbei.ice.services.rest.ManuscriptResource
    • org.jbei.ice.services.rest.MessageResource
    • org.jbei.ice.services.rest.PartnerResource
    • org.jbei.ice.services.rest.PartResource
    • org.jbei.ice.services.rest.PermissionResource
    • org.jbei.ice.services.rest.SampleResource
    • org.jbei.ice.services.rest.SearchResource
    • org.jbei.ice.services.rest.UserResource
    • org.jbei.ice.services.rest.WebResource
  • org.jbei.ice.lib.dto.common.Results<T> (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.storage.model.Sample (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.entry.sample.SampleCreator
  • org.jbei.ice.lib.bulkupload.SampleHeaderValue (implements org.jbei.ice.lib.bulkupload.HeaderValue)
  • org.jbei.ice.lib.dto.sample.SampleRequest (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.entry.sequence.composers.formatters.SBOL2Visitor
  • org.sbolstandard.core.util.SBOLBaseVisitor<T> (implements org.sbolstandard.core.SBOLVisitor<T>)
    • org.jbei.ice.lib.parsers.sbol.ICESBOLParserVisitor
  • org.jbei.ice.lib.entry.sequence.composers.formatters.SBOLVisitor
  • org.jbei.ice.lib.search.SearchController
  • org.jbei.ice.lib.search.filter.SearchFieldFactory
  • org.jbei.ice.lib.dto.search.SearchQuery (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.search.SearchQuery.Parameters (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.search.SearchResults (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.storage.model.SelectionMarker (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.storage.model.Sequence (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.entry.sequence.SequenceAnalysisController
  • org.jbei.ice.storage.model.SequenceFeature (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.storage.model.SequenceFeatureAttribute (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.entry.sequence.composers.formatters.SequenceFeatureComparator (implements java.util.Comparator<T>)
  • org.jbei.ice.lib.dto.entry.SequenceInfo (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.utils.SequenceUtils
  • org.jbei.ice.lib.dto.Setting (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.entry.SharedEntries
  • org.jbei.ice.storage.model.ShotgunSequence (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.dto.ShotgunSequenceDTO (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.config.SiteSettings (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.storage.model.Storage (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.dto.StorageLocation (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.entry.StrainData (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.experiment.Study (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.parsers.genbank.Tag
    • org.jbei.ice.lib.parsers.genbank.FeaturesTag
    • org.jbei.ice.lib.parsers.genbank.OriginTag
    • org.jbei.ice.lib.parsers.genbank.ReferenceTag
  • org.jbei.ice.lib.executor.Task
    • org.jbei.ice.lib.entry.sequence.annotation.AutoAnnotationBlastDbBuildTask
    • org.jbei.ice.lib.bulkupload.BulkUploadDeleteTask
    • org.jbei.ice.lib.entry.EntryPermissionTask
    • org.jbei.ice.lib.search.blast.RebuildBlastIndexTask
    • org.jbei.ice.lib.search.RebuildLuceneIndexTask
    • org.jbei.ice.lib.executor.TransferTask
    • org.jbei.ice.lib.net.WebOfRegistriesTask
    • org.jbei.ice.lib.search.WebSearch.SearchTask
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.jbei.ice.lib.account.authentication.AuthenticationException
      • org.jbei.ice.lib.search.blast.BlastException
      • org.jbei.ice.lib.entry.sequence.composers.formatters.FormatterException
      • org.jbei.ice.lib.account.authentication.InvalidCredentialsException
      • org.jbei.ice.lib.parsers.InvalidFormatParserException
      • org.jbei.ice.lib.search.blast.ProgramTookTooLongException
      • java.lang.RuntimeException
        • org.jbei.ice.lib.access.AuthorizationException
        • org.jbei.ice.storage.DAOException
        • org.jbei.ice.lib.access.PermissionException
      • org.jbei.ice.lib.utils.UtilityException
  • org.jbei.ice.lib.account.TokenHash
  • org.jbei.ice.lib.access.TokenVerification
  • org.jbei.ice.storage.model.TraceSequence (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.storage.model.TraceSequenceAlignment (implements org.jbei.ice.storage.DataModel)
  • org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.entry.sequence.TraceSequences
  • org.jbei.ice.lib.net.TransferredParts
  • org.jbei.ice.lib.account.UserApiKeys
  • org.jbei.ice.lib.dto.comment.UserComment (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.folder.UserFolder
  • org.jbei.ice.lib.dto.group.UserGroup (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.account.authentication.UserIdAuthentication (implements org.jbei.ice.lib.account.authentication.IAuthentication)
  • org.jbei.ice.lib.dto.user.UserPreferences (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.dto.sample.UserSamples (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.account.UserSessions
  • org.jbei.ice.lib.utils.Utils
  • org.jbei.ice.lib.entry.VisibleEntries
  • org.jbei.ice.lib.dto.web.WebEntries
  • org.jbei.ice.lib.dto.web.WebOfRegistries (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.net.WebPartners
  • org.jbei.ice.lib.search.WebResult (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.search.WebSearch
  • org.jbei.ice.lib.search.WebSearchResults (implements org.jbei.ice.storage.IDataTransferModel)
  • org.jbei.ice.lib.net.WoRController

Interface Hierarchy

• org.jbei.auth.Authorization
• org.jbei.ice.storage.DataModel
• org.jbei.ice.lib.bulkupload.HeaderValue
• org.jbei.auth.hmac.HmacSignature
• org.jbei.ice.lib.account.authentication.IAuthentication
• org.jbei.ice.lib.entry.sequence.composers.formatters.IFormatter
• org.jbei.ice.storage.IRepository<T>
• org.jbei.auth.KeyTable
• java.io.Serializable
  • org.jbei.ice.storage.IDataTransferModel

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.jbei.ice.lib.executor.TaskStatus
    • org.jbei.ice.lib.shared.BioSafetyOption (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.shared.StatusType
    • org.jbei.ice.lib.shared.ColumnField (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.folder.collection.CollectionType
    • org.jbei.ice.lib.bulkupload.BulkUploadStatus (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.manuscript.ManuscriptStatus
    • org.jbei.ice.lib.account.AccountType (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.entry.LinkType
    • org.jbei.ice.lib.entry.EntrySelectionType
    • org.jbei.ice.lib.entry.sequence.SequenceFormat
    • org.jbei.ice.lib.search.QueryType
    • org.jbei.ice.lib.message.MessageStatus
    • org.jbei.ice.lib.access.Article
    • org.jbei.ice.lib.access.AccessType
    • org.jbei.ice.lib.access.AccessStatus
    • org.jbei.ice.lib.email.Type
    • org.jbei.ice.lib.dto.ConfigurationKey (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.AuditType
    • org.jbei.ice.lib.dto.folder.FolderType (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.user.PreferenceKey
    • org.jbei.ice.lib.dto.bulkupload.EditMode (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.bulkupload.SampleField
    • org.jbei.ice.lib.dto.sample.SampleRequestType (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.sample.SampleType
    • org.jbei.ice.lib.dto.sample.SampleRequestStatus (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.group.GroupType
    • org.jbei.ice.lib.dto.entry.PlantType (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.entry.EntryField (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.entry.AutoCompleteField
    • org.jbei.ice.lib.dto.entry.Generation (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.entry.EntryType
    • org.jbei.ice.lib.dto.entry.Visibility
    • org.jbei.ice.lib.dto.search.SearchBoostField
    • org.jbei.ice.lib.dto.search.BlastProgram (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.search.IndexType (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.web.RemotePartnerStatus (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.access.AccessPermission.Type (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.dto.access.AccessPermission.Article (implements org.jbei.ice.storage.IDataTransferModel)
    • org.jbei.ice.lib.parsers.genbank.Tag.Type
    • org.jbei.ice.storage.model.Storage.StorageType
    • org.jbei.ice.storage.model.Part.AssemblyStandard
    • org.jbei.ice.storage.model.SequenceFeature.AnnotationType