Hierarchy For All Packages

Package Hierarchies:

• ca.corefacility.bioinformatics.irida,
• ca.corefacility.bioinformatics.irida.config.analysis,
• ca.corefacility.bioinformatics.irida.config.data,
• ca.corefacility.bioinformatics.irida.config.environment,
• ca.corefacility.bioinformatics.irida.config.repository,
• ca.corefacility.bioinformatics.irida.config.security,
• ca.corefacility.bioinformatics.irida.config.services,
• ca.corefacility.bioinformatics.irida.config.services.scheduled,
• ca.corefacility.bioinformatics.irida.config.web,
• ca.corefacility.bioinformatics.irida.config.workflow,
• ca.corefacility.bioinformatics.irida.constraints,
• ca.corefacility.bioinformatics.irida.constraints.impl,
• ca.corefacility.bioinformatics.irida.database.changesets,
• ca.corefacility.bioinformatics.irida.events,
• ca.corefacility.bioinformatics.irida.events.annotations,
• ca.corefacility.bioinformatics.irida.exceptions,
• ca.corefacility.bioinformatics.irida.exceptions.galaxy,
• ca.corefacility.bioinformatics.irida.exceptions.pipelines,
• ca.corefacility.bioinformatics.irida.jackson2.mixin,
• ca.corefacility.bioinformatics.irida.model,
• ca.corefacility.bioinformatics.irida.model.announcements,
• ca.corefacility.bioinformatics.irida.model.assembly,
• ca.corefacility.bioinformatics.irida.model.enums,
• ca.corefacility.bioinformatics.irida.model.event,
• ca.corefacility.bioinformatics.irida.model.export,
• ca.corefacility.bioinformatics.irida.model.irida,
• ca.corefacility.bioinformatics.irida.model.joins,
• ca.corefacility.bioinformatics.irida.model.joins.impl,
• ca.corefacility.bioinformatics.irida.model.project,
• ca.corefacility.bioinformatics.irida.model.remote,
• ca.corefacility.bioinformatics.irida.model.remote.resource,
• ca.corefacility.bioinformatics.irida.model.run,
• ca.corefacility.bioinformatics.irida.model.sample,
• ca.corefacility.bioinformatics.irida.model.sample.metadata,
• ca.corefacility.bioinformatics.irida.model.sequenceFile,
• ca.corefacility.bioinformatics.irida.model.subscription,
• ca.corefacility.bioinformatics.irida.model.upload,
• ca.corefacility.bioinformatics.irida.model.upload.galaxy,
• ca.corefacility.bioinformatics.irida.model.user,
• ca.corefacility.bioinformatics.irida.model.user.group,
• ca.corefacility.bioinformatics.irida.model.workflow,
• ca.corefacility.bioinformatics.irida.model.workflow.analysis,
• ca.corefacility.bioinformatics.irida.model.workflow.analysis.type,
• ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.config,
• ca.corefacility.bioinformatics.irida.model.workflow.config,
• ca.corefacility.bioinformatics.irida.model.workflow.description,
• ca.corefacility.bioinformatics.irida.model.workflow.execution,
• ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy,
• ca.corefacility.bioinformatics.irida.model.workflow.manager,
• ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy,
• ca.corefacility.bioinformatics.irida.model.workflow.structure,
• ca.corefacility.bioinformatics.irida.model.workflow.submission,
• ca.corefacility.bioinformatics.irida.oauth2,
• ca.corefacility.bioinformatics.irida.pipeline.results,
• ca.corefacility.bioinformatics.irida.pipeline.results.impl,
• ca.corefacility.bioinformatics.irida.pipeline.results.updater,
• ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl,
• ca.corefacility.bioinformatics.irida.pipeline.upload,
• ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy,
• ca.corefacility.bioinformatics.irida.plugins,
• ca.corefacility.bioinformatics.irida.processing,
• ca.corefacility.bioinformatics.irida.processing.concatenate,
• ca.corefacility.bioinformatics.irida.processing.concatenate.impl,
• ca.corefacility.bioinformatics.irida.processing.impl,
• ca.corefacility.bioinformatics.irida.repositories,
• ca.corefacility.bioinformatics.irida.repositories.analysis,
• ca.corefacility.bioinformatics.irida.repositories.analysis.submission,
• ca.corefacility.bioinformatics.irida.repositories.assembly,
• ca.corefacility.bioinformatics.irida.repositories.filesystem,
• ca.corefacility.bioinformatics.irida.repositories.joins.announcement,
• ca.corefacility.bioinformatics.irida.repositories.joins.project,
• ca.corefacility.bioinformatics.irida.repositories.joins.sample,
• ca.corefacility.bioinformatics.irida.repositories.referencefile,
• ca.corefacility.bioinformatics.irida.repositories.relational.auditing,
• ca.corefacility.bioinformatics.irida.repositories.remote,
• ca.corefacility.bioinformatics.irida.repositories.remote.impl,
• ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate,
• ca.corefacility.bioinformatics.irida.repositories.sample,
• ca.corefacility.bioinformatics.irida.repositories.sequencefile,
• ca.corefacility.bioinformatics.irida.repositories.specification,
• ca.corefacility.bioinformatics.irida.repositories.user,
• ca.corefacility.bioinformatics.irida.ria.config,
• ca.corefacility.bioinformatics.irida.ria.config.filters,
• ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker,
• ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor,
• ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util,
• ca.corefacility.bioinformatics.irida.ria.security,
• ca.corefacility.bioinformatics.irida.ria.utilities,
• ca.corefacility.bioinformatics.irida.ria.utilities.components,
• ca.corefacility.bioinformatics.irida.ria.utilities.converters,
• ca.corefacility.bioinformatics.irida.ria.web,
• ca.corefacility.bioinformatics.irida.ria.web.activities,
• ca.corefacility.bioinformatics.irida.ria.web.activities.dto,
• ca.corefacility.bioinformatics.irida.ria.web.admin,
• ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics,
• ca.corefacility.bioinformatics.irida.ria.web.ajax,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.dto,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.ontologies,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.projects,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.exceptions,
• ca.corefacility.bioinformatics.irida.ria.web.ajax.users,
• ca.corefacility.bioinformatics.irida.ria.web.analyses,
• ca.corefacility.bioinformatics.irida.ria.web.analysis,
• ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing,
• ca.corefacility.bioinformatics.irida.ria.web.analysis.dto,
• ca.corefacility.bioinformatics.irida.ria.web.announcements,
• ca.corefacility.bioinformatics.irida.ria.web.announcements.dto,
• ca.corefacility.bioinformatics.irida.ria.web.cart,
• ca.corefacility.bioinformatics.irida.ria.web.cart.dto,
• ca.corefacility.bioinformatics.irida.ria.web.components,
• ca.corefacility.bioinformatics.irida.ria.web.components.agGrid,
• ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification,
• ca.corefacility.bioinformatics.irida.ria.web.components.ant.table,
• ca.corefacility.bioinformatics.irida.ria.web.components.datatables,
• ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config,
• ca.corefacility.bioinformatics.irida.ria.web.components.datatables.export,
• ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models,
• ca.corefacility.bioinformatics.irida.ria.web.dto,
• ca.corefacility.bioinformatics.irida.ria.web.dto.list,
• ca.corefacility.bioinformatics.irida.ria.web.errors,
• ca.corefacility.bioinformatics.irida.ria.web.exceptions,
• ca.corefacility.bioinformatics.irida.ria.web.files,
• ca.corefacility.bioinformatics.irida.ria.web.files.dto,
• ca.corefacility.bioinformatics.irida.ria.web.launchPipeline,
• ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos,
• ca.corefacility.bioinformatics.irida.ria.web.linelist,
• ca.corefacility.bioinformatics.irida.ria.web.linelist.dto,
• ca.corefacility.bioinformatics.irida.ria.web.login,
• ca.corefacility.bioinformatics.irida.ria.web.models,
• ca.corefacility.bioinformatics.irida.ria.web.models.datatables,
• ca.corefacility.bioinformatics.irida.ria.web.models.export,
• ca.corefacility.bioinformatics.irida.ria.web.models.project,
• ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile,
• ca.corefacility.bioinformatics.irida.ria.web.models.tables,
• ca.corefacility.bioinformatics.irida.ria.web.models.user,
• ca.corefacility.bioinformatics.irida.ria.web.oauth,
• ca.corefacility.bioinformatics.irida.ria.web.pipelines,
• ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto,
• ca.corefacility.bioinformatics.irida.ria.web.projects,
• ca.corefacility.bioinformatics.irida.ria.web.projects.dto,
• ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples,
• ca.corefacility.bioinformatics.irida.ria.web.projects.error,
• ca.corefacility.bioinformatics.irida.ria.web.projects.metadata,
• ca.corefacility.bioinformatics.irida.ria.web.projects.settings,
• ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto,
• ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto,
• ca.corefacility.bioinformatics.irida.ria.web.samples,
• ca.corefacility.bioinformatics.irida.ria.web.samples.dto,
• ca.corefacility.bioinformatics.irida.ria.web.search,
• ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns,
• ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto,
• ca.corefacility.bioinformatics.irida.ria.web.services,
• ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs,
• ca.corefacility.bioinformatics.irida.ria.web.settings,
• ca.corefacility.bioinformatics.irida.ria.web.settings.dto,
• ca.corefacility.bioinformatics.irida.ria.web.users,
• ca.corefacility.bioinformatics.irida.ria.web.users.dto,
• ca.corefacility.bioinformatics.irida.ria.web.utilities,
• ca.corefacility.bioinformatics.irida.security,
• ca.corefacility.bioinformatics.irida.security.permissions,
• ca.corefacility.bioinformatics.irida.security.permissions.analysis,
• ca.corefacility.bioinformatics.irida.security.permissions.files,
• ca.corefacility.bioinformatics.irida.security.permissions.metadata,
• ca.corefacility.bioinformatics.irida.security.permissions.project,
• ca.corefacility.bioinformatics.irida.security.permissions.sample,
• ca.corefacility.bioinformatics.irida.security.permissions.user,
• ca.corefacility.bioinformatics.irida.service,
• ca.corefacility.bioinformatics.irida.service.analysis.annotations,
• ca.corefacility.bioinformatics.irida.service.analysis.execution,
• ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy,
• ca.corefacility.bioinformatics.irida.service.analysis.workspace,
• ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy,
• ca.corefacility.bioinformatics.irida.service.export,
• ca.corefacility.bioinformatics.irida.service.impl,
• ca.corefacility.bioinformatics.irida.service.impl.analysis.submission,
• ca.corefacility.bioinformatics.irida.service.impl.export,
• ca.corefacility.bioinformatics.irida.service.impl.processor,
• ca.corefacility.bioinformatics.irida.service.impl.sample,
• ca.corefacility.bioinformatics.irida.service.impl.user,
• ca.corefacility.bioinformatics.irida.service.impl.workflow,
• ca.corefacility.bioinformatics.irida.service.remote,
• ca.corefacility.bioinformatics.irida.service.remote.impl,
• ca.corefacility.bioinformatics.irida.service.sample,
• ca.corefacility.bioinformatics.irida.service.user,
• ca.corefacility.bioinformatics.irida.service.util,
• ca.corefacility.bioinformatics.irida.service.util.impl,
• ca.corefacility.bioinformatics.irida.service.workflow,
• ca.corefacility.bioinformatics.irida.util,
• ca.corefacility.bioinformatics.irida.validators,
• ca.corefacility.bioinformatics.irida.validators.annotations,
• ca.corefacility.bioinformatics.irida.validators.annotations.validators,
• ca.corefacility.bioinformatics.irida.validators.groups,
• ca.corefacility.bioinformatics.irida.web.assembler.resource,
• ca.corefacility.bioinformatics.irida.web.assembler.resource.sample,
• ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile,
• ca.corefacility.bioinformatics.irida.web.controller.api,
• ca.corefacility.bioinformatics.irida.web.controller.api.exception,
• ca.corefacility.bioinformatics.irida.web.controller.api.json,
• ca.corefacility.bioinformatics.irida.web.controller.api.projects,
• ca.corefacility.bioinformatics.irida.web.controller.api.samples,
• ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun,
• ca.corefacility.bioinformatics.irida.web.filter,
• ca.corefacility.bioinformatics.irida.web.spring.view

Class Hierarchy

• java.lang.Object
  • ca.corefacility.bioinformatics.irida.database.changesets.AbsoluteToRelativePaths (implements liquibase.change.custom.CustomSqlChange)
  • org.springframework.security.web.authentication.AbstractAuthenticationTargetUrlRequestHandler
    • org.springframework.security.web.authentication.SimpleUrlAuthenticationSuccessHandler (implements org.springframework.security.web.authentication.AuthenticationSuccessHandler)
      • org.springframework.security.web.authentication.SavedRequestAwareAuthenticationSuccessHandler
        • ca.corefacility.bioinformatics.irida.ria.security.LoginSuccessHandler
  • org.springframework.security.authentication.AbstractAuthenticationToken (implements org.springframework.security.core.Authentication, org.springframework.security.core.CredentialsContainer)
    • org.springframework.security.oauth2.server.authorization.authentication.OAuth2AuthorizationGrantAuthenticationToken
      • ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationToken
    • org.springframework.security.web.authentication.preauth.PreAuthenticatedAuthenticationToken
      • ca.corefacility.bioinformatics.irida.security.ProjectSynchronizationAuthenticationToken
  • org.thymeleaf.dialect.AbstractDialect (implements org.thymeleaf.dialect.IDialect)
    • org.thymeleaf.dialect.AbstractProcessorDialect (implements org.thymeleaf.dialect.IProcessorDialect)
      • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.WebpackerDialect
  • ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.AbstractExportModel
    • ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel
  • liquibase.AbstractExtensibleObject (implements liquibase.ExtensibleObject)
    • liquibase.resource.AbstractResourceAccessor (implements liquibase.resource.ResourceAccessor)
      • liquibase.integration.spring.SpringResourceAccessor
        • ca.corefacility.bioinformatics.irida.config.data.IridaApiJdbcDataSourceConfig.ApplicationContextAwareSpringLiquibase.ApplicationContextSpringResourceOpener
  • 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)
      • ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs.Cart
      • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleFilesResponse
      • ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata
  • org.thymeleaf.processor.AbstractProcessor (implements org.thymeleaf.processor.IProcessor)
    • org.thymeleaf.processor.element.AbstractElementTagProcessor (implements org.thymeleaf.processor.element.IElementTagProcessor)
      • org.thymeleaf.processor.element.AbstractAttributeTagProcessor
        • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor.WebpackerScriptAttributeTagProcessor
      • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor.WebpackerCSSElementTagProcessor
      • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor.WebpackerJavascriptElementTagProcessor
  • ca.corefacility.bioinformatics.irida.ria.web.activities.ActivitiesAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.activities.dto.ActivityItem
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse
  • ca.corefacility.bioinformatics.irida.ria.web.cart.dto.AddToCartRequest
  • ca.corefacility.bioinformatics.irida.ria.web.admin.AdminBaseController
  • ca.corefacility.bioinformatics.irida.ria.web.admin.AdminStatisticsAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn
    • ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataField
    • ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataFieldDefault
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxResponse
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxCreateItemSuccessResponse
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxErrorResponse
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxFormErrorResponse
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxSuccessResponse
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxUpdateItemSuccessResponse
    • ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSamplesByUserPermissions
    • ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartUpdateResponse
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.CreateNamedParameterSetAjaxResponse
    • ca.corefacility.bioinformatics.irida.ria.web.dto.list.PagedListResponse
    • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse
    • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleFiles
    • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.SavedMetadataErrorResponse
    • ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.StatisticsResponse
    • ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UploadReferenceFilesResponse
    • ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesResponse
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesFilters
  • ca.corefacility.bioinformatics.irida.ria.web.analyses.AnalysesOutputsAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysesTableAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing.AnalysisAudit
  • ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisCollectionServiceGalaxy
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisEmailPipelineResult
  • ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl (implements ca.corefacility.bioinformatics.irida.service.AnalysisExecutionScheduledTask)
  • ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionServiceAspect
  • ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig
  • ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxy (implements ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService)
  • ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync
  • ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyCleanupAsync
  • ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInputFiles
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisJobError
  • ca.corefacility.bioinformatics.irida.ria.web.components.AnalysisOutputFileDownloadManager
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo
  • ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisParameterServiceGalaxy (implements ca.corefacility.bioinformatics.irida.service.analysis.workspace.AnalysisParameterService<WorkflowInputsType>)
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProjectShare
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProvenanceResponse
  • ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisProvenanceServiceGalaxy
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSampleProject
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples
  • ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSistrResults
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisStateModel
  • ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder
  • ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionCleanupServiceImpl (implements ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionCleanupService)
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSubmissionInfo
  • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryCustom)
  • ca.corefacility.bioinformatics.irida.pipeline.results.impl.AnalysisSubmissionSampleProcessorImpl (implements ca.corefacility.bioinformatics.irida.pipeline.results.AnalysisSubmissionSampleProcessor)
  • ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService.AnalysisServiceStatus
  • ca.corefacility.bioinformatics.irida.repositories.specification.AnalysisSubmissionSpecification
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.AnalysisTemplate
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecution
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecutionParameters
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTreeResponse
  • ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTypeModel
  • ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.config.AnalysisTypeSet
  • ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl (implements ca.corefacility.bioinformatics.irida.service.AnalysisTypesService)
  • ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisWorkspaceServiceGalaxy (implements ca.corefacility.bioinformatics.irida.service.analysis.workspace.AnalysisWorkspaceService)
  • ca.corefacility.bioinformatics.irida.ria.config.AnalyticsHandlerInterceptor (implements org.springframework.web.servlet.AsyncHandlerInterceptor)
  • ca.corefacility.bioinformatics.irida.model.announcements.Announcement (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.IridaThing)
  • ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest
  • ca.corefacility.bioinformatics.irida.repositories.specification.AnnouncementSpecification
  • ca.corefacility.bioinformatics.irida.model.announcements.AnnouncementUserJoin (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserReadDetails (implements java.lang.Comparable<T>)
  • ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntPagination
  • ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSearch
  • ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSort
  • ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableItem
    • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSampleTableItem
  • ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableRequest
    • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSamplesTableRequest
  • ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableResponse<T>
  • 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)
        • ca.corefacility.bioinformatics.irida.web.spring.view.CSVView
        • ca.corefacility.bioinformatics.irida.web.spring.view.FastaView
        • ca.corefacility.bioinformatics.irida.web.spring.view.FastqView
        • ca.corefacility.bioinformatics.irida.web.spring.view.GenbankView
        • ca.corefacility.bioinformatics.irida.web.spring.view.NewickFileView
  • ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.AssemblySampleUpdater (implements ca.corefacility.bioinformatics.irida.pipeline.results.updater.AnalysisSampleUpdater)
  • ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.AssociatedProject
  • ca.corefacility.bioinformatics.irida.processing.impl.AutomatedAnalysisFileProcessor (implements ca.corefacility.bioinformatics.irida.processing.FileProcessor)
  • ca.corefacility.bioinformatics.irida.database.changesets.AutomatedAnalysisToTemplate (implements liquibase.change.custom.CustomSqlChange)
  • ca.corefacility.bioinformatics.irida.database.changesets.AutomatedSISTRUpdate (implements liquibase.change.custom.CustomSqlChange)
  • ca.corefacility.bioinformatics.irida.ria.web.BaseController
    • ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementsController
    • ca.corefacility.bioinformatics.irida.ria.web.login.LoginController
    • ca.corefacility.bioinformatics.irida.ria.web.pipelines.PipelineController
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.RemoteAPIAjaxController
    • ca.corefacility.bioinformatics.irida.ria.web.oauth.RemoteAPIController
  • ca.corefacility.bioinformatics.irida.ria.web.models.BaseModel
    • ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.PairedEndSequenceFileModel
    • ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.SequenceFileModel
    • ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.SingleEndSequenceFileModel
  • ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse
  • ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.BioHanselSampleUpdater (implements ca.corefacility.bioinformatics.irida.pipeline.results.updater.AnalysisSampleUpdater)
  • ca.corefacility.bioinformatics.irida.service.util.impl.BioJavaSequenceFileUtilitiesImpl (implements ca.corefacility.bioinformatics.irida.service.util.SequenceFileUtilities)
  • ca.corefacility.bioinformatics.irida.ria.config.BreadCrumbInterceptor (implements org.springframework.web.servlet.AsyncHandlerInterceptor)
  • ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes
  • ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.cart.CartController
  • ca.corefacility.bioinformatics.irida.ria.web.cart.CartGalaxyController
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart.CartProjectModel
  • ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartProjectSample
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CartSampleModel
  • ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSampleRequest
  • ca.corefacility.bioinformatics.irida.processing.impl.ChecksumFileProcessor (implements ca.corefacility.bioinformatics.irida.processing.FileProcessor)
  • ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.CleanupAnalysisSubmissionConditionAge (implements ca.corefacility.bioinformatics.irida.service.CleanupAnalysisSubmissionCondition)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.ClientsAjaxController
  • ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Coverage
  • ca.corefacility.bioinformatics.irida.processing.impl.CoverageFileProcessor (implements ca.corefacility.bioinformatics.irida.processing.FileProcessor)
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.CreateRemoteProjectRequest
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdateSampleRequest
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails
  • ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl<KeyType,ValueType> (implements ca.corefacility.bioinformatics.irida.service.CRUDService<IdentifierType,Type>)
    • ca.corefacility.bioinformatics.irida.service.impl.AnalysisServiceImpl (implements ca.corefacility.bioinformatics.irida.service.AnalysisService)
    • ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl (implements ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService)
    • ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl (implements ca.corefacility.bioinformatics.irida.service.AnnouncementService)
    • ca.corefacility.bioinformatics.irida.service.impl.GenomeAssemblyServiceImpl (implements ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService)
    • ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl (implements ca.corefacility.bioinformatics.irida.service.IridaClientDetailsService)
    • ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl (implements ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService)
    • ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl (implements ca.corefacility.bioinformatics.irida.service.export.NcbiExportSubmissionService)
    • ca.corefacility.bioinformatics.irida.service.impl.user.PasswordResetServiceImpl (implements ca.corefacility.bioinformatics.irida.service.user.PasswordResetService)
    • ca.corefacility.bioinformatics.irida.service.impl.ProjectEventServiceImpl (implements ca.corefacility.bioinformatics.irida.service.ProjectEventService)
    • ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl (implements ca.corefacility.bioinformatics.irida.service.ProjectService)
    • ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl (implements ca.corefacility.bioinformatics.irida.service.ProjectSubscriptionService)
    • ca.corefacility.bioinformatics.irida.service.impl.ReferenceFileServiceImpl (implements ca.corefacility.bioinformatics.irida.service.ReferenceFileService)
    • ca.corefacility.bioinformatics.irida.service.impl.RemoteAPIServiceImpl (implements ca.corefacility.bioinformatics.irida.service.RemoteAPIService)
    • ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl (implements ca.corefacility.bioinformatics.irida.service.sample.SampleService)
    • ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl (implements ca.corefacility.bioinformatics.irida.service.SequencingObjectService)
    • ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl (implements ca.corefacility.bioinformatics.irida.service.SequencingRunService)
    • ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl (implements ca.corefacility.bioinformatics.irida.service.user.UserGroupService)
    • ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl (implements ca.corefacility.bioinformatics.irida.service.user.UserService)
    • ca.corefacility.bioinformatics.irida.service.impl.workflow.WorkflowNamedParametersServiceImpl (implements ca.corefacility.bioinformatics.irida.service.workflow.WorkflowNamedParametersService)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CurrentUser
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.CurrentUserAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.DashboardController
  • ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable
  • ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesColumnDefinitions
  • ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportToFile
  • ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams
  • ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config.DataTablesRequestResolver (implements org.springframework.web.method.support.HandlerMethodArgumentResolver)
  • ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesResponse
  • ca.corefacility.bioinformatics.irida.web.controller.api.json.DateJson
  • ca.corefacility.bioinformatics.irida.ria.web.utilities.DateUtilities
  • ca.corefacility.bioinformatics.irida.processing.impl.DefaultFileProcessingChain (implements ca.corefacility.bioinformatics.irida.processing.FileProcessingChain)
  • org.springframework.web.client.DefaultResponseErrorHandler (implements org.springframework.web.client.ResponseErrorHandler)
    • ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.IridaOAuthErrorHandler
  • org.hibernate.envers.DefaultRevisionEntity (implements java.io.Serializable)
    • ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevEntity
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.DownloadRequest
  • ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProject (implements ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.DataTablesResponseModel)
  • ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples (implements ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportable, ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.DataTablesResponseModel)
  • ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl (implements ca.corefacility.bioinformatics.irida.service.EmailController)
    • ca.corefacility.bioinformatics.irida.service.impl.TestEmailController
  • ca.corefacility.bioinformatics.irida.config.services.scheduled.EmailScheduledTaskConfig
  • ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.EntriesResponse
  • ca.corefacility.bioinformatics.irida.web.controller.api.exception.ErrorResponse
  • ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol
  • ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData
  • ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelHeader
  • ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelRow
  • ca.corefacility.bioinformatics.irida.ria.utilities.ExceptionPropertyAndMessage
  • ca.corefacility.bioinformatics.irida.ria.web.utilities.ExceptionUtilities
  • ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig
  • ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy.ExecutionManagerGalaxy (implements ca.corefacility.bioinformatics.irida.model.workflow.manager.ExecutionManager)
  • ca.corefacility.bioinformatics.irida.config.services.scheduled.ExecutorConfig
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel
  • ca.corefacility.bioinformatics.irida.service.export.ExportUploadService
  • ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCDetailsResponse
  • ca.corefacility.bioinformatics.irida.processing.impl.FastqcFileProcessor (implements ca.corefacility.bioinformatics.irida.processing.FileProcessor)
  • ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse
  • ca.corefacility.bioinformatics.irida.database.changesets.FastqcToFilesystem (implements liquibase.change.custom.CustomSqlChange)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.FieldUpdate
  • ca.corefacility.bioinformatics.irida.config.services.scheduled.FileProcessingScheduledTaskConfig
  • ca.corefacility.bioinformatics.irida.ria.utilities.converters.FileSizeConverter (implements org.springframework.core.convert.converter.Converter<S,T>)
  • ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl<Type> (implements ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
    • ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisOutputFileRepositoryImpl
    • ca.corefacility.bioinformatics.irida.repositories.assembly.GenomeAssemblyRepositoryImpl
    • ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepositoryImpl
    • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepositoryImpl
  • ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl.RelativePathTranslatorListener
  • ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities
  • ca.corefacility.bioinformatics.irida.util.FileUtils
  • ca.corefacility.bioinformatics.irida.config.repository.ForbidJpqlUpdateDeletePostProcessor (implements org.springframework.beans.factory.config.BeanPostProcessor, org.springframework.core.PriorityOrdered)
  • ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyAccountEmail (implements ca.corefacility.bioinformatics.irida.model.upload.UploaderAccountName)
  • ca.corefacility.bioinformatics.irida.ria.web.cart.dto.GalaxyExportAuthentication
  • ca.corefacility.bioinformatics.irida.ria.web.cart.dto.GalaxyExportSample
  • ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService
  • ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyJobErrorsService
  • ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService
  • ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName (implements ca.corefacility.bioinformatics.irida.model.upload.UploadProjectName)
  • ca.corefacility.bioinformatics.irida.ria.web.oauth.GalaxyRedirectionEndpointController
  • ca.corefacility.bioinformatics.irida.ria.config.GalaxySessionInterceptor (implements org.springframework.web.servlet.AsyncHandlerInterceptor)
  • ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyToolDataService
  • ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyWorkflowService
  • ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus
  • ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus.GalaxyWorkflowStatusBuilder
  • org.springframework.web.filter.GenericFilterBean (implements org.springframework.beans.factory.BeanNameAware, org.springframework.beans.factory.DisposableBean, org.springframework.context.EnvironmentAware, org.springframework.core.env.EnvironmentCapable, javax.servlet.Filter, org.springframework.beans.factory.InitializingBean, org.springframework.web.context.ServletContextAware)
    • org.springframework.security.web.authentication.AnonymousAuthenticationFilter (implements org.springframework.beans.factory.InitializingBean)
      • ca.corefacility.bioinformatics.irida.web.filter.UnauthenticatedAnonymousAuthenticationFilter
    • ca.corefacility.bioinformatics.irida.ria.config.filters.SessionFilter
  • ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.GenericStatModel
  • org.springframework.security.config.annotation.method.configuration.GlobalMethodSecurityConfiguration (implements org.springframework.beans.factory.BeanFactoryAware, org.springframework.context.annotation.ImportAware, org.springframework.beans.factory.SmartInitializingSingleton)
    • ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig
  • ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor (implements ca.corefacility.bioinformatics.irida.processing.FileProcessor)
  • org.springframework.http.client.support.HttpAccessor
    • org.springframework.http.client.support.InterceptingHttpAccessor
      • org.springframework.web.client.RestTemplate (implements org.springframework.web.client.RestOperations)
        • ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.OAuthTokenRestTemplate
  • ca.corefacility.bioinformatics.irida.web.filter.HttpHeadFilter (implements javax.servlet.Filter)
  • ca.corefacility.bioinformatics.irida.service.impl.InMemoryTaxonomyService (implements ca.corefacility.bioinformatics.irida.service.TaxonomyService)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.Input
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.InputWithOptions
  • ca.corefacility.bioinformatics.irida.config.workflow.IridaAnalysisTypesServiceConfig
  • ca.corefacility.bioinformatics.irida.config.services.IridaApiAspectsConfig
  • ca.corefacility.bioinformatics.irida.config.repository.IridaApiFilesystemRepositoryConfig
  • ca.corefacility.bioinformatics.irida.config.data.IridaApiJdbcDataSourceConfig
  • ca.corefacility.bioinformatics.irida.config.services.IridaApiPropertyPlaceholderConfig
  • ca.corefacility.bioinformatics.irida.config.repository.IridaApiRepositoriesConfig
  • ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig
  • ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig.IridaLocaleList
  • ca.corefacility.bioinformatics.irida.IridaApplication
  • ca.corefacility.bioinformatics.irida.model.IridaClientDetails (implements ca.corefacility.bioinformatics.irida.model.MutableIridaThing)
  • ca.corefacility.bioinformatics.irida.repositories.specification.IridaClientDetailsSpecification
  • ca.corefacility.bioinformatics.irida.config.environment.IridaEnvironmentPostProcessor (implements org.springframework.boot.env.EnvironmentPostProcessor, org.springframework.core.Ordered)
  • ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig
  • ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.AuthorizationServerConfig
  • ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.JWKConfig
  • ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.ResourceServerConfig
  • ca.corefacility.bioinformatics.irida.security.permissions.IridaPermissionEvaluator (implements org.springframework.security.access.PermissionEvaluator)
  • ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig
  • ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig.IridaPluginList
  • ca.corefacility.bioinformatics.irida.util.IridaPluginMessageSource (implements org.springframework.context.HierarchicalMessageSource)
  • ca.corefacility.bioinformatics.irida.security.IridaPostAuthenicationChecker (implements org.springframework.security.core.userdetails.UserDetailsChecker)
  • ca.corefacility.bioinformatics.irida.oauth2.IridaRegisteredClientsRepository (implements org.springframework.security.oauth2.server.authorization.client.RegisteredClientRepository)
  • ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel
    • ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission (implements ca.corefacility.bioinformatics.irida.model.MutableIridaThing)
      • ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission (implements java.lang.Comparable<T>)
      • ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate (implements java.lang.Comparable<T>)
    • ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis (implements ca.corefacility.bioinformatics.irida.model.IridaThing)
      • ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC
    • ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile (implements ca.corefacility.bioinformatics.irida.model.IridaThing, ca.corefacility.bioinformatics.irida.model.VersionedFileFields<VersionType>)
    • ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly (implements ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile, ca.corefacility.bioinformatics.irida.model.IridaThing, ca.corefacility.bioinformatics.irida.model.VersionedFileFields<VersionType>)
      • ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis
      • ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly
    • ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.IridaThing)
    • ca.corefacility.bioinformatics.irida.web.assembler.resource.LabelledRelationshipResource<Owner,Child>
    • ca.corefacility.bioinformatics.irida.model.project.Project (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.MutableIridaThing, ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable)
    • ca.corefacility.bioinformatics.irida.web.assembler.resource.ProjectHashResource
    • ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceCollection<Type> (implements java.lang.Iterable<T>)
    • ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceList<Type>
    • ca.corefacility.bioinformatics.irida.model.sample.Sample (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.MutableIridaThing, ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable)
    • ca.corefacility.bioinformatics.irida.web.assembler.resource.sample.SampleMetadataResponse
    • ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile, ca.corefacility.bioinformatics.irida.model.MutableIridaThing, ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable, ca.corefacility.bioinformatics.irida.model.VersionedFileFields<VersionType>)
    • ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject (implements ca.corefacility.bioinformatics.irida.model.MutableIridaThing, ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable)
      • ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object
      • ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair
      • ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile
    • ca.corefacility.bioinformatics.irida.model.run.SequencingRun (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.MutableIridaThing)
    • ca.corefacility.bioinformatics.irida.model.user.User (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.MutableIridaThing, org.springframework.security.core.userdetails.UserDetails)
  • ca.corefacility.bioinformatics.irida.config.web.IridaRestApiWebConfig (implements org.springframework.web.servlet.config.annotation.WebMvcConfigurer)
  • ca.corefacility.bioinformatics.irida.config.services.scheduled.IridaScheduledTasksConfig (implements org.springframework.scheduling.annotation.SchedulingConfigurer)
  • ca.corefacility.bioinformatics.irida.ria.web.settings.IRIDASettingsAjaxController
  • ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter
  • ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig (implements org.springframework.context.ApplicationContextAware, org.springframework.web.servlet.config.annotation.WebMvcConfigurer)
  • ca.corefacility.bioinformatics.irida.config.security.IridaWebSecurityConfig
  • ca.corefacility.bioinformatics.irida.config.security.IridaWebSecurityConfig.UISecurityConfig
  • ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow
  • ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription
  • ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDynamicSourceGalaxy
  • ca.corefacility.bioinformatics.irida.model.workflow.config.IridaWorkflowIdSet
  • ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowInput
  • ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowLoaderService
  • ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters (implements ca.corefacility.bioinformatics.irida.model.IridaThing)
  • ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowOutput
  • ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter
  • ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameterChoice
  • ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig
  • ca.corefacility.bioinformatics.irida.model.workflow.config.IridaWorkflowSet
  • ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService
  • ca.corefacility.bioinformatics.irida.model.workflow.structure.IridaWorkflowStructure
  • ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository
  • org.springframework.mail.javamail.JavaMailSenderImpl (implements org.springframework.mail.javamail.JavaMailSender)
    • ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig.ConfigurableJavaMailSenderImpl (implements ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig.ConfigurableJavaMailSender)
  • org.springframework.security.oauth2.server.authorization.JdbcOAuth2AuthorizationService (implements org.springframework.security.oauth2.server.authorization.OAuth2AuthorizationService)
    • ca.corefacility.bioinformatics.irida.oauth2.IridaOAuth2AuthorizationService
  • com.fasterxml.jackson.databind.JsonDeserializer<T> (implements com.fasterxml.jackson.databind.deser.NullValueProvider)
    • com.fasterxml.jackson.databind.deser.std.StdDeserializer<T> (implements java.io.Serializable, com.fasterxml.jackson.databind.deser.ValueInstantiator.Gettable)
      • ca.corefacility.bioinformatics.irida.web.controller.api.json.DateJson.DateDeserializer
      • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackAssetsManifestDeserializer
      • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntryDeserializer
  • com.fasterxml.jackson.databind.JsonSerializer<T> (implements com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatVisitable)
    • com.fasterxml.jackson.databind.ser.std.StdSerializer<T> (implements com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatVisitable, com.fasterxml.jackson.databind.jsonschema.SchemaAware, java.io.Serializable)
      • ca.corefacility.bioinformatics.irida.web.controller.api.json.DateJson.DateSerializer
      • ca.corefacility.bioinformatics.irida.web.controller.api.json.PathJson.PathSerializer
      • ca.corefacility.bioinformatics.irida.web.controller.api.json.TimestampJson.TimestampSerializer
  • ca.corefacility.bioinformatics.irida.validators.annotations.validators.LatitudeValidator (implements javax.validation.ConstraintValidator<A,T>)
  • ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchController
  • ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest
  • ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchSample
  • ca.corefacility.bioinformatics.irida.ria.web.linelist.LineListController
  • ca.corefacility.bioinformatics.irida.ria.web.dto.list.ListItem
    • ca.corefacility.bioinformatics.irida.ria.web.activities.dto.Activity
  • ca.corefacility.bioinformatics.irida.model.remote.resource.ListResourceWrapper<Type>
  • ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Locale
  • ca.corefacility.bioinformatics.irida.validators.annotations.validators.LongitudeValidator (implements javax.validation.ConstraintValidator<A,T>)
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.MergeRequest
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController
  • ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry
    • ca.corefacility.bioinformatics.irida.model.sample.metadata.PipelineProvidedMetadataEntry
  • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepositoryCustom)
  • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepositoryCustom)
  • ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataRestriction
  • ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate (implements ca.corefacility.bioinformatics.irida.model.MutableIridaThing)
  • ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField
    • ca.corefacility.bioinformatics.irida.model.sample.StaticMetadataTemplateField
  • ca.corefacility.bioinformatics.irida.events.MethodEvent
  • ca.corefacility.bioinformatics.irida.ria.web.models.MinimalModel
    • ca.corefacility.bioinformatics.irida.ria.web.models.project.ProjectMinimalModel
    • ca.corefacility.bioinformatics.irida.ria.web.models.user.UserMinimalModel
  • ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController
  • ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles
  • ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder
  • ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel
  • ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission (implements ca.corefacility.bioinformatics.irida.model.MutableIridaThing)
  • ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatformInstrumentModel
  • ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel
  • ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest
  • ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample
  • ca.corefacility.bioinformatics.irida.config.services.scheduled.NcbiUploadScheduledTaskConfig
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NewMemberRequest
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.NewProjectMetadataRestriction
  • ca.corefacility.bioinformatics.irida.ria.web.projects.NGSLinkerAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.NGSLinkerCmdRequest
  • ca.corefacility.bioinformatics.irida.ria.web.services.NGSLinkerService
  • ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.Notification
    • ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.ErrorNotification
    • ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.InfoNotification
    • ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.SuccessNotification
    • ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.WarnNotification
  • ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationConverter (implements org.springframework.security.web.authentication.AuthenticationConverter)
  • ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationProvider (implements org.springframework.security.authentication.AuthenticationProvider)
  • ca.corefacility.bioinformatics.irida.ria.web.oauth.OltuAuthorizationController
  • ca.corefacility.bioinformatics.irida.config.web.OpenAPIConfig
  • ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.IridaThing)
  • ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy
  • ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy.ParameterId
  • ca.corefacility.bioinformatics.irida.security.PasswordExpiryChecker (implements org.springframework.security.core.userdetails.UserDetailsChecker)
  • ca.corefacility.bioinformatics.irida.model.user.PasswordReset (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.Timestamped<Identifier>)
  • ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetController
  • ca.corefacility.bioinformatics.irida.model.PathConverter (implements javax.persistence.AttributeConverter<X,Y>)
  • ca.corefacility.bioinformatics.irida.web.controller.api.json.PathJson
  • ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto.Pipeline
  • ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy (implements ca.corefacility.bioinformatics.irida.model.workflow.execution.PreparedWorkflow<WorkflowInputsType>)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Priorities
  • ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin (implements ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectAssociatedProjectsAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectCartSample
  • ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectControllerUtils
  • ca.corefacility.bioinformatics.irida.ria.web.users.dto.ProjectCurrentUserModel
  • ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectDetailsAjaxController
  • ca.corefacility.bioinformatics.irida.model.event.ProjectEvent (implements ca.corefacility.bioinformatics.irida.model.IridaThing)
    • ca.corefacility.bioinformatics.irida.model.event.DataAddedToSampleProjectEvent
    • ca.corefacility.bioinformatics.irida.model.event.SampleAddedProjectEvent
    • ca.corefacility.bioinformatics.irida.model.event.SampleRemovedProjectEvent
    • ca.corefacility.bioinformatics.irida.model.enums.UserGroupRemovedProjectEvent
    • ca.corefacility.bioinformatics.irida.model.event.UserGroupRoleSetProjectEvent
    • ca.corefacility.bioinformatics.irida.model.event.UserRemovedProjectEvent
    • ca.corefacility.bioinformatics.irida.model.event.UserRoleSetProjectEvent
  • ca.corefacility.bioinformatics.irida.events.ProjectEventAspect (implements org.springframework.core.Ordered)
  • ca.corefacility.bioinformatics.irida.service.impl.ProjectEventEmailScheduledTaskImpl (implements ca.corefacility.bioinformatics.irida.service.ProjectEventEmailScheduledTask)
  • ca.corefacility.bioinformatics.irida.events.ProjectEventHandler
  • ca.corefacility.bioinformatics.irida.service.remote.ProjectHashingService
  • ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectLineListController
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectMembersAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField
  • ca.corefacility.bioinformatics.irida.model.sample.metadata.ProjectMetadataResponse
  • ca.corefacility.bioinformatics.irida.constraints.impl.ProjectMetadataRoleValidator (implements javax.validation.ConstraintValidator<A,T>)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.ProjectObject
  • ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectReferenceFileController
  • ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin (implements ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.repositories.ProjectRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.ProjectRepositoryCustom)
  • ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsAjaxController
  • ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo
  • ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin (implements ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.repositories.specification.ProjectSampleJoinSpecification (implements org.springframework.data.jpa.domain.Specification<T>)
  • ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSampleMetadataAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.ProjectSamplesFilter
  • ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSamplesMetadataTemplateController
  • ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.ProjectSettingsAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectSettingsRemoteAjaxController
  • ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription (implements ca.corefacility.bioinformatics.irida.model.IridaThing)
  • ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectSubscriptionsAjaxController
  • ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService
  • ca.corefacility.bioinformatics.irida.config.services.scheduled.ProjectSyncScheduledTaskConfig
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectUserGroupsAjaxController
  • ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin (implements ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.model.sample.QCEntry
    • ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry
    • ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry
  • ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadProjectMetadataResponsePermission (implements ca.corefacility.bioinformatics.irida.security.permissions.BasePermission<DomainObjectType>)
  • ca.corefacility.bioinformatics.irida.util.RecursiveDeleteVisitor (implements java.nio.file.FileVisitor<T>)
  • ca.corefacility.bioinformatics.irida.model.project.ReferenceFile (implements ca.corefacility.bioinformatics.irida.model.MutableIridaThing, ca.corefacility.bioinformatics.irida.model.VersionedFileFields<VersionType>)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.ReferenceFileAjaxController
  • ca.corefacility.bioinformatics.irida.model.joins.impl.RelatedProjectJoin (implements ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.model.RemoteAPI (implements java.lang.Comparable<T>, ca.corefacility.bioinformatics.irida.model.MutableIridaThing)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteAPIModel
  • ca.corefacility.bioinformatics.irida.repositories.specification.RemoteAPISpecification
  • ca.corefacility.bioinformatics.irida.model.RemoteAPIToken
  • ca.corefacility.bioinformatics.irida.service.impl.RemoteAPITokenServiceImpl (implements ca.corefacility.bioinformatics.irida.service.RemoteAPITokenService)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectModel
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest
  • ca.corefacility.bioinformatics.irida.repositories.remote.impl.RemoteRepositoryImpl<Type> (implements ca.corefacility.bioinformatics.irida.repositories.remote.RemoteRepository<Type>)
    • ca.corefacility.bioinformatics.irida.repositories.remote.impl.Fast5ObjectRemoteRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.remote.Fast5ObjectRemoteRepository)
    • ca.corefacility.bioinformatics.irida.repositories.remote.impl.GenomeAssemblyRemoteRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.remote.GenomeAssemblyRemoteRepository)
    • ca.corefacility.bioinformatics.irida.repositories.remote.impl.ProjectRemoteRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.remote.ProjectRemoteRepository)
    • ca.corefacility.bioinformatics.irida.repositories.remote.impl.SampleRemoteRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.remote.SampleRemoteRepository)
    • ca.corefacility.bioinformatics.irida.repositories.remote.impl.SequenceFilePairRemoteRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.remote.SequenceFilePairRemoteRepository)
    • ca.corefacility.bioinformatics.irida.repositories.remote.impl.SequenceFileRemoteRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.remote.SequenceFileRemoteRepository)
    • ca.corefacility.bioinformatics.irida.repositories.remote.impl.SingleEndSequenceFileRemoteRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.remote.SingleEndSequenceFileRemoteRepository)
  • ca.corefacility.bioinformatics.irida.service.remote.impl.RemoteServiceImpl<Type> (implements ca.corefacility.bioinformatics.irida.service.remote.RemoteService<Type>)
    • ca.corefacility.bioinformatics.irida.service.remote.impl.GenomeAssemblyRemoteServiceImpl (implements ca.corefacility.bioinformatics.irida.service.remote.GenomeAssemblyRemoteService)
    • ca.corefacility.bioinformatics.irida.service.remote.impl.ProjectRemoteServiceImpl (implements ca.corefacility.bioinformatics.irida.service.remote.ProjectRemoteService)
    • ca.corefacility.bioinformatics.irida.service.remote.impl.SampleRemoteServiceImpl (implements ca.corefacility.bioinformatics.irida.service.remote.SampleRemoteService)
    • ca.corefacility.bioinformatics.irida.service.remote.impl.SequencingObjectRemoteServiceImpl<Type> (implements ca.corefacility.bioinformatics.irida.service.remote.SequencingObjectRemoteService<Type>)
      • ca.corefacility.bioinformatics.irida.service.remote.impl.Fast5ObjectRemoteServiceImpl (implements ca.corefacility.bioinformatics.irida.service.remote.Fast5ObjectRemoteService)
      • ca.corefacility.bioinformatics.irida.service.remote.impl.SequenceFilePairRemoteServiceImpl (implements ca.corefacility.bioinformatics.irida.service.remote.SequenceFilePairRemoteService)
      • ca.corefacility.bioinformatics.irida.service.remote.impl.SingleEndSequenceFileRemoteServiceImpl (implements ca.corefacility.bioinformatics.irida.service.remote.SingleEndSequenceFileRemoteService)
  • ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.RemoveSamplesRequest
  • ca.corefacility.bioinformatics.irida.security.permissions.RepositoryBackedPermission<DomainObjectType,IdentifierType> (implements ca.corefacility.bioinformatics.irida.security.permissions.BasePermission<DomainObjectType>)
    • ca.corefacility.bioinformatics.irida.security.permissions.project.ModifyProjectPermission
      • ca.corefacility.bioinformatics.irida.security.permissions.project.ManageLocalProjectSettingsPermission
      • ca.corefacility.bioinformatics.irida.security.permissions.project.ProjectOwnerPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.analysis.ReadAnalysisPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.analysis.ReadAnalysisSubmissionPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.project.ReadExportSubmissionPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataEntryPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataTemplatePermission
    • ca.corefacility.bioinformatics.irida.security.permissions.project.ReadProjectPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.files.ReadReferenceFilePermission
    • ca.corefacility.bioinformatics.irida.security.permissions.sample.ReadSamplePermission
    • ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingObjectPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingRunPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateAnalysisSubmissionPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.metadata.UpdateMetadataTemplatePermission
    • ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateReferenceFilePermission
    • ca.corefacility.bioinformatics.irida.security.permissions.sample.UpdateSamplePermission
    • ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateSamplesFromAnalysisSubmissionPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateSequencingRunPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.user.UpdateUserGroupPermission
    • ca.corefacility.bioinformatics.irida.security.permissions.user.UpdateUserPermission
  • org.springframework.hateoas.RepresentationModel<T>
    • ca.corefacility.bioinformatics.irida.web.assembler.resource.RootResource
  • ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceAdditionalProperties<Type>
  • ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceWrapper<Type>
  • ca.corefacility.bioinformatics.irida.ria.web.dto.ResponseDetails
  • org.springframework.web.servlet.mvc.method.annotation.ResponseEntityExceptionHandler
    • ca.corefacility.bioinformatics.irida.ria.web.errors.IridaCustomExceptionHandler
  • ca.corefacility.bioinformatics.irida.web.assembler.resource.ResponseProjectResource<Type>
  • ca.corefacility.bioinformatics.irida.web.assembler.resource.ResponseResource<Type>
  • ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController<Type>
    • ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController
    • ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController
    • ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController
    • ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController
  • ca.corefacility.bioinformatics.irida.web.controller.api.RESTOAuthAuthorizationConsentController
  • ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectAnalysisController
  • ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController
  • ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController
  • ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController
  • ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController.ResponseVersion
  • ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController
  • ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController
  • ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController
  • ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunSequenceFilesController
  • ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.Role
  • ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role
  • ca.corefacility.bioinformatics.irida.jackson2.mixin.RoleMixin
  • ca.corefacility.bioinformatics.irida.ria.web.utilities.RoleUtilities
  • ca.corefacility.bioinformatics.irida.service.analysis.annotations.RunAsUserAspect
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleAnalyses
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleDetails
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleExportFiles
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleGenomeAssemblyFileModel
  • ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin (implements ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadata
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry
  • ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage
  • ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleNameValidationResponse
  • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.SampleObject
  • ca.corefacility.bioinformatics.irida.ria.web.samples.SamplePairer
  • ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepositoryImpl (implements ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepositoryCustom)
  • ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel
  • ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin (implements ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.repositories.specification.SampleSequencingObjectSpecification
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavedPipelineParameters
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavePipelineParametersRequest
  • ca.corefacility.bioinformatics.irida.util.SchemaExporter
  • ca.corefacility.bioinformatics.irida.ria.web.search.SearchController
  • ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.SelectOption
  • ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceConcatenation (implements ca.corefacility.bioinformatics.irida.model.IridaThing)
  • ca.corefacility.bioinformatics.irida.ria.web.files.SequenceFileAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails (implements java.lang.Comparable<T>)
  • ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.SequenceFileMessageConverter (implements org.springframework.http.converter.HttpMessageConverter<T>)
  • ca.corefacility.bioinformatics.irida.service.impl.processor.SequenceFileProcessorLauncher (implements java.lang.Runnable)
  • ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile.SequenceFileResource
  • ca.corefacility.bioinformatics.irida.processing.concatenate.SequencingObjectConcatenator<Type>
    • ca.corefacility.bioinformatics.irida.processing.concatenate.impl.SequenceFilePairConcatenator
    • ca.corefacility.bioinformatics.irida.processing.concatenate.impl.SingleEndSequenceFileConcatenator
  • ca.corefacility.bioinformatics.irida.processing.concatenate.SequencingObjectConcatenatorFactory
  • ca.corefacility.bioinformatics.irida.service.SequencingObjectProcessingService
  • ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunController
  • ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareMetadataRestriction
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest
  • org.springframework.security.web.authentication.SimpleUrlAuthenticationFailureHandler (implements org.springframework.security.web.authentication.AuthenticationFailureHandler)
    • ca.corefacility.bioinformatics.irida.ria.security.IridaPostAuthenticationFailureHandler
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult
  • ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.SISTRSampleUpdater (implements ca.corefacility.bioinformatics.irida.pipeline.results.updater.AnalysisSampleUpdater)
  • ca.corefacility.bioinformatics.irida.web.filter.SlashFilter (implements javax.servlet.Filter)
  • org.springframework.boot.web.servlet.support.SpringBootServletInitializer (implements org.springframework.web.WebApplicationInitializer)
    • ca.corefacility.bioinformatics.irida.ServletInitializer
  • liquibase.integration.spring.SpringLiquibase (implements org.springframework.beans.factory.BeanNameAware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ResourceLoaderAware)
    • ca.corefacility.bioinformatics.irida.config.data.IridaApiJdbcDataSourceConfig.ApplicationContextAwareSpringLiquibase
  • ca.corefacility.bioinformatics.irida.ria.web.analysis.StateFilter
  • ca.corefacility.bioinformatics.irida.ria.web.components.SubmissionIds
  • ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableModel
    • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectModel
  • ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableModel
    • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisModel
    • ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementTableModel
    • ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserTableModel
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.ClientTableModel
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NcbiExportSubmissionTableModel
      • ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiExportSubmissionAdminTableModel
    • ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectMemberTableModel
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ProjectUserGroupsTableModel
    • ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto.RemoteAPITableModel
      • ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto.RemoteAPITableAdminModel
    • ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunModel
    • ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupProjectTableModel
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupTableModel
    • ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserProjectDetailsModel
  • ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest
  • ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest
    • ca.corefacility.bioinformatics.irida.ria.web.users.dto.AdminUsersTableRequest
    • ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesListRequest
    • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.ClientTableRequest
    • ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunsListRequest
  • ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableResponse
  • ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableResponse<T>
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.ontologies.TaxonomyAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.TaxonomyEntry
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Error
      • ca.corefacility.bioinformatics.irida.ria.web.errors.AjaxItemNotFoundException
      • ca.corefacility.bioinformatics.irida.exceptions.UnsupportedReferenceFileContentError
    • java.lang.Exception
      • ca.corefacility.bioinformatics.irida.exceptions.AnalysisAlreadySetException
      • ca.corefacility.bioinformatics.irida.exceptions.ConcatenateException
      • ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerConfigurationException
      • ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException
        • ca.corefacility.bioinformatics.irida.exceptions.galaxy.DeleteGalaxyObjectFailedException
        • ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerDownloadException
        • ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetException
          • ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetNotFoundException
        • ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyToolDataTableException
        • ca.corefacility.bioinformatics.irida.exceptions.UploadException
          • ca.corefacility.bioinformatics.irida.exceptions.galaxy.CreateLibraryException
          • ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerObjectNotFoundException
            • ca.corefacility.bioinformatics.irida.exceptions.galaxy.NoGalaxyHistoryException
          • ca.corefacility.bioinformatics.irida.exceptions.UploadConnectionException
          • ca.corefacility.bioinformatics.irida.exceptions.UploadErrorException
          • ca.corefacility.bioinformatics.irida.exceptions.UploadTimeoutException
        • ca.corefacility.bioinformatics.irida.exceptions.WorkflowException
          • ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyOutputsForWorkflowException
          • ca.corefacility.bioinformatics.irida.exceptions.NoPercentageCompleteException
          • ca.corefacility.bioinformatics.irida.exceptions.WorkflowInvalidException
          • ca.corefacility.bioinformatics.irida.exceptions.WorkflowPreprationException
            • ca.corefacility.bioinformatics.irida.exceptions.SampleAnalysisDuplicateException
        • ca.corefacility.bioinformatics.irida.exceptions.galaxy.WorkflowUploadException
      • ca.corefacility.bioinformatics.irida.exceptions.FileProcessorTimeoutException
      • ca.corefacility.bioinformatics.irida.exceptions.IridaAccountDisabledException
      • ca.corefacility.bioinformatics.irida.plugins.IridaPluginException
      • ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowException
        • ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowAnalysisTypeException
        • ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowDefaultException
        • ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowLoadException
          • ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNotDisplayableException
          • ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNotFoundException
        • ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowParameterException
          • ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNoParameterException
      • ca.corefacility.bioinformatics.irida.exceptions.pipelines.MissingRequiredParametersException
      • ca.corefacility.bioinformatics.irida.exceptions.NcbiXmlParseException
      • ca.corefacility.bioinformatics.irida.exceptions.NoSuchValueException
      • ca.corefacility.bioinformatics.irida.exceptions.PostProcessingException
      • ca.corefacility.bioinformatics.irida.exceptions.ProjectWithoutOwnerException
        • ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIProjectWithoutOwnerException
      • ca.corefacility.bioinformatics.irida.exceptions.pipelines.ReferenceFileRequiredException
      • java.lang.RuntimeException
        • org.springframework.security.core.AuthenticationException
          • org.springframework.security.authentication.AccountStatusException
            • ca.corefacility.bioinformatics.irida.security.SequencerUILoginException
        • ca.corefacility.bioinformatics.irida.exceptions.DuplicateSampleException
        • ca.corefacility.bioinformatics.irida.exceptions.EntityExistsException
          • ca.corefacility.bioinformatics.irida.exceptions.ExistingSampleNameException
        • ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException
          • ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIEntityNotFoundException
        • ca.corefacility.bioinformatics.irida.ria.web.components.datatables.export.ExportFormatException
        • ca.corefacility.bioinformatics.irida.processing.FileProcessorException
        • ca.corefacility.bioinformatics.irida.web.controller.api.exception.GenericsException
        • ca.corefacility.bioinformatics.irida.exceptions.InvalidPropertyException
        • ca.corefacility.bioinformatics.irida.exceptions.IridaOAuthException
        • ca.corefacility.bioinformatics.irida.exceptions.LinkNotFoundException
        • ca.corefacility.bioinformatics.irida.exceptions.MetadataImportFileTypeNotSupportedError
        • org.springframework.core.NestedRuntimeException
          • org.springframework.mail.MailException
            • org.springframework.mail.MailSendException
              • ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIEmailSendException
        • ca.corefacility.bioinformatics.irida.exceptions.PasswordReusedException
        • ca.corefacility.bioinformatics.irida.exceptions.ProjectSynchronizationException
        • ca.corefacility.bioinformatics.irida.exceptions.RemoteFileNotCachedException
        • ca.corefacility.bioinformatics.irida.exceptions.StorageException
        • ca.corefacility.bioinformatics.irida.security.permissions.UndefinedPermissionException
        • ca.corefacility.bioinformatics.irida.exceptions.WebpackParserException
      • ca.corefacility.bioinformatics.irida.ria.web.projects.error.SampleMergeException
      • ca.corefacility.bioinformatics.irida.ria.web.errors.SavedMetadataException
      • ca.corefacility.bioinformatics.irida.exceptions.SequenceFileAnalysisException
      • ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIAddAssociatedProjectException
      • ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIConstraintViolationException
      • ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIRemoveAssociatedProjectException
      • ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIShareSamplesException
      • ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIUserFormException
      • ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIUserStatusException
      • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.exceptions.UpdateException
      • ca.corefacility.bioinformatics.irida.exceptions.UserGroupWithoutOwnerException
  • ca.corefacility.bioinformatics.irida.web.controller.api.json.TimestampJson
  • ca.corefacility.bioinformatics.irida.jackson2.mixin.TimestampMixin
  • ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution (implements ca.corefacility.bioinformatics.irida.model.IridaThing)
  • ca.corefacility.bioinformatics.irida.util.ToolsListExporter
  • ca.corefacility.bioinformatics.irida.util.TreeNode<ValueType>
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIActivitiesService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIAdminStatisticsService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesOutputsService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIAssociatedProjectsService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UICartService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIClientService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataFileImportService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataImportService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService
  • ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataTemplate
  • ca.corefacility.bioinformatics.irida.ria.web.services.UINcbiService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIPasswordResetService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineSampleService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineStartService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectMembersService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectReferenceFileService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSampleService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSubscriptionService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectUserGroupsService
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UIReferenceFile
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteAPIService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteProjectService
  • ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter
  • ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UISequencingRunService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UISettingsService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIUsersService
  • ca.corefacility.bioinformatics.irida.ria.web.services.UIUserStatisticsService
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress
  • ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.UpdateProjectAttributeRequest
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleAttributeRequest
  • ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest
  • ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest
  • ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserEditRequest
  • ca.corefacility.bioinformatics.irida.model.user.group.UserGroup (implements ca.corefacility.bioinformatics.irida.model.MutableIridaThing)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails
  • ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin (implements ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupMember
  • ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin (implements ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>)
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupRole
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.UserGroupsController
  • ca.corefacility.bioinformatics.irida.repositories.specification.UserGroupSpecification
  • ca.corefacility.bioinformatics.irida.jackson2.mixin.UserMixin
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserPasswordResetDetails
  • ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryImpl (implements org.springframework.security.core.userdetails.UserDetailsService, ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryCustom)
  • ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevListener (implements org.springframework.context.ApplicationContextAware, org.hibernate.envers.RevisionListener)
  • ca.corefacility.bioinformatics.irida.ria.web.users.UsersAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.users.UsersController
  • ca.corefacility.bioinformatics.irida.ria.config.UserSecurityInterceptor (implements org.springframework.web.servlet.AsyncHandlerInterceptor)
  • ca.corefacility.bioinformatics.irida.repositories.specification.UserSpecification
  • ca.corefacility.bioinformatics.irida.ria.web.users.UserStatisticsAjaxController
  • ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserStatisticsResponse
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNameModel
  • ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesRequest
  • ca.corefacility.bioinformatics.irida.validators.ValidMethodParametersAspect
  • ca.corefacility.bioinformatics.irida.validators.annotations.ValidProjectName.ValidProjectNameBlocklist
  • ca.corefacility.bioinformatics.irida.validators.annotations.ValidSampleName.ValidSampleNameBlocklist
  • ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig
  • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackAssetsManifest
  • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntry
  • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerManifestParser
  • ca.corefacility.bioinformatics.irida.ria.config.WebStylesConfig
  • ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.WorkflowInputsGalaxy (implements ca.corefacility.bioinformatics.irida.model.workflow.execution.WorkflowInputsGeneric)

Interface Hierarchy

• ca.corefacility.bioinformatics.irida.service.AnalysisExecutionScheduledTask
• ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService
• ca.corefacility.bioinformatics.irida.service.analysis.workspace.AnalysisParameterService<WorkflowInputsType>
• ca.corefacility.bioinformatics.irida.pipeline.results.updater.AnalysisSampleUpdater
• ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionCleanupService
• ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryCustom
• ca.corefacility.bioinformatics.irida.pipeline.results.AnalysisSubmissionSampleProcessor
• ca.corefacility.bioinformatics.irida.service.AnalysisTypesService
• ca.corefacility.bioinformatics.irida.service.analysis.workspace.AnalysisWorkspaceService
• ca.corefacility.bioinformatics.irida.security.permissions.BasePermission<DomainObjectType>
• ca.corefacility.bioinformatics.irida.service.CleanupAnalysisSubmissionCondition
• ca.corefacility.bioinformatics.irida.service.CRUDService<IdentifierType,Type>
  • ca.corefacility.bioinformatics.irida.service.AnalysisService
  • ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService
  • ca.corefacility.bioinformatics.irida.service.AnnouncementService
  • ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService
  • ca.corefacility.bioinformatics.irida.service.IridaClientDetailsService
  • ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService
  • ca.corefacility.bioinformatics.irida.service.export.NcbiExportSubmissionService
  • ca.corefacility.bioinformatics.irida.service.user.PasswordResetService
  • ca.corefacility.bioinformatics.irida.service.ProjectEventService
  • ca.corefacility.bioinformatics.irida.service.ProjectService
  • ca.corefacility.bioinformatics.irida.service.ProjectSubscriptionService
  • ca.corefacility.bioinformatics.irida.service.ReferenceFileService
  • ca.corefacility.bioinformatics.irida.service.RemoteAPIService
  • ca.corefacility.bioinformatics.irida.service.sample.SampleService
  • ca.corefacility.bioinformatics.irida.service.SequencingObjectService
  • ca.corefacility.bioinformatics.irida.service.SequencingRunService
  • ca.corefacility.bioinformatics.irida.service.user.UserGroupService
  • ca.corefacility.bioinformatics.irida.service.user.UserService (also extends org.springframework.security.core.userdetails.UserDetailsService)
  • ca.corefacility.bioinformatics.irida.service.workflow.WorkflowNamedParametersService
• ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportable
• ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.DataTablesResponseModel
• javax.validation.groups.Default
  • ca.corefacility.bioinformatics.irida.validators.groups.NCBISubmission
  • ca.corefacility.bioinformatics.irida.validators.groups.NCBISubmissionOneOf
• ca.corefacility.bioinformatics.irida.service.EmailController
• ca.corefacility.bioinformatics.irida.model.workflow.manager.ExecutionManager
• org.pf4j.ExtensionPoint
  • ca.corefacility.bioinformatics.irida.plugins.IridaPlugin
• ca.corefacility.bioinformatics.irida.processing.FileProcessingChain
• ca.corefacility.bioinformatics.irida.processing.FileProcessor
• ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>
  • ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisOutputFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>)
  • ca.corefacility.bioinformatics.irida.repositories.assembly.GenomeAssemblyRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>)
  • ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>)
  • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>)
• ca.corefacility.bioinformatics.irida.ria.utilities.Formats
• ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile
• org.springframework.data.jpa.repository.JpaSpecificationExecutor<T>
  • ca.corefacility.bioinformatics.irida.repositories.joins.announcement.AnnouncementUserJoinRepository (also extends org.springframework.data.repository.PagingAndSortingRepository<T,ID>)
  • ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier> (also extends org.springframework.data.repository.PagingAndSortingRepository<T,ID>, org.springframework.data.repository.history.RevisionRepository<T,ID,N>)
    • ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisOutputFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
    • ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisRepository
    • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository
    • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionTemplateRepository
    • ca.corefacility.bioinformatics.irida.repositories.AnnouncementRepository
    • ca.corefacility.bioinformatics.irida.repositories.assembly.GenomeAssemblyRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
    • ca.corefacility.bioinformatics.irida.repositories.IridaClientDetailsRepository
    • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.JobErrorRepository
    • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository (also extends ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepositoryCustom)
    • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepository (also extends ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepositoryCustom)
    • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataRestrictionRepository
    • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataTemplateRepository
    • ca.corefacility.bioinformatics.irida.repositories.NcbiExportSubmissionRepository
    • ca.corefacility.bioinformatics.irida.repositories.user.PasswordResetRepository
    • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.ProjectAnalysisSubmissionJoinRepository
    • ca.corefacility.bioinformatics.irida.repositories.ProjectEventRepository
    • ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectReferenceFileJoinRepository
    • ca.corefacility.bioinformatics.irida.repositories.ProjectRepository (also extends ca.corefacility.bioinformatics.irida.repositories.ProjectRepositoryCustom)
    • ca.corefacility.bioinformatics.irida.repositories.ProjectSubscriptionRepository
    • ca.corefacility.bioinformatics.irida.repositories.sample.QCEntryRepository
    • ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
    • ca.corefacility.bioinformatics.irida.repositories.RemoteAPIRepository
    • ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository (also extends ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepositoryCustom)
    • ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleSequencingObjectJoinRepository
    • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceConcatenationRepository
    • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
    • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository
    • ca.corefacility.bioinformatics.irida.repositories.SequencingRunRepository
    • ca.corefacility.bioinformatics.irida.repositories.user.UserGroupJoinRepository
    • ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository
    • ca.corefacility.bioinformatics.irida.repositories.user.UserGroupRepository
    • ca.corefacility.bioinformatics.irida.repositories.user.UserRepository (also extends org.springframework.security.core.userdetails.UserDetailsService, ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryCustom)
    • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.WorkflowNamedParametersRepository
  • ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository (also extends org.springframework.data.repository.PagingAndSortingRepository<T,ID>)
  • ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository (also extends org.springframework.data.repository.CrudRepository<T,ID>)
• org.springframework.mail.MailSender
  • org.springframework.mail.javamail.JavaMailSender
    • ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig.ConfigurableJavaMailSender
• ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepositoryCustom
  • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>)
• ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepositoryCustom
  • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>)
• ca.corefacility.bioinformatics.irida.model.workflow.execution.PreparedWorkflow<WorkflowInputsType>
• ca.corefacility.bioinformatics.irida.service.ProjectEventEmailScheduledTask
• ca.corefacility.bioinformatics.irida.repositories.ProjectRepositoryCustom
  • ca.corefacility.bioinformatics.irida.repositories.ProjectRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>)
• ca.corefacility.bioinformatics.irida.service.RemoteAPITokenService
• ca.corefacility.bioinformatics.irida.repositories.remote.RemoteRepository<Type>
  • ca.corefacility.bioinformatics.irida.repositories.remote.Fast5ObjectRemoteRepository
  • ca.corefacility.bioinformatics.irida.repositories.remote.GenomeAssemblyRemoteRepository
  • ca.corefacility.bioinformatics.irida.repositories.remote.ProjectRemoteRepository
  • ca.corefacility.bioinformatics.irida.repositories.remote.SampleRemoteRepository
  • ca.corefacility.bioinformatics.irida.repositories.remote.SequenceFilePairRemoteRepository
  • ca.corefacility.bioinformatics.irida.repositories.remote.SequenceFileRemoteRepository
  • ca.corefacility.bioinformatics.irida.repositories.remote.SingleEndSequenceFileRemoteRepository
• ca.corefacility.bioinformatics.irida.service.remote.RemoteService<Type>
  • ca.corefacility.bioinformatics.irida.service.remote.GenomeAssemblyRemoteService
  • ca.corefacility.bioinformatics.irida.service.remote.ProjectRemoteService
  • ca.corefacility.bioinformatics.irida.service.remote.SampleRemoteService
  • ca.corefacility.bioinformatics.irida.service.remote.SequencingObjectRemoteService<Type>
    • ca.corefacility.bioinformatics.irida.service.remote.Fast5ObjectRemoteService
    • ca.corefacility.bioinformatics.irida.service.remote.SequenceFilePairRemoteService
    • ca.corefacility.bioinformatics.irida.service.remote.SingleEndSequenceFileRemoteService
• ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable
• org.springframework.data.repository.Repository<T,ID>
  • org.springframework.data.repository.CrudRepository<T,ID>
    • org.springframework.data.repository.PagingAndSortingRepository<T,ID>
      • ca.corefacility.bioinformatics.irida.repositories.joins.announcement.AnnouncementUserJoinRepository (also extends org.springframework.data.jpa.repository.JpaSpecificationExecutor<T>)
      • ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier> (also extends org.springframework.data.jpa.repository.JpaSpecificationExecutor<T>, org.springframework.data.repository.history.RevisionRepository<T,ID,N>)
        • ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisOutputFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
        • ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisRepository
        • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository
        • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionTemplateRepository
        • ca.corefacility.bioinformatics.irida.repositories.AnnouncementRepository
        • ca.corefacility.bioinformatics.irida.repositories.assembly.GenomeAssemblyRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
        • ca.corefacility.bioinformatics.irida.repositories.IridaClientDetailsRepository
        • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.JobErrorRepository
        • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository (also extends ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepositoryCustom)
        • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepository (also extends ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepositoryCustom)
        • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataRestrictionRepository
        • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataTemplateRepository
        • ca.corefacility.bioinformatics.irida.repositories.NcbiExportSubmissionRepository
        • ca.corefacility.bioinformatics.irida.repositories.user.PasswordResetRepository
        • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.ProjectAnalysisSubmissionJoinRepository
        • ca.corefacility.bioinformatics.irida.repositories.ProjectEventRepository
        • ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectReferenceFileJoinRepository
        • ca.corefacility.bioinformatics.irida.repositories.ProjectRepository (also extends ca.corefacility.bioinformatics.irida.repositories.ProjectRepositoryCustom)
        • ca.corefacility.bioinformatics.irida.repositories.ProjectSubscriptionRepository
        • ca.corefacility.bioinformatics.irida.repositories.sample.QCEntryRepository
        • ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
        • ca.corefacility.bioinformatics.irida.repositories.RemoteAPIRepository
        • ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository (also extends ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepositoryCustom)
        • ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleSequencingObjectJoinRepository
        • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceConcatenationRepository
        • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
        • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository
        • ca.corefacility.bioinformatics.irida.repositories.SequencingRunRepository
        • ca.corefacility.bioinformatics.irida.repositories.user.UserGroupJoinRepository
        • ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository
        • ca.corefacility.bioinformatics.irida.repositories.user.UserGroupRepository
        • ca.corefacility.bioinformatics.irida.repositories.user.UserRepository (also extends org.springframework.security.core.userdetails.UserDetailsService, ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryCustom)
        • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.WorkflowNamedParametersRepository
      • ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository (also extends org.springframework.data.jpa.repository.JpaSpecificationExecutor<T>)
    • ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository (also extends org.springframework.data.jpa.repository.JpaSpecificationExecutor<T>)
    • ca.corefacility.bioinformatics.irida.repositories.joins.project.RelatedProjectRepository
    • ca.corefacility.bioinformatics.irida.repositories.RemoteApiTokenRepository (also extends org.springframework.data.repository.history.RevisionRepository<T,ID,N>)
    • ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleGenomeAssemblyJoinRepository
  • org.springframework.data.repository.history.RevisionRepository<T,ID,N>
    • ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier> (also extends org.springframework.data.jpa.repository.JpaSpecificationExecutor<T>, org.springframework.data.repository.PagingAndSortingRepository<T,ID>)
      • ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisOutputFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
      • ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisRepository
      • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository
      • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionTemplateRepository
      • ca.corefacility.bioinformatics.irida.repositories.AnnouncementRepository
      • ca.corefacility.bioinformatics.irida.repositories.assembly.GenomeAssemblyRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
      • ca.corefacility.bioinformatics.irida.repositories.IridaClientDetailsRepository
      • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.JobErrorRepository
      • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository (also extends ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepositoryCustom)
      • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepository (also extends ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepositoryCustom)
      • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataRestrictionRepository
      • ca.corefacility.bioinformatics.irida.repositories.sample.MetadataTemplateRepository
      • ca.corefacility.bioinformatics.irida.repositories.NcbiExportSubmissionRepository
      • ca.corefacility.bioinformatics.irida.repositories.user.PasswordResetRepository
      • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.ProjectAnalysisSubmissionJoinRepository
      • ca.corefacility.bioinformatics.irida.repositories.ProjectEventRepository
      • ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectReferenceFileJoinRepository
      • ca.corefacility.bioinformatics.irida.repositories.ProjectRepository (also extends ca.corefacility.bioinformatics.irida.repositories.ProjectRepositoryCustom)
      • ca.corefacility.bioinformatics.irida.repositories.ProjectSubscriptionRepository
      • ca.corefacility.bioinformatics.irida.repositories.sample.QCEntryRepository
      • ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
      • ca.corefacility.bioinformatics.irida.repositories.RemoteAPIRepository
      • ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository (also extends ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepositoryCustom)
      • ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleSequencingObjectJoinRepository
      • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceConcatenationRepository
      • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository (also extends ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository<Type>)
      • ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository
      • ca.corefacility.bioinformatics.irida.repositories.SequencingRunRepository
      • ca.corefacility.bioinformatics.irida.repositories.user.UserGroupJoinRepository
      • ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository
      • ca.corefacility.bioinformatics.irida.repositories.user.UserGroupRepository
      • ca.corefacility.bioinformatics.irida.repositories.user.UserRepository (also extends org.springframework.security.core.userdetails.UserDetailsService, ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryCustom)
      • ca.corefacility.bioinformatics.irida.repositories.analysis.submission.WorkflowNamedParametersRepository
    • ca.corefacility.bioinformatics.irida.repositories.RemoteApiTokenRepository (also extends org.springframework.data.repository.CrudRepository<T,ID>)
• ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepositoryCustom
  • ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>)
• ca.corefacility.bioinformatics.irida.service.util.SequenceFileUtilities
• ca.corefacility.bioinformatics.irida.service.TaxonomyService
• ca.corefacility.bioinformatics.irida.model.Timestamped<Identifier>
  • ca.corefacility.bioinformatics.irida.model.IridaThing
    • ca.corefacility.bioinformatics.irida.model.joins.Join<SubjectType,ObjectType>
    • ca.corefacility.bioinformatics.irida.model.MutableIridaThing
• ca.corefacility.bioinformatics.irida.model.upload.UploaderAccountName
• ca.corefacility.bioinformatics.irida.model.upload.UploadProjectName
• org.springframework.security.core.userdetails.UserDetailsService
  • ca.corefacility.bioinformatics.irida.repositories.user.UserRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>, ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryCustom)
  • ca.corefacility.bioinformatics.irida.service.user.UserService (also extends ca.corefacility.bioinformatics.irida.service.CRUDService<IdentifierType,Type>)
• ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryCustom
  • ca.corefacility.bioinformatics.irida.repositories.user.UserRepository (also extends ca.corefacility.bioinformatics.irida.repositories.IridaJpaRepository<Type,Identifier>, org.springframework.security.core.userdetails.UserDetailsService)
• ca.corefacility.bioinformatics.irida.model.VersionedFileFields<VersionType>
• ca.corefacility.bioinformatics.irida.model.workflow.execution.WorkflowInputsGeneric

Annotation Type Hierarchy

• ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config.DataTablesRequest (implements java.lang.annotation.Annotation)
• ca.corefacility.bioinformatics.irida.validators.annotations.Latitude (implements java.lang.annotation.Annotation)
• ca.corefacility.bioinformatics.irida.events.annotations.LaunchesProjectEvent (implements java.lang.annotation.Annotation)
• ca.corefacility.bioinformatics.irida.validators.annotations.Longitude (implements java.lang.annotation.Annotation)
• ca.corefacility.bioinformatics.irida.constraints.MetadataRoleValidate (implements java.lang.annotation.Annotation)
• ca.corefacility.bioinformatics.irida.service.analysis.annotations.RunAsUser (implements java.lang.annotation.Annotation)
• ca.corefacility.bioinformatics.irida.validators.annotations.ValidProjectName (implements java.lang.annotation.Annotation)
• ca.corefacility.bioinformatics.irida.validators.annotations.ValidSampleName (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType
    • ca.corefacility.bioinformatics.irida.model.enums.AnalysisCleanedState
    • ca.corefacility.bioinformatics.irida.model.enums.AnalysisState
    • ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Priority
    • ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.DatasetCollectionType
    • ca.corefacility.bioinformatics.irida.pipeline.upload.DataStorage
    • ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportTypes
    • ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState
    • ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object.Fast5Type
    • ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState
    • ca.corefacility.bioinformatics.irida.model.workflow.execution.InputFileType
    • ca.corefacility.bioinformatics.irida.ria.web.models.ModelKeys
    • ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel
    • ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection
    • ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource
    • ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy
    • ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform
    • ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.NotificationType
    • ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole
    • ca.corefacility.bioinformatics.irida.model.enums.ProjectRole
    • ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency
    • ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryStatus
    • ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryType
    • ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus
    • ca.corefacility.bioinformatics.irida.model.user.Role (implements org.springframework.security.core.GrantedAuthority)
    • ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation
    • ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject.ProcessingState
    • ca.corefacility.bioinformatics.irida.model.run.SequencingRun.LayoutType
    • ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus
    • ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod
    • ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin.UserGroupRole
    • ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerTagType