Hierarchy For All Packages

Class Hierarchy

• java.lang.Object
  • io.seqware.webservice.generated.controller.AbstractFacade<T>
    • io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST
      • io.seqware.webservice.controller.CustomExpenseAttributeFacadeREST
    • io.seqware.webservice.generated.controller.ExpenseFacadeREST
      • io.seqware.webservice.controller.CustomExpenseFacadeREST
    • io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST
      • io.seqware.webservice.controller.CustomExperimentAttributeFacadeREST
    • io.seqware.webservice.generated.controller.ExperimentFacadeREST
      • io.seqware.webservice.controller.CustomExperimentFacadeREST
    • io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST
      • io.seqware.webservice.controller.CustomExperimentLibraryDesignFacadeREST
    • io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST
      • io.seqware.webservice.controller.CustomExperimentLinkFacadeREST
    • io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST
      • io.seqware.webservice.controller.CustomExperimentSpotDesignFacadeREST
    • io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST
      • io.seqware.webservice.controller.CustomExperimentSpotDesignReadSpecFacadeREST
    • io.seqware.webservice.generated.controller.FileAttributeFacadeREST
      • io.seqware.webservice.controller.CustomFileAttributeFacadeREST
    • io.seqware.webservice.generated.controller.FileFacadeREST
      • io.seqware.webservice.controller.CustomFileFacadeREST
    • io.seqware.webservice.generated.controller.FileReportFacadeREST
      • io.seqware.webservice.controller.CustomFileReportFacadeREST
    • io.seqware.webservice.generated.controller.FileTypeFacadeREST
      • io.seqware.webservice.controller.CustomFileTypeFacadeREST
    • io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST
      • io.seqware.webservice.controller.CustomInvoiceAttributeFacadeREST
    • io.seqware.webservice.generated.controller.InvoiceFacadeREST
      • io.seqware.webservice.controller.CustomInvoiceFacadeREST
    • io.seqware.webservice.generated.controller.IusAttributeFacadeREST
      • io.seqware.webservice.controller.CustomIusAttributeFacadeREST
    • io.seqware.webservice.generated.controller.IusFacadeREST
      • io.seqware.webservice.controller.CustomIusFacadeREST
    • io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST
      • io.seqware.webservice.controller.CustomIusWorkflowRunsFacadeREST
    • io.seqware.webservice.generated.controller.LaneAttributeFacadeREST
      • io.seqware.webservice.controller.CustomLaneAttributeFacadeREST
    • io.seqware.webservice.generated.controller.LaneFacadeREST
      • io.seqware.webservice.controller.CustomLaneFacadeREST
    • io.seqware.webservice.generated.controller.LaneTypeFacadeREST
      • io.seqware.webservice.controller.CustomLaneTypeFacadeREST
    • io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST
      • io.seqware.webservice.controller.CustomLaneWorkflowRunsFacadeREST
    • io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST
      • io.seqware.webservice.controller.CustomLibrarySelectionFacadeREST
    • io.seqware.webservice.generated.controller.LibrarySourceFacadeREST
      • io.seqware.webservice.controller.CustomLibrarySourceFacadeREST
    • io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST
      • io.seqware.webservice.controller.CustomLibraryStrategyFacadeREST
    • io.seqware.webservice.generated.controller.OrganismFacadeREST
      • io.seqware.webservice.controller.CustomOrganismFacadeREST
    • io.seqware.webservice.generated.controller.PlatformFacadeREST
      • io.seqware.webservice.controller.CustomPlatformFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST
      • io.seqware.webservice.controller.CustomProcessingAttributeFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST
      • io.seqware.webservice.controller.CustomProcessingExperimentsFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingFacadeREST
      • io.seqware.webservice.controller.CustomProcessingFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST
      • io.seqware.webservice.controller.CustomProcessingFilesFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingIusFacadeREST
      • io.seqware.webservice.controller.CustomProcessingIusFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST
      • io.seqware.webservice.controller.CustomProcessingLanesFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST
      • io.seqware.webservice.controller.CustomProcessingRelationshipFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST
      • io.seqware.webservice.controller.CustomProcessingSamplesFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST
      • io.seqware.webservice.controller.CustomProcessingSequencerRunsFacadeREST
    • io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST
      • io.seqware.webservice.controller.CustomProcessingStudiesFacadeREST
    • io.seqware.webservice.generated.controller.RegistrationFacadeREST
      • io.seqware.webservice.controller.CustomRegistrationFacadeREST
    • io.seqware.webservice.generated.controller.SampleAttributeFacadeREST
      • io.seqware.webservice.controller.CustomSampleAttributeFacadeREST
    • io.seqware.webservice.generated.controller.SampleFacadeREST
      • io.seqware.webservice.controller.CustomSampleFacadeREST
    • io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST
      • io.seqware.webservice.controller.CustomSampleRelationshipFacadeREST
    • io.seqware.webservice.generated.controller.SampleReportFacadeREST
      • io.seqware.webservice.controller.CustomSampleReportFacadeREST
    • io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST
      • io.seqware.webservice.controller.CustomSequencerRunAttributeFacadeREST
    • io.seqware.webservice.generated.controller.SequencerRunFacadeREST
      • io.seqware.webservice.controller.CustomSequencerRunFacadeREST
    • io.seqware.webservice.generated.controller.ShareStudyFacadeREST
      • io.seqware.webservice.controller.CustomShareStudyFacadeREST
    • io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST
      • io.seqware.webservice.controller.CustomShareWorkflowRunFacadeREST
    • io.seqware.webservice.generated.controller.StudyAttributeFacadeREST
      • io.seqware.webservice.controller.CustomStudyAttributeFacadeREST
    • io.seqware.webservice.generated.controller.StudyFacadeREST
      • io.seqware.webservice.controller.CustomStudyFacadeREST
    • io.seqware.webservice.generated.controller.StudyTypeFacadeREST
      • io.seqware.webservice.controller.CustomStudyTypeFacadeREST
    • io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST
      • io.seqware.webservice.controller.CustomWorkflowAttributeFacadeREST
    • io.seqware.webservice.generated.controller.WorkflowFacadeREST
      • io.seqware.webservice.controller.CustomWorkflowFacadeREST
    • io.seqware.webservice.generated.controller.WorkflowParamFacadeREST
      • io.seqware.webservice.controller.CustomWorkflowParamFacadeREST
    • io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST
      • io.seqware.webservice.controller.CustomWorkflowParamValueFacadeREST
    • io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST
      • io.seqware.webservice.controller.CustomWorkflowRunAttributeFacadeREST
    • io.seqware.webservice.generated.controller.WorkflowRunFacadeREST
      • io.seqware.webservice.controller.CustomWorkflowRunFacadeREST
    • io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST
      • io.seqware.webservice.controller.CustomWorkflowRunParamFacadeREST
  • net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob (implements net.sourceforge.seqware.pipeline.workflowV2.model.Job)
    • net.sourceforge.seqware.pipeline.workflowV2.model.BashJob
    • net.sourceforge.seqware.pipeline.workflowV2.model.JavaJob
    • net.sourceforge.seqware.pipeline.workflowV2.model.JavaSeqwareModuleJob
    • net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
    • net.sourceforge.seqware.pipeline.workflowV2.model.PerlJob
  • net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
  • org.springframework.context.support.ApplicationObjectSupport (implements org.springframework.context.ApplicationContextAware)
    • net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
    • org.springframework.web.context.support.WebApplicationObjectSupport (implements org.springframework.web.context.ServletContextAware)
      • org.springframework.web.servlet.support.WebContentGenerator
        • org.springframework.web.servlet.mvc.AbstractController (implements org.springframework.web.servlet.mvc.Controller)
          • org.springframework.web.servlet.mvc.BaseCommandController
            • net.sourceforge.solexatools.webapp.controller.AbortLoadIndexPageController
            • org.springframework.web.servlet.mvc.AbstractFormController
              • org.springframework.web.servlet.mvc.SimpleFormController
                • net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
                • net.sourceforge.solexatools.webapp.controller.LoginController
            • net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
            • net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
            • net.sourceforge.solexatools.webapp.controller.AnalisysListController
            • net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
            • net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
            • net.sourceforge.solexatools.webapp.controller.AnalisysTableController
            • net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
            • net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
            • net.sourceforge.solexatools.webapp.controller.BulkDownloaderSizeValidatorController
            • net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
            • net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
            • net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
            • net.sourceforge.solexatools.webapp.controller.CancelBulkDownloaderController
            • net.sourceforge.solexatools.webapp.controller.CancelInputDownloaderController
            • net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
            • net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
            • net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
            • net.sourceforge.solexatools.webapp.controller.DownloaderController
            • net.sourceforge.solexatools.webapp.controller.DownloadFileListController
            • net.sourceforge.solexatools.webapp.controller.EntityController
            • net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
            • net.sourceforge.solexatools.webapp.controller.FileSetupController
            • net.sourceforge.solexatools.webapp.controller.InviteNewUserController
            • net.sourceforge.solexatools.webapp.controller.InviteNewUserSetupController
            • net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
            • net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
            • net.sourceforge.solexatools.webapp.controller.IUSSetupController
            • net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
            • net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
            • net.sourceforge.solexatools.webapp.controller.LaneSetupController
            • net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
            • net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
            • net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
            • net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
            • net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
            • net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
            • net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
            • net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
            • net.sourceforge.solexatools.webapp.controller.RetryAnalysisWorkflowController
            • net.sourceforge.solexatools.webapp.controller.SampleSetupController
            • net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
            • net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
            • net.sourceforge.solexatools.webapp.controller.SearchController
            • net.sourceforge.solexatools.webapp.controller.SearchResultsController
            • net.sourceforge.solexatools.webapp.controller.SearchResultsListController
            • net.sourceforge.solexatools.webapp.controller.SelectInputListController
            • net.sourceforge.solexatools.webapp.controller.SequencerRunListController
            • net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
            • net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
            • net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
            • net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
            • net.sourceforge.solexatools.webapp.controller.ShareValidatorController
            • net.sourceforge.solexatools.webapp.controller.SignUpController
            • net.sourceforge.solexatools.webapp.controller.StudyListController
            • net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
            • net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
            • net.sourceforge.solexatools.webapp.controller.StudyReportController
            • net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
            • net.sourceforge.solexatools.webapp.controller.StudyReportTableController
            • net.sourceforge.solexatools.webapp.controller.StudySetupController
            • net.sourceforge.solexatools.webapp.controller.StudyTableController
            • net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails
            • net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
            • net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
            • net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
            • net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
            • net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
            • net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
            • net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
            • net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
          • net.sourceforge.solexatools.webapp.controller.LogoutController
          • org.springframework.web.servlet.mvc.multiaction.MultiActionController (implements org.springframework.web.servlet.mvc.LastModified)
            • net.sourceforge.solexatools.webapp.controller.AnalisysEventController
            • net.sourceforge.solexatools.webapp.controller.ExperimentController
            • net.sourceforge.solexatools.webapp.controller.FileController
            • net.sourceforge.solexatools.webapp.controller.IUSController
            • net.sourceforge.solexatools.webapp.controller.LaneController
            • net.sourceforge.solexatools.webapp.controller.ProcessingController
            • net.sourceforge.solexatools.webapp.controller.RegistrationController
            • net.sourceforge.solexatools.webapp.controller.SampleController
            • net.sourceforge.solexatools.webapp.controller.SelectInputController
            • net.sourceforge.solexatools.webapp.controller.SequencerRunController
            • net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
            • net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
            • net.sourceforge.solexatools.webapp.controller.StudyController
            • net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
            • net.sourceforge.solexatools.webapp.controller.UploadFileController
            • net.sourceforge.solexatools.webapp.controller.UploadSequenceController
            • net.sourceforge.solexatools.webapp.controller.WorkflowController
            • net.sourceforge.solexatools.webapp.controller.WorkflowParamController
            • net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
            • net.sourceforge.solexatools.webapp.controller.WorkflowRunController
  • net.sourceforge.seqware.pipeline.workflowV2.model.Argument
  • net.sourceforge.seqware.common.model.Attribute<T,S> (implements java.lang.Comparable<T>)
    • net.sourceforge.seqware.common.model.ExperimentAttribute (implements java.io.Serializable)
    • net.sourceforge.seqware.common.model.FileAttribute (implements java.io.Serializable)
    • net.sourceforge.seqware.common.model.IUSAttribute (implements java.io.Serializable)
    • net.sourceforge.seqware.common.model.LaneAttribute (implements java.io.Serializable)
    • net.sourceforge.seqware.common.model.ProcessingAttribute (implements java.io.Serializable)
    • net.sourceforge.seqware.common.model.SampleAttribute (implements java.io.Serializable)
    • net.sourceforge.seqware.common.model.SequencerRunAttribute (implements java.io.Serializable)
    • net.sourceforge.seqware.common.model.StudyAttribute (implements java.io.Serializable)
    • net.sourceforge.seqware.common.model.WorkflowAttribute (implements java.io.Serializable)
    • net.sourceforge.seqware.common.model.WorkflowRunAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.AttributePlugin (implements net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface)
  • net.sourceforge.solexatools.authentication.Authentication
    • net.sourceforge.solexatools.authentication.OICRLdapAuthentication
    • net.sourceforge.solexatools.authentication.UNCKerberos
  • net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreatorWrapper
  • net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
    • net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.CreateFromScratch
    • net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.ParseMiseqFile
  • net.sourceforge.seqware.common.factory.BeanFactory
  • org.apache.commons.beanutils.BeanUtilsBean
    • net.sourceforge.seqware.common.util.NullBeanUtils
  • net.sourceforge.seqware.common.util.Bool
  • net.sourceforge.solexatools.util.BulkUtil
  • net.sourceforge.seqware.pipeline.bundle.Bundle
  • io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • net.sourceforge.seqware.pipeline.bundle.BundleInfo
  • net.sourceforge.seqware.common.hibernate.CheckForCycles
  • io.seqware.pipeline.plugins.sanity.checks.CLICheck (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • io.seqware.pipeline.plugins.sanity.checks.ClientServerConsistencyCheck (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • net.sourceforge.seqware.pipeline.workflowV2.model.Command
  • net.sourceforge.seqware.common.util.configtools.ConfigTools
  • net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
  • net.sourceforge.solexatools.util.Constant
  • net.sourceforge.seqware.common.ContextImpl
  • net.sourceforge.solexatools.util.ControllerUtil
  • org.springframework.dao.support.DaoSupport (implements org.springframework.beans.factory.InitializingBean)
    • org.springframework.orm.hibernate3.support.HibernateDaoSupport
      • net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate (implements net.sourceforge.seqware.common.dao.ExperimentAttributeDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate (implements net.sourceforge.seqware.common.dao.ExperimentDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate (implements net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate (implements net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate (implements net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO)
      • net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate (implements net.sourceforge.seqware.common.dao.FileDAO)
      • net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate (implements net.sourceforge.seqware.common.dao.FileReportDAO)
      • net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate (implements net.sourceforge.seqware.common.dao.FileTypeDAO)
      • net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate (implements net.sourceforge.seqware.common.dao.InvoiceDAO)
      • net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate (implements net.sourceforge.seqware.common.dao.IUSAttributeDAO)
      • net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate (implements net.sourceforge.seqware.common.dao.IUSDAO)
      • net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate (implements net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO)
      • net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate (implements net.sourceforge.seqware.common.dao.LaneDAO)
      • net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate (implements net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO)
      • net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate (implements net.sourceforge.seqware.common.dao.LibrarySelectionDAO)
      • net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate (implements net.sourceforge.seqware.common.dao.LibrarySourceDAO)
      • net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate (implements net.sourceforge.seqware.common.dao.LibraryStrategyDAO)
      • net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate (implements net.sourceforge.seqware.common.dao.OrganismDAO)
      • net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate (implements net.sourceforge.seqware.common.dao.PlatformDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate (implements net.sourceforge.seqware.common.dao.ProcessingAttributeDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate (implements net.sourceforge.seqware.common.dao.ProcessingDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate (implements net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate (implements net.sourceforge.seqware.common.dao.ProcessingIUSDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate (implements net.sourceforge.seqware.common.dao.ProcessingLanesDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate (implements net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate (implements net.sourceforge.seqware.common.dao.ProcessingSamplesDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate (implements net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate (implements net.sourceforge.seqware.common.dao.ProcessingStudiesDAO)
      • net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate (implements net.sourceforge.seqware.common.dao.RegistrationDAO)
      • net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate (implements net.sourceforge.seqware.common.dao.SampleAttributeDAO)
      • net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate (implements net.sourceforge.seqware.common.dao.SampleDAO)
      • net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate (implements net.sourceforge.seqware.common.dao.SampleReportDAO)
      • net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate (implements net.sourceforge.seqware.common.dao.SequencerRunDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate (implements net.sourceforge.seqware.common.dao.ShareStudyDAO)
      • net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate (implements net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO)
      • net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate (implements net.sourceforge.seqware.common.dao.StudyAttributeDAO)
      • net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate (implements net.sourceforge.seqware.common.dao.StudyDAO)
      • net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate (implements net.sourceforge.seqware.common.dao.StudyTypeDAO)
      • net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate (implements net.sourceforge.seqware.common.dao.WorkflowDAO)
      • net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate (implements net.sourceforge.seqware.common.dao.WorkflowParamDAO)
      • net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate (implements net.sourceforge.seqware.common.dao.WorkflowParamValueDAO)
      • net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate (implements net.sourceforge.seqware.common.dao.WorkflowRunDAO)
      • net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate (implements net.sourceforge.seqware.common.dao.WorkflowRunParamDAO)
  • io.seqware.pipeline.plugins.sanity.checks.DB_Check (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • net.sourceforge.seqware.common.factory.DBAccess
  • net.sourceforge.solexatools.Debug
  • io.seqware.Engines
  • net.sourceforge.seqware.pipeline.workflowV2.model.Environment
  • net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
  • io.seqware.webservice.generated.model.Expense (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ExpenseAttribute (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.Experiment (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ExperimentAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.ExperimentLibraryDesign (implements java.lang.Comparable<T>, net.sourceforge.seqware.common.model.SecondTierModel, java.io.Serializable)
  • io.seqware.webservice.generated.model.ExperimentLibraryDesign (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList
  • net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl (implements net.sourceforge.seqware.common.business.ExperimentLibraryDesignService)
  • io.seqware.webservice.generated.model.ExperimentLink (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.ExperimentList
  • net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl (implements net.sourceforge.seqware.common.business.ExperimentService)
  • net.sourceforge.seqware.common.model.ExperimentSpotDesign (implements java.lang.Comparable<T>, net.sourceforge.seqware.common.model.SecondTierModel, java.io.Serializable)
  • io.seqware.webservice.generated.model.ExperimentSpotDesign (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList
  • net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec (implements java.lang.Comparable<T>, net.sourceforge.seqware.common.model.SecondTierModel, java.io.Serializable)
  • io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.comparator.ExperimentSpotDesignReadSpecComparator (implements java.util.Comparator<T>)
  • net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList
  • net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl (implements net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService)
  • net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl (implements net.sourceforge.seqware.common.business.ExperimentSpotDesignService)
  • net.sourceforge.solexatools.validation.ExperimentValidator (implements org.springframework.validation.Validator)
    • net.sourceforge.solexatools.validation.ExperimentUpdateValidator
  • io.seqware.webservice.generated.model.File (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.FileAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate (implements net.sourceforge.seqware.common.dao.FileAttributeDAO)
  • net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl (implements net.sourceforge.seqware.common.business.FileAttributeService)
  • net.sourceforge.solexatools.util.FileFinder
  • net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
  • net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser
  • net.sourceforge.seqware.common.model.lists.FileList
  • net.sourceforge.seqware.common.module.FileMetadata
  • io.seqware.webservice.generated.model.FileReport (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.FileReportRow (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.FileReportServiceImpl (implements net.sourceforge.seqware.common.business.FileReportService)
  • net.sourceforge.seqware.common.business.impl.FileServiceImpl (implements net.sourceforge.seqware.common.business.FileService)
  • net.sourceforge.seqware.common.util.filetools.FileTools
  • net.sourceforge.seqware.common.util.filetools.FileTools.LocalhostPair
  • net.sourceforge.seqware.common.model.FileType (implements java.lang.Comparable<T>, java.io.Serializable)
  • io.seqware.webservice.generated.model.FileType (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl (implements net.sourceforge.seqware.common.business.FileTypeService)
  • net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl (implements net.sourceforge.seqware.common.business.FileUploadService)
  • net.sourceforge.seqware.common.hibernate.FindAllTheFiles
  • net.sourceforge.solexatools.util.FindChildUtil
  • net.sourceforge.solexatools.util.FindRootUtil
  • net.sourceforge.solexatools.webapp.metamodel.Flexigrid
  • net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
  • net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
  • io.seqware.pipeline.plugins.sanity.checks.HDFS_Check (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • net.sourceforge.solexatools.util.HTMLTagValidator
  • net.sourceforge.seqware.common.hibernate.InSessionExecutions
  • net.sourceforge.seqware.common.model.lists.IntegerList
  • net.sourceforge.seqware.common.invitation.InvitationParams
  • io.seqware.webservice.generated.model.Invoice (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.InvoiceAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl (implements net.sourceforge.seqware.common.business.InvoiceService)
  • net.sourceforge.seqware.pipeline.plugins.ITUtility
  • io.seqware.webservice.generated.model.Ius (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.IusAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.IUSList
  • net.sourceforge.seqware.common.business.impl.IUSServiceImpl (implements net.sourceforge.seqware.common.business.IUSService)
  • io.seqware.webservice.generated.model.IusWorkflowRuns (implements java.io.Serializable)
  • net.sourceforge.seqware.common.util.xmltools.JaxbObject<T>
  • net.sourceforge.seqware.common.util.testtools.JndiDatasourceCreator
  • net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
  • net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
  • net.sourceforge.seqware.common.util.jsontools.JSONHelper
  • net.sourceforge.seqware.common.util.jsontools.JsonUtil
  • io.seqware.webservice.generated.model.Lane (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.LaneAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo (implements java.lang.Comparable<T>)
  • net.sourceforge.seqware.common.model.lists.LaneList
  • net.sourceforge.seqware.common.business.impl.LaneServiceImpl (implements net.sourceforge.seqware.common.business.LaneService)
  • io.seqware.webservice.generated.model.LaneType (implements java.io.Serializable)
  • net.sourceforge.solexatools.validation.LaneValidator (implements org.springframework.validation.Validator)
  • io.seqware.webservice.generated.model.LaneWorkflowRuns (implements java.io.Serializable)
  • net.sourceforge.solexatools.util.LaunchWorkflowUtil
  • net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate (implements net.sourceforge.seqware.common.dao.LibraryDAO)
  • net.sourceforge.seqware.common.model.LibrarySelection (implements java.lang.Comparable<T>, net.sourceforge.seqware.common.model.SecondTierModel, java.io.Serializable)
  • io.seqware.webservice.generated.model.LibrarySelection (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.LibrarySelectionList
  • net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl (implements net.sourceforge.seqware.common.business.LibrarySelectionService)
  • net.sourceforge.seqware.common.business.impl.LibraryServiceImpl (implements net.sourceforge.seqware.common.business.LibraryService)
  • net.sourceforge.seqware.common.model.LibrarySource (implements java.lang.Comparable<T>, net.sourceforge.seqware.common.model.SecondTierModel, java.io.Serializable)
  • io.seqware.webservice.generated.model.LibrarySource (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.LibrarySourceList
  • net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl (implements net.sourceforge.seqware.common.business.LibrarySourceService)
  • net.sourceforge.seqware.common.model.LibraryStrategy (implements java.lang.Comparable<T>, net.sourceforge.seqware.common.model.SecondTierModel, java.io.Serializable)
  • io.seqware.webservice.generated.model.LibraryStrategy (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.LibraryStrategyList
  • net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl (implements net.sourceforge.seqware.common.business.LibraryStrategyService)
  • net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools
  • net.sourceforge.seqware.common.util.Log
  • net.sourceforge.solexatools.validation.LoginValidator (implements org.springframework.validation.Validator)
    • net.sourceforge.solexatools.validation.FileValidator
    • net.sourceforge.solexatools.validation.RegistrationValidator
  • io.seqware.cli.Main
  • net.sourceforge.seqware.common.util.maptools.MapTools
  • net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.MarkDownFormatter (implements joptsimple.HelpFormatter)
  • net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.ModuleComparator (implements java.util.Comparator<T>)
  • net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.PluginComparator (implements java.util.Comparator<T>)
  • net.sourceforge.seqware.common.util.MD5Generator
  • net.sourceforge.seqware.common.metadata.MetadataDB (implements net.sourceforge.seqware.common.metadata.Metadata)
  • net.sourceforge.seqware.common.metadata.MetadataDB.IntByIndex (implements org.apache.commons.dbutils.ResultSetHandler<T>)
  • net.sourceforge.seqware.common.metadata.MetadataDB.IntByName (implements org.apache.commons.dbutils.ResultSetHandler<T>)
  • net.sourceforge.seqware.common.metadata.MetadataFactory
  • net.sourceforge.seqware.common.metadata.MetadataInMemory (implements net.sourceforge.seqware.common.metadata.Metadata)
  • net.sourceforge.seqware.common.metadata.MetadataNoConnection (implements net.sourceforge.seqware.common.metadata.Metadata)
  • net.sourceforge.seqware.common.metadata.MetadataWS (implements net.sourceforge.seqware.common.metadata.Metadata)
  • net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
  • io.seqware.webservice.controller.ModelAccessionIDTuple (implements java.lang.Comparable<T>)
  • io.seqware.webservice.generated.controller.ModelAccessionIDTuple (implements java.lang.Comparable<T>)
  • net.sourceforge.solexatools.util.ModelUtil
  • net.sourceforge.seqware.pipeline.module.Module (implements net.sourceforge.seqware.pipeline.module.ModuleInterface)
    • net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
    • net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
    • net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
    • net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
    • net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
    • net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
    • net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
    • net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
    • net.sourceforge.seqware.pipeline.module.TestModule
  • net.sourceforge.solexatools.util.NodeHtmlUtil
  • io.seqware.pipeline.plugins.sanity.checks.Oozie_Check (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob (implements java.lang.Comparable<T>)
    • net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob
    • net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob
    • net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob
    • net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
  • net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine (implements io.seqware.pipeline.api.WorkflowEngine)
  • net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowXmlGenerator
  • net.sourceforge.seqware.common.model.Organism (implements java.lang.Comparable<T>, net.sourceforge.seqware.common.model.SecondTierModel, java.io.Serializable)
  • io.seqware.webservice.generated.model.Organism (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.OrganismList
  • net.sourceforge.seqware.common.business.impl.OrganismServiceImpl (implements net.sourceforge.seqware.common.business.OrganismService)
  • net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.OrphanCheckerPlugin (implements net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface)
  • net.sourceforge.solexatools.util.PageInfo
  • net.sourceforge.solexatools.util.PaginationUtil
  • net.sourceforge.seqware.common.security.PermissionsAware
    • net.sourceforge.seqware.common.model.Expense (implements java.lang.Comparable<T>, java.io.Serializable)
    • net.sourceforge.seqware.common.model.Experiment (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, net.sourceforge.seqware.common.model.ParentAccessionModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.File (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.Invoice (implements java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.IUS (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, net.sourceforge.seqware.common.model.ParentAccessionModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.Lane (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, net.sourceforge.seqware.common.model.ParentAccessionModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.Processing (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, net.sourceforge.seqware.common.model.ParentAccessionModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.Registration (implements java.lang.Comparable<T>, java.io.Serializable)
      • net.sourceforge.seqware.common.model.RegistrationDTO
    • net.sourceforge.seqware.common.model.Sample (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, net.sourceforge.seqware.common.model.ParentAccessionModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.SequencerRun (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, net.sourceforge.seqware.common.model.ParentAccessionModel, java.io.Serializable)
      • net.sourceforge.seqware.common.model.SequencerRunWizardDTO
    • net.sourceforge.seqware.common.model.Study (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, net.sourceforge.seqware.common.model.ParentAccessionModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.Workflow (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.WorkflowParam (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
    • net.sourceforge.seqware.common.model.WorkflowParamValue (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
    • net.sourceforge.seqware.common.model.WorkflowRun (implements net.sourceforge.seqware.common.model.Annotatable<T>, java.lang.Comparable<T>, net.sourceforge.seqware.common.model.FirstTierModel, java.io.Serializable)
    • net.sourceforge.seqware.common.model.WorkflowRunParam (implements java.lang.Comparable<T>, java.io.Serializable)
  • io.seqware.pipeline.engines.whitestar.Persistence
  • net.sourceforge.seqware.common.model.Platform (implements java.lang.Comparable<T>, net.sourceforge.seqware.common.model.SecondTierModel, java.io.Serializable)
  • io.seqware.webservice.generated.model.Platform (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.PlatformList
  • net.sourceforge.seqware.common.business.impl.PlatformServiceImpl (implements net.sourceforge.seqware.common.business.PlatformService)
  • net.sourceforge.seqware.pipeline.plugin.Plugin (implements net.sourceforge.seqware.pipeline.plugin.PluginInterface)
    • net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
    • net.sourceforge.seqware.pipeline.deciders.BasicDecider (implements net.sourceforge.seqware.pipeline.decider.DeciderInterface)
    • net.sourceforge.seqware.pipeline.plugins.BundleManager
    • net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB
    • net.sourceforge.seqware.pipeline.plugins.CycleChecker
    • net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB
    • net.sourceforge.seqware.pipeline.plugins.FileLinker
    • io.seqware.pipeline.plugins.FileProvenanceQueryTool
    • net.sourceforge.seqware.pipeline.plugins.fileprovenance.FileProvenanceReporter
    • net.sourceforge.seqware.pipeline.plugins.HelloWorld
    • net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
    • net.sourceforge.seqware.pipeline.plugins.Metadata
      • net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
    • net.sourceforge.seqware.pipeline.plugins.ModuleRunner
    • net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot
    • net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
    • io.seqware.pipeline.plugins.sanity.SanityCheck
    • io.seqware.pipeline.plugins.UserSettingsPlugin
    • io.seqware.pipeline.plugins.WorkflowLauncher
    • io.seqware.pipeline.plugins.WorkflowLifecycle
    • io.seqware.pipeline.plugins.WorkflowRelauncher
    • io.seqware.pipeline.plugins.WorkflowRescheduler
    • net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
    • net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
    • io.seqware.pipeline.plugins.WorkflowScheduler
    • net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
    • io.seqware.pipeline.plugins.WorkflowWatcher
  • net.sourceforge.seqware.pipeline.runner.PluginRunner
  • net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource.IntListByName (implements org.apache.commons.dbutils.ResultSetHandler<T>)
  • io.seqware.webservice.generated.model.Processing (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ProcessingAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.ProcessingExperiments (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ProcessingExperiments (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl (implements net.sourceforge.seqware.common.business.ProcessingExperimentsService)
  • io.seqware.webservice.generated.model.ProcessingFiles (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.ProcessingIus (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ProcessingIus (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl (implements net.sourceforge.seqware.common.business.ProcessingIUSService)
  • net.sourceforge.seqware.common.model.ProcessingLanes (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ProcessingLanes (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl (implements net.sourceforge.seqware.common.business.ProcessingLanesService)
  • net.sourceforge.seqware.common.model.lists.ProcessingList
  • net.sourceforge.seqware.common.model.ProcessingRelationship (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ProcessingRelationship (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl (implements net.sourceforge.seqware.common.business.ProcessingRelationshipService)
  • net.sourceforge.seqware.common.model.ProcessingSamples (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ProcessingSamples (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl (implements net.sourceforge.seqware.common.business.ProcessingSamplesService)
  • net.sourceforge.seqware.common.model.ProcessingSequencerRuns (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ProcessingSequencerRuns (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl (implements net.sourceforge.seqware.common.business.ProcessingSequencerRunsService)
  • net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl (implements net.sourceforge.seqware.common.business.ProcessingService)
  • net.sourceforge.seqware.common.model.ProcessingStudies (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.ProcessingStudies (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl (implements net.sourceforge.seqware.common.business.ProcessingStudiesService)
  • net.sourceforge.seqware.common.util.processtools.ProcessTools
  • net.sourceforge.seqware.common.hibernate.PropagateOwnership
  • java.beans.PropertyEditorSupport (implements java.beans.PropertyEditor)
    • net.sourceforge.solexatools.validation.CustomIntegerEditor
  • net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility
  • io.seqware.pipeline.plugins.sanity.ProvidedBundleUserPhase5
    • io.seqware.pipeline.plugins.sanity.ProvidedBundleCLIUserPhase5
  • net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
  • io.seqware.pipeline.plugins.sanity.QueryRunner
  • net.sourceforge.seqware.common.invitation.RandomInvitationCode
  • net.sourceforge.solexatools.util.RandomInvitationCode
  • io.seqware.webservice.generated.model.Registration (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl (implements net.sourceforge.seqware.common.business.RegistrationService)
  • io.seqware.Reports
  • net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
  • org.restlet.resource.Resource
    • org.restlet.resource.ServerResource
      • org.restlet.ext.wadl.WadlServerResource
        • net.sourceforge.seqware.webservice.resources.BasicResource
          • net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
            • net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
            • net.sourceforge.seqware.webservice.resources.tables.FileIDResource
            • net.sourceforge.seqware.webservice.resources.tables.IusIDResource
            • net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
            • net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
            • net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
            • net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
            • net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
            • net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
            • net.sourceforge.seqware.webservice.resources.tables.WorkflowParamIDResource
            • net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueIDResource
            • net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
          • net.sourceforge.seqware.webservice.resources.tables.DatabaseResource
            • net.sourceforge.seqware.webservice.resources.tables.ExperimentLibraryDesignResource
            • net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
            • net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignReadSpecResource
            • net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignResource
            • net.sourceforge.seqware.webservice.resources.tables.FileChildLimitedWorkflowRunsResource
            • net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource
            • net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource
            • net.sourceforge.seqware.webservice.resources.tables.FileResource
            • net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource
            • net.sourceforge.seqware.webservice.resources.tables.IusResource
            • net.sourceforge.seqware.webservice.resources.tables.LaneResource
            • net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource
            • net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource
            • net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource
            • net.sourceforge.seqware.webservice.resources.tables.OrganismResource
            • net.sourceforge.seqware.webservice.resources.tables.PlatformResource
            • net.sourceforge.seqware.webservice.resources.tables.ProcessResource
            • net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
            • net.sourceforge.seqware.webservice.resources.tables.SampleResource
            • net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
            • net.sourceforge.seqware.webservice.resources.tables.StudyResource
            • net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource
            • net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource
            • net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource
            • net.sourceforge.seqware.webservice.resources.tables.WorkflowResource
            • net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
          • net.sourceforge.seqware.webservice.resources.queries.EnvironmentResource
          • net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
          • net.sourceforge.seqware.webservice.resources.filters.IUSIDFilter
          • net.sourceforge.seqware.webservice.resources.filters.LaneIDFilter
          • net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
          • net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
          • net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
  • org.restlet.Restlet (implements org.restlet.Uniform)
    • org.restlet.Application
      • org.restlet.ext.wadl.WadlApplication
        • net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
    • net.sourceforge.seqware.webservice.resources.BasicRestlet
      • net.sourceforge.seqware.webservice.resources.queries.CycleCheckResource
      • net.sourceforge.seqware.webservice.resources.queries.FileProvenanceResource
      • net.sourceforge.seqware.webservice.resources.queries.ProcessIdProcessResource
      • net.sourceforge.seqware.webservice.resources.tables.ProcessingStructureResource
      • net.sourceforge.seqware.webservice.resources.queries.RunWorkflowResource
      • net.sourceforge.seqware.webservice.resources.queries.SampleHierarchyResource
      • net.sourceforge.seqware.webservice.resources.queries.TriggerFileProvenanceResource
      • net.sourceforge.seqware.webservice.resources.queries.WorkflowReportResource
      • net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource
      • net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource
      • net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDWorkflowResource
      • net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
      • net.sourceforge.seqware.webservice.resources.queries.WorkflowRuntimeResource
    • net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
  • net.sourceforge.seqware.common.util.Rethrow
  • net.sourceforge.seqware.common.module.ReturnValue (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.ReturnValueList
  • net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
  • net.sourceforge.seqware.pipeline.tools.RunLock
  • net.sourceforge.seqware.pipeline.runner.Runner
  • net.sourceforge.seqware.common.util.runtools.RunTools
  • io.seqware.webservice.generated.model.Sample (implements com.sun.xml.bind.CycleRecoverable, java.io.Serializable)
  • io.seqware.webservice.generated.model.SampleAttribute (implements java.io.Serializable)
  • net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
  • net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
  • net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
  • net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
  • net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.SampleHierarchyPlugin (implements net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface)
  • net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo (implements java.lang.Comparable<T>)
  • net.sourceforge.seqware.common.model.lists.SampleList
  • io.seqware.webservice.generated.model.SampleRelationship (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.SampleReport (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.SampleReportRow
  • net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl (implements net.sourceforge.seqware.common.business.SampleReportService)
  • net.sourceforge.seqware.common.business.impl.SampleServiceImpl (implements net.sourceforge.seqware.common.business.SampleService)
  • net.sourceforge.solexatools.validation.SampleValidator (implements org.springframework.validation.Validator)
  • io.seqware.pipeline.api.Scheduler
  • io.seqware.pipeline.plugins.sanity.checks.Script_Check (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • org.restlet.security.SecretVerifier (implements org.restlet.security.Verifier)
    • net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier
  • net.sourceforge.solexatools.Security
  • java.lang.SecurityManager
    • net.sourceforge.seqware.common.util.NoExitSecurityManager
  • net.sourceforge.seqware.pipeline.plugins.checkdb.SelectQueryRunner
  • io.seqware.webservice.generated.model.SequencerRun (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.SequencerRunAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.SequencerRunDTO (implements java.io.Serializable)
  • net.sourceforge.solexatools.util.SequencerRunHtmlUtil
  • net.sourceforge.seqware.common.model.lists.SequencerRunList
  • net.sourceforge.seqware.common.model.SequencerRunReportId
  • net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
  • net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl (implements net.sourceforge.seqware.common.business.SequencerRunService)
  • net.sourceforge.solexatools.validation.SequencerRunValidator (implements org.springframework.validation.Validator)
    • net.sourceforge.solexatools.validation.SequencerRunWizardValidator
  • io.seqware.webservice.generated.client.SeqWareWebserviceClient
    • io.seqware.webservice.client.SeqWareWebServiceClient
  • net.sourceforge.solexatools.util.SetNodeIdInSession
  • net.sourceforge.seqware.pipeline.tools.SetOperations
  • net.sourceforge.seqware.common.model.ShareStudy (implements java.lang.Comparable<T>, java.io.Serializable)
  • io.seqware.webservice.generated.model.ShareStudy (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl (implements net.sourceforge.seqware.common.business.ShareStudyService)
  • net.sourceforge.seqware.common.model.ShareWorkflowRun (implements java.lang.Comparable<T>, java.io.Serializable)
  • io.seqware.webservice.generated.model.ShareWorkflowRun (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl (implements net.sourceforge.seqware.common.business.ShareWorkflowRunService)
  • net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
  • net.sourceforge.seqware.common.util.Str
  • net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.StringTruncator
  • io.seqware.Studies
  • io.seqware.webservice.generated.model.Study (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.StudyAttribute (implements java.io.Serializable)
  • net.sourceforge.solexatools.util.StudyBuildTree
  • net.sourceforge.solexatools.util.StudyHtmlUtil
  • net.sourceforge.seqware.common.model.lists.StudyList
  • net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem (implements java.lang.Comparable<T>)
  • net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem (implements java.lang.Comparable<T>)
  • net.sourceforge.seqware.common.business.impl.StudyServiceImpl (implements net.sourceforge.seqware.common.business.StudyService)
  • net.sourceforge.seqware.common.model.StudyType (implements net.sourceforge.seqware.common.model.SecondTierModel, java.io.Serializable)
  • io.seqware.webservice.generated.model.StudyType (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.StudyTypeList
  • net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl (implements net.sourceforge.seqware.common.business.StudyTypeService)
  • net.sourceforge.solexatools.validation.StudyValidator (implements org.springframework.validation.Validator)
    • net.sourceforge.solexatools.validation.StudyUpdateValidator
  • net.sourceforge.solexatools.util.SummaryData
  • net.sourceforge.solexatools.util.SummaryLine
  • net.sourceforge.seqware.common.util.TabExpansionUtil
  • net.sourceforge.solexatools.util.TagUtils
  • net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit (implements java.lang.Comparable<T>)
  • io.seqware.metadb.util.TestDatabaseCreator
    • net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator
    • net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator
  • java.lang.Thread (implements java.lang.Runnable)
    • net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLineException
        • net.sourceforge.seqware.common.err.NotFoundException
        • net.sourceforge.seqware.pipeline.runner.PluginRunner.ExitException
        • java.lang.SecurityException
          • net.sourceforge.seqware.common.util.ExitException
        • net.sourceforge.seqware.common.util.Str.UnsafeName
  • net.sourceforge.solexatools.util.TreeNodeHtmlUtil
  • io.seqware.pipeline.plugins.sanity.checks.TutorialCheck (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • net.sourceforge.solexatools.authentication.UNCKerberos.NamePasswordCallbackHandler (implements javax.security.auth.callback.CallbackHandler)
  • net.sourceforge.seqware.pipeline.tools.UnZip
  • net.sourceforge.seqware.common.business.UploadFile (implements java.io.Serializable)
  • net.sourceforge.solexatools.validation.UploadFileValidator (implements org.springframework.validation.Validator)
    • net.sourceforge.solexatools.validation.UploadSequenceValidator (implements org.springframework.validation.Validator)
  • net.sourceforge.seqware.common.model.UploadSequence (implements java.io.Serializable)
  • io.seqware.webservice.controller.UtilityREST
  • net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl (implements net.sourceforge.seqware.common.business.ValidationReportService)
  • net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
  • io.seqware.pipeline.engines.whitestar.WhiteStarWorkflowEngine (implements io.seqware.pipeline.api.WorkflowEngine)
  • io.seqware.webservice.generated.model.Workflow (implements java.io.Serializable)
  • net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
  • net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp
  • io.seqware.webservice.generated.model.WorkflowAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate (implements net.sourceforge.seqware.common.dao.WorkflowAttributeDAO)
  • net.sourceforge.seqware.pipeline.workflowV2.WorkflowClassFinder
  • net.sourceforge.seqware.pipeline.workflowV2.WorkflowDataModelFactory
  • net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
  • net.sourceforge.seqware.common.model.lists.WorkflowList
  • io.seqware.webservice.generated.model.WorkflowParam (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.WorkflowParamList
  • net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl (implements net.sourceforge.seqware.common.business.WorkflowParamService)
  • net.sourceforge.solexatools.validation.WorkflowParamValidator (implements org.springframework.validation.Validator)
  • io.seqware.webservice.generated.model.WorkflowParamValue (implements java.io.Serializable)
  • net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
  • net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl (implements net.sourceforge.seqware.common.business.WorkflowParamValueService)
  • net.sourceforge.seqware.common.hibernate.WorkflowReport
  • io.seqware.webservice.generated.model.WorkflowRun (implements java.io.Serializable)
  • io.seqware.webservice.generated.model.WorkflowRunAttribute (implements java.io.Serializable)
  • net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate (implements net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO)
  • net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.WorkflowRunConventionsPlugin (implements net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface)
  • net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
  • net.sourceforge.seqware.common.model.lists.WorkflowRunList
  • net.sourceforge.seqware.common.model.lists.WorkflowRunList2
  • io.seqware.webservice.generated.model.WorkflowRunParam (implements java.io.Serializable)
  • net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl (implements net.sourceforge.seqware.common.business.WorkflowRunParamService)
  • net.sourceforge.seqware.common.hibernate.WorkflowRunReport
  • net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
  • io.seqware.WorkflowRuns
  • net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl (implements net.sourceforge.seqware.common.business.WorkflowRunService)
  • net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl (implements net.sourceforge.seqware.common.business.WorkflowService)
  • io.seqware.pipeline.api.WorkflowTools
  • net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
  • net.sourceforge.solexatools.validation.WorkflowValidator (implements org.springframework.validation.Validator)
  • io.seqware.pipeline.plugins.sanity.checks.WS_Check (implements io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface)
  • javax.xml.bind.annotation.adapters.XmlAdapter<ValueType,BoundType>
    • io.seqware.webservice.adapter.DateFormatterAdapter
    • io.seqware.webservice.adapter.TimestampFormatterAdapter
    • net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
    • net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
    • net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
    • net.sourceforge.seqware.common.model.adapters.XmlizeXML
  • net.sourceforge.seqware.common.util.xmltools.XmlTools
  • net.sourceforge.seqware.pipeline.tools.Zip
  • net.sourceforge.solexatools.util.ZipFileUtil

Interface Hierarchy

• net.sourceforge.seqware.common.model.Annotatable<T>
• net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface
• net.sourceforge.seqware.pipeline.decider.DeciderInterface
• net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
• net.sourceforge.seqware.common.dao.ExperimentDAO
• net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
• net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
• net.sourceforge.seqware.common.business.ExperimentService
• net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
• net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
• net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
• net.sourceforge.seqware.common.business.ExperimentSpotDesignService
• net.sourceforge.seqware.common.dao.FileAttributeDAO
• net.sourceforge.seqware.common.business.FileAttributeService
• net.sourceforge.seqware.common.dao.FileDAO
• net.sourceforge.seqware.common.dao.FileReportDAO
• net.sourceforge.seqware.common.business.FileReportService
• net.sourceforge.seqware.common.business.FileService
• net.sourceforge.seqware.common.dao.FileTypeDAO
• net.sourceforge.seqware.common.business.FileTypeService
• net.sourceforge.seqware.common.business.FileUploadService
• net.sourceforge.seqware.common.model.FirstTierModel
• net.sourceforge.seqware.common.dao.InvoiceDAO
• net.sourceforge.seqware.common.business.InvoiceService
• net.sourceforge.seqware.common.dao.IUSAttributeDAO
• net.sourceforge.seqware.common.dao.IUSDAO
• net.sourceforge.seqware.common.business.IUSService
• net.sourceforge.seqware.pipeline.workflowV2.model.Job
• net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO
• net.sourceforge.seqware.common.dao.LaneDAO
• net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO
• net.sourceforge.seqware.common.business.LaneService
• net.sourceforge.seqware.common.dao.LibraryDAO
• net.sourceforge.seqware.common.dao.LibrarySelectionDAO
• net.sourceforge.seqware.common.business.LibrarySelectionService
• net.sourceforge.seqware.common.business.LibraryService
• net.sourceforge.seqware.common.dao.LibrarySourceDAO
• net.sourceforge.seqware.common.business.LibrarySourceService
• net.sourceforge.seqware.common.dao.LibraryStrategyDAO
• net.sourceforge.seqware.common.business.LibraryStrategyService
• net.sourceforge.seqware.common.metadata.Metadata
• net.sourceforge.seqware.pipeline.module.ModuleInterface
• net.sourceforge.seqware.common.dao.OrganismDAO
• net.sourceforge.seqware.common.business.OrganismService
• net.sourceforge.seqware.common.model.ParentAccessionModel
• net.sourceforge.seqware.common.dao.PlatformDAO
• net.sourceforge.seqware.common.business.PlatformService
• net.sourceforge.seqware.pipeline.plugin.PluginInterface
• net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
• net.sourceforge.seqware.common.dao.ProcessingDAO
• net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
• net.sourceforge.seqware.common.business.ProcessingExperimentsService
• net.sourceforge.seqware.common.dao.ProcessingIUSDAO
• net.sourceforge.seqware.common.business.ProcessingIUSService
• net.sourceforge.seqware.common.dao.ProcessingLanesDAO
• net.sourceforge.seqware.common.business.ProcessingLanesService
• net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
• net.sourceforge.seqware.common.business.ProcessingRelationshipService
• net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
• net.sourceforge.seqware.common.business.ProcessingSamplesService
• net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
• net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
• net.sourceforge.seqware.common.business.ProcessingService
• net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
• net.sourceforge.seqware.common.business.ProcessingStudiesService
• net.sourceforge.seqware.pipeline.module.RedirectAware
• net.sourceforge.seqware.common.dao.RegistrationDAO
• net.sourceforge.seqware.common.business.RegistrationService
• net.sourceforge.seqware.common.dao.SampleAttributeDAO
• net.sourceforge.seqware.common.dao.SampleDAO
• net.sourceforge.seqware.common.dao.SampleReportDAO
• net.sourceforge.seqware.common.business.SampleReportService
• net.sourceforge.seqware.common.business.SampleService
• io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface
• net.sourceforge.seqware.common.model.SecondTierModel
• net.sourceforge.seqware.common.dao.SequencerRunDAO
• net.sourceforge.seqware.common.business.SequencerRunService
• net.sourceforge.seqware.common.dao.ShareStudyDAO
• net.sourceforge.seqware.common.business.ShareStudyService
• net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
• net.sourceforge.seqware.common.business.ShareWorkflowRunService
• net.sourceforge.seqware.common.dao.StudyAttributeDAO
• net.sourceforge.seqware.common.dao.StudyDAO
• net.sourceforge.seqware.common.business.StudyService
• net.sourceforge.seqware.common.dao.StudyTypeDAO
• net.sourceforge.seqware.common.business.StudyTypeService
• net.sourceforge.seqware.common.business.ValidationReportService
• net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
• net.sourceforge.seqware.common.dao.WorkflowDAO
• io.seqware.pipeline.api.WorkflowEngine
• net.sourceforge.seqware.common.dao.WorkflowParamDAO
• net.sourceforge.seqware.common.business.WorkflowParamService
• net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
• net.sourceforge.seqware.common.business.WorkflowParamValueService
• net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
• net.sourceforge.seqware.common.dao.WorkflowRunDAO
• net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
• net.sourceforge.seqware.common.business.WorkflowRunParamService
• net.sourceforge.seqware.common.business.WorkflowRunService
• net.sourceforge.seqware.common.business.WorkflowService

Annotation Type Hierarchy

• net.sourceforge.seqware.pipeline.module.StderrRedirect (implements java.lang.annotation.Annotation)
• net.sourceforge.seqware.pipeline.module.StdoutRedirect (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • io.seqware.common.model.ProcessingStatus
    • io.seqware.common.model.SequencerRunStatus
    • io.seqware.common.model.WorkflowRunStatus
    • net.sourceforge.seqware.common.business.SampleReportService.Status
    • net.sourceforge.seqware.common.util.maptools.ReservedIniKeys
    • net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
    • net.sourceforge.seqware.common.model.FileProvenanceParam
    • net.sourceforge.seqware.common.model.InvoiceState
    • net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
    • io.seqware.Engines.TYPES
    • io.seqware.pipeline.SqwKeys
    • io.seqware.pipeline.SqwKeys.Categories
    • net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser.Field
    • net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface.Level
    • net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters
    • net.sourceforge.seqware.pipeline.workflowV2.model.Requirement.Type
    • net.sourceforge.seqware.pipeline.workflowV2.model.Module
    • net.sourceforge.seqware.pipeline.deciders.BasicDecider.FILE_STATUS
    • net.sourceforge.seqware.pipeline.deciders.BasicDecider.PREVIOUS_RUN_STATUS
    • net.sourceforge.seqware.pipeline.module.ModuleMethod
    • net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource.SEARCH_TYPE
    • net.sourceforge.seqware.webservice.resources.TomcatVersion