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