boolean isInitializingBeans
IProgressMonitor currentMonitor
java.util.Set<E> alreadyMonitoredBeans
boolean includeEmptySeconds
boolean includeReferenceSystem
boolean includeEmptySeconds
boolean includeReferenceSystem
java.util.List<E> exceptions
java.util.Set<E> relatedObjects
java.util.Set<E> deletedObjects
UpdateResult.Status status
java.util.Collection<E> exceptions
java.util.Set<E> updatedObjects
java.util.Set<E> updatedCdmIds
java.util.Set<E> unchangedObjects
CdmBase cdmEntity
java.util.List<E> classList
IProgressMonitor monitor
boolean updateCacheStrategies
boolean isCheck
boolean recursiveAggregation
boolean includeDefault
boolean includeLiterature
SpecimenOrObservationType specimenType
java.util.UUID associatedTaxonUuid
java.util.UUID associatedTaxonNameUuid
java.lang.String significantIdentifier
boolean retrieveIndirectlyAssociatedSpecimens
AssignmentStatus assignmentStatus
boolean includeUnpublished
boolean doTaxa
boolean doSynonyms
boolean doTaxaByCommonNames
boolean doNamesWithoutTaxa
boolean doMisappliedNames
boolean doIncludeAuthors
Classification classification
TaxonNode subtree
java.util.List<E> taxonPropertyPath
java.util.List<E> synonymPropertyPath
java.util.List<E> taxonNamePropertyPath
java.util.List<E> commonNamePropertyPath
java.util.Set<E> namedAreas
NameSearchOrder order
java.util.UUID subtreeUuid
boolean includeAcceptedTaxa
boolean includeSynonyms
boolean includeSharedTaxa
IProgressMonitor monitor
java.lang.String titleSearchString
MatchMode matchMode
java.lang.Integer pageSize
java.lang.Integer pageNumber
java.lang.Class<T> clazz
java.util.List<E> criteria
java.util.List<E> restrictions
java.util.List<E> propertyPaths
java.util.List<E> orderHints
boolean deleteFromDescription
boolean deleteFromEveryWhere
boolean onlyRemoveFromGallery
CdmBase deleteFrom
boolean removeAllNameRelationships
boolean ignoreIsBasionymFor
boolean ignoreIsReplacedSynonymFor
boolean ignoreHasBasionym
boolean ignoreHasReplacedSynonym
boolean removeAllNameTypeDesignations
NodeDeletionConfigurator.ChildHandling childHandling
boolean deleteElement
boolean publish
boolean includeMisapplications
boolean includeProParteSynonyms
boolean includeHybrids
java.util.Set<E> includedRelationTypes
Reference newSecundum
boolean overwriteExistingAccepted
boolean overwriteExistingSynonyms
boolean emptySecundumDetail
java.util.UUID subtreeUuid
Reference newSecundum
boolean includeAcceptedTaxa
boolean includeSynonyms
boolean overwriteExistingAccepted
boolean overwriteExistingSynonyms
boolean emptySecundumDetail
boolean includeSharedTaxa
IRemotingProgressMonitor monitor
boolean doTaxonNode
boolean doTermNode
boolean doPolytomousKeyNode
IProgressMonitor monitor
boolean deleteChildren
true
all sub derivates of the specimen are deleted.boolean deleteFromTypeDesignation
true
the SpecimenTypeDesignation
which
uses the specimen.boolean deleteFromIndividualsAssociation
true
theboolean deleteFromDescription
boolean isDeleteMolecularData
true
then attached molecular data like amplification results
and sequences are deletedboolean newHomotypicGroupIfNeeded
boolean deleteNameIfPossible
boolean deleteSynonymRelations
NameDeletionConfigurator nameDeletionConfig
boolean deleteSynonymsIfPossible
boolean deleteMisappliedNamesAndInvalidDesignations
boolean deleteConceptRelationships
TaxonNodeDeletionConfigurator taxonNodeConfig
boolean deleteTaxonNodes
boolean deleteTaxonRelationships
boolean deleteDescriptions
boolean deleteInAllClassifications
java.util.UUID classificationUuid
boolean deleteIncludedTerms
boolean deleteIncludedRelations
boolean deletePartOfRelations
boolean deleteGeneralizationOfRelations
boolean deleteKindOfRelations
boolean deleteMediaIfPossible
TaxonNodeFilter taxonNodeFilter
AggregationSourceMode toParentSourceMode
AggregationSourceMode withinTaxonSourceMode
java.util.List<E> aggregationModes
boolean adaptBatchSize
boolean doClearExistingDescription
boolean doReuseDescriptions
boolean doReuseDescriptionElements
boolean doReuseSources
IProgressMonitor monitor
java.util.EnumSet<E extends java.lang.Enum<E>> aggregatingSourceTypes
java.util.List<E> superAreasUuids
TermCollection<TERM extends DefinedTermBase,REL extends TermRelationBase> statusOrder
boolean ignoreAbsentStatusByArea
boolean ignoreAbsentStatusByRank
java.util.List<E> byAreaIgnoreStatusList
java.util.List<E> byRankIgnoreStatusList
java.util.UUID datasetUuid
boolean aggregateToHigherRanks
boolean includeDefault
boolean includeLiterature
MissingMinimumMode missingMinimumMode
MissingMaximumMode missingMaximumMode
int id
java.lang.Class<T> cdmClass
java.lang.String code
java.lang.String codeStandard
java.lang.String institute
java.lang.String townOrLocation
java.util.List<E> specimenScans
java.util.List<E> molecularDataList
java.util.List<E> detailImages
java.util.List<E> specimenScanUuids
java.util.List<E> detailImageUuids
DerivateDataDTO.Link contigLink
java.util.List<E> primerLinks
java.lang.String linkText
java.net.URI uri
DerivateDataDTO.Link providerLink
java.util.List<E> contigFiles
java.util.TreeSet<E> characterData
DerivateDataDTO derivateDataDTO
java.lang.String taxonName
java.lang.String listLabel
java.lang.String citation
boolean hasDetailImage
boolean hasCharacterData
boolean hasDna
boolean hasSpecimenScan
java.lang.String recordBase
java.lang.String kindOfUnit
CollectionDTO collection
java.lang.String catalogNumber
java.lang.String collectorsNumber
java.lang.String barcode
java.lang.String preservationMethod
java.util.Set<E> derivates
java.util.Set<E> specimenTypeDesignations
DerivationEventDTO derivationEvent
java.util.Set<E> sources
java.util.List<E> listOfMedia
java.lang.String derivationEventType
java.lang.String derivationEventActor
java.lang.String derivationEventInstitute
java.util.Set<E> sequences
java.util.Set<E> amplificationResults
DnaQuality dnaQuality
EntityDTOBase.CdmEntity cdmEntity
CdmBase entity
java.lang.String country
java.lang.String collectingString
java.lang.String date
java.lang.String collectionString
boolean hasType
GatheringEventDTO gatheringEvent
java.lang.String locality
Point exactLocation
java.lang.String country
java.util.Set<E> collectingAreas
java.lang.String collectingMethod
java.lang.Integer absoluteElevation
java.lang.Integer absoluteElevationMax
java.lang.String absoluteElevationText
java.lang.Double distanceToGround
java.lang.Double distanceToGroundMax
java.lang.String distanceToGroundText
java.lang.Double distanceToWaterSurface
java.lang.Double distanceToWaterSurfaceMax
java.lang.String collector
java.lang.String distanceToWaterSurfaceText
IdentifiedEntityDTO.AlternativeIdentifier identifier
java.util.UUID typeUuid
java.lang.String typeLabel
java.lang.String identifier
MarkedEntityDTO.Marker marker
java.lang.String uri
java.lang.String title_l10n
java.lang.String mimeType
java.lang.Integer size
java.lang.String accessionNumber
java.net.URI preferredStableUri
java.util.List<E> associatedTaxa
java.util.Map<K,V> types
java.util.List<E> determinedNames
DescriptionBase<S extends IIdentifiableEntityCacheStrategy> description
TaxonNodeDto taxonNode
java.util.Map<K,V> featureToElementMap
java.util.Map<K,V> featureToDisplayDataMap
Media contigFile
SequenceString consensusSequence
java.lang.Boolean isBarcode
SequenceString barcodeSequencePart
java.lang.String geneticAccessionNumber
java.lang.String boldProcessId
java.util.Set<E> singleReadAlignments
java.lang.String dnaMarker
java.lang.String haplotype
java.util.Set<E> citations
java.net.URI boldUri
java.net.URI ddbjUri
java.net.URI emblUri
java.net.URI genBankUri
TaxonRowWrapperDTO defaultDescription
SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy<?>> specimen
FieldUnit fieldUnit
java.lang.String identifier
NamedArea country
java.util.List<E> names
DerivateDTO typeSpecimen
java.lang.String typeStatus
java.util.UUID taxonUUID
java.util.Set<E> descriptions
java.util.UUID taxonUUID
java.lang.String nameCache
java.lang.Integer rankOrderIndex
java.lang.String rankLabel
TaxonDescriptionDTO descriptionsWrapper
java.lang.String concatenatedSynonyms
java.util.List<E> problems
java.lang.String workingSetRepresentation
TypedEntityReference<T> baseEntityReference
VersionableEntity baseEntity
java.util.List<E> derivedUnits
java.lang.Integer pagesAvailable
java.lang.Integer prevIndex
java.lang.Integer nextIndex
java.lang.Integer currentIndex
java.util.Map<K,V> pageNumbers
java.lang.Integer firstRecord
java.lang.Integer lastRecord
java.lang.Long count
java.util.List<E> records
java.lang.String suggestion
java.util.ArrayList<E> indices
java.lang.Integer pageSize
INameService nameService
ITaxonService taxonService
IClassificationService classificationService
IReferenceService referenceService
IAgentService agentService
IOccurrenceService occurrenceService
ITermService termService
IDescriptionService descriptionService
ICollectionService collectionService
ITermTreeService termTreeService
IVocabularyService vocabularyService
IPolytomousKeyService polytomousKeyService
IMediaService mediaService
IProgressMonitorService progressMonitorService
org.springframework.orm.hibernate5.HibernateTransactionManager transactionManager
ITaxonService repository
ICdmPermissionEvaluator permissionEvaluator
CdmRepository repo
org.springframework.security.authentication.AuthenticationProvider runAsAuthenticationProvider
RunAsAuthenticator runAsAutheticator
SecurityContextAccess securityContextAccess
java.lang.String className
java.lang.String parentClassName
java.util.List<E> fields
java.lang.String prefix_registrantCode
java.lang.String suffix
java.util.List<E> errors
java.util.List<E> warnings
java.util.List<E> exceptions
java.lang.String message
java.lang.Exception exception
java.lang.String codeLocation
java.lang.String dataLocation
boolean isCanceled
java.lang.String taskName
int totalWork
double workDone
java.lang.String subTask
java.io.Serializable feedback
boolean isWaitingForFeedback
long feedbackWaitStartTime
java.math.BigDecimal lastPercentage
long feedbackWaitTimeout
java.lang.String owner
IProgressMonitor progressMonitor
java.io.Serializable result
java.util.List<E> reports
boolean serviceDone
boolean isFailed
boolean isDone
java.lang.String origin
int parentTicks
double sentToParent
double scale
int nestedBeginTasks
boolean usedUp
boolean hasSubTask
int style
java.lang.String mainTaskLabel
java.lang.String sourceName
boolean invalidFilter
java.lang.String problem
java.lang.String externalService
java.util.Set<E> tripleIds
java.lang.String taxonName
java.lang.String higherTaxon
java.lang.String collector
java.lang.String collectorsNumber
java.lang.String accessionNumber
java.lang.String herbarium
java.lang.String country
java.lang.String locality
java.util.Calendar dateFrom
java.util.Calendar dateTo
boolean hasImage
java.net.URI itemUri
java.net.URI titleUri
MobotOpenUrlServiceWrapper.ReferenceType referenceType
LogicFilter.Op operator
java.util.UUID uuid
java.lang.String treeIndex
java.lang.Class<T> clazz
java.util.List<E> subtrees
java.util.List<E> taxonNodes
java.util.List<E> classifications
java.util.List<E> taxa
LogicFilter<T extends CdmBase> rankMin
LogicFilter<T extends CdmBase> rankMax
java.util.List<E> areaFilter
java.util.List<E> distributionStatusFilter
boolean includeRootNodes
boolean includeUnpublished
TaxonNodeFilter.ORDER orderBy
java.lang.Class<T> clazz
java.lang.Class<T> clazz
Cdm2CdmImportState state
java.util.Map<K,V> sessionCache
java.util.Map<K,V> existingObjects
java.util.Set<E> toSave
TaxonNodeFilter taxonNodeFilter
ITaxonNodeOutStreamPartitioner partitioner
boolean concurrent
boolean doTaxa
boolean doDescriptions
boolean addSources
boolean removeImportSources
java.util.Map<K,V> sessionCache
java.util.Map<K,V> permanentCache
java.util.Set<E> movedObjects
java.util.Set<E> toSave
IEditGeoService geoService
CsvIOConfigurator csvIOConfig
boolean isHighlightPrimaryCollector
boolean createZipFile
boolean isFilterIntextReferences
boolean isFilterImportSources
java.util.Comparator<T> comparator
boolean updateCacheStrategies
java.util.List<E> classList
java.io.ByteArrayOutputStream exportStream
java.util.Set<E> observers
java.lang.String ioName
java.lang.String encoding
java.lang.String linesTerminatedBy
java.lang.String fieldsEnclosedBy
boolean hasHeaderLines
java.lang.String fieldsTerminatedBy
DbExportConfiguratorBase.IdType idType
java.lang.String dbTableName
java.lang.String pluralString
java.lang.reflect.Method userTransformationMethod
int recordsPerTransaction
boolean doReferences
boolean doAuthors
IExportConfigurator.CHECK check
IExportConfigurator.TARGET target
ICdmDataSource source
java.lang.Object destination
IDatabase sourceReference
java.lang.Class<T>[] ioClassList
TaxonNodeFilter taxonNodeFilter
ExportResultType resultType
IExportTransformer transformer
java.lang.Object exportData
ExportResultType type
ExportResult.ExportResultState state
ExportDataWrapper<T> data
ExportType exportType
IImportConfigurator.CHECK check
IInputTransformer transformer
java.util.UUID uuidFeatureTree
java.lang.String featureTreeTitle
NomenclaturalCode nomenclaturalCode
java.util.Map<K,V> featureMap
java.lang.String classificationName
java.util.UUID classificationUuid
java.util.UUID secUuid
java.lang.Object sourceSecId
java.lang.Object source
Reference sourceReference
java.util.UUID sourceRefUuid
ICdmDataSource destination
Person commentator
java.lang.Class<T>[] ioClassList
ICdmIO<STATE extends IoStateBase>[] ioList
java.lang.String[] ioBeans
boolean askUserForHelp
java.util.List<E> reports
java.util.Map<K,V> newRecords
java.util.Map<K,V> updatedRecords
java.util.Map<K,V> deletedRecords
ImportResult.ImportResultState state
boolean useClassification
DbSchemaValidation dbSchemaValidation
ICdmRepository cdmApp
org.springframework.security.authentication.UsernamePasswordAuthenticationToken authenticationToken
HibernateConfiguration hibernateConfig
IProgressMonitor progressMonitor
java.lang.String userFriendlyIOName
java.util.Set<E> observers
java.util.UUID subtreeUuid
Reference newSecundum
boolean includeAcceptedTaxa
boolean includeSynonyms
boolean overwriteExistingAccepted
boolean overwriteExistingSynonyms
boolean emptySecundumDetail
boolean includeSharedTaxa
IProgressMonitor monitor
boolean doTaxonNode
boolean doFeatureNode
boolean doPolytomousKeyNode
java.lang.String subTreeIndex
XmlExportConfiguratorBase.IdType idType
IEditGeoService geoService
java.util.HashMap<K,V> familyMap
java.util.HashMap<K,V> genusMap
java.util.List<E> nameRecords
java.lang.String NOT_DESIGNATED
org.springframework.transaction.TransactionStatus txStatus
java.io.ByteArrayOutputStream byteOutputStream
boolean namesOnly
java.util.UUID classificationUUID
boolean condensedDistribution
boolean invalidNamesQuoted
CsvIOConfigurator csvIOConfig
Rank rank
char fieldSeparator
int transactionLineCount
java.net.URI originalUri
java.util.Set<E> existingRecordIds
java.util.Set<E> existingRecordUuids
java.lang.String encoding
java.lang.String linesTerminatedBy
java.lang.String fieldsEnclosedBy
boolean hasHeaderLines
java.lang.String fieldsTerminatedBy
boolean doTaxa
boolean doDistributions
java.io.ByteArrayOutputStream baos
boolean isUseIdWherePossible
boolean includeBasionymsInResourceRelations
boolean includeMisappliedNamesInResourceRelations
java.lang.String defaultBibliographicCitation
java.util.List<E> featureExclusions
java.util.Set<E> classificationUuids
boolean withHigherClassification
java.lang.String setSeparator
boolean doGeographicalFilter
boolean doDemoExport
boolean doTaxonConceptExport
boolean classification
boolean taxonName
boolean taxonNameID
boolean author
boolean rank
boolean taxonStatus
boolean taxonConceptID
boolean synonyms
boolean distributions
boolean redlistFeatures
boolean acceptedName
boolean parentID
boolean externalID
boolean lastChange
java.util.List<E> recordList
java.util.List<E> features
java.lang.String classificationTitleCache
java.util.List<E> areas
java.lang.Integer pageSize
java.lang.Integer pageNumber
int taxonNodeListSize
java.util.Set<E> existingRecordIds
java.util.Set<E> existingRecordUuids
java.lang.String encoding
java.lang.String linesTerminatedBy
java.lang.String fieldsEnclosedBy
boolean hasHeaderLines
java.lang.String fieldsTerminatedBy
boolean doTaxa
boolean doDistributions
java.io.ByteArrayOutputStream baos
boolean isUseIdWherePossible
boolean includeBasionymsInResourceRelations
boolean includeMisappliedNamesInResourceRelations
boolean includeUnpublished
java.lang.String defaultBibliographicCitation
java.util.List<E> featureExclusions
java.util.Set<E> taxonNodeUuids
boolean withHigherClassification
java.lang.String setSeparator
java.util.List<E> features
java.lang.String classificationTitleCache
java.util.List<E> areas
eu.etaxonomy.cdm.model.term.FeatureTree<T extends DefinedTermBase> featureTree
java.util.List<E> featureTreeUuids
java.util.List<E> vocabularyUuids
TermTree<T extends DefinedTermBase> featureTree
java.util.UUID areaVocabularyUuid
boolean createNewDistribution
au.com.bytecode.opencsv.CSVReader csvReader
ArchiveEntryBase archiveEntry
eu.etaxonomy.cdm.io.dwca.TermUri term
int line
StreamItem next
boolean doSplitRelationshipImport
boolean doSynonymRelationships
boolean doHigherRankRelationships
boolean doLowerRankRelationships
boolean deduplicateNamePublishedIn
boolean scientificNameIdAsOriginalSourceId
DwcaDataImportConfiguratorBase.DatasetUse datasetUse
boolean useSourceReferenceAsSec
boolean useParentAsAcceptedIfAcceptedNotExists
boolean excludeLocality
boolean guessNomenclaturalReferences
boolean handleAllRefsAsCitation
boolean validateRankConsistency
boolean isNoQuotes
boolean doTaxa
boolean doTaxonRelationships
boolean doExtensions
boolean keepMappingForFurtherImports
DwcaMetaDataRecord metaRecord
DwcaMetaDataRecord metaRecord
java.lang.String emlNamespace
java.lang.String mdNamespace
java.lang.String projNamespace
java.lang.String datasetNamespace
java.lang.String resNamespace
java.lang.String dcNamespace
java.lang.String xsiNamespace
java.lang.String schemaLocation
DwcaTaxExportFile file
DwcaMetaDataRecord metaRecord
DwcaMetaDataRecord metaRecord
DwcaMetaDataRecord metaRecord
ITaxonNodeService taxonNodeService
java.lang.String encoding
java.lang.String linesTerminatedBy
java.lang.String fieldsEnclosedBy
boolean hasHeaderLines
java.lang.String fieldsTerminatedBy
boolean doTaxa
boolean doResourceRelation
boolean doTypesAndSpecimen
boolean doVernacularNames
boolean doReferences
boolean doDescriptions
boolean doDistributions
boolean doImages
boolean doMetaData
boolean doEml
boolean doSynonyms
boolean doMisappliedNames
boolean isUseIdWherePossible
boolean includeBasionymsInResourceRelations
boolean includeMisappliedNamesInResourceRelations
java.lang.String defaultBibliographicCitation
DwcaEmlRecord emlRecord
java.util.List<E> featureExclusions
java.lang.String defaultTaxonSource
boolean withHigherClassification
java.lang.String setSeparator
DwcaMetaDataRecord metaRecord
DwcaMetaDataRecord metaRecord
DwcaMetaDataRecord metaRecord
java.util.List<E> recordList
ExcelImportConfiguratorBase configurator
byte[] stream
boolean deduplicateReferences
boolean deduplicateAuthors
java.lang.String worksheetName
java.util.ArrayList<E> recordList
ExcelImportConfiguratorBase configurator
java.util.Map<K,V> myDescriptions
java.util.List<E> innerStream
int index
eu.etaxonomy.cdm.io.dwca.TermUri termUri
java.lang.String streamLocation
java.util.ArrayList<E> recordList
java.io.InputStream stream
java.util.Map<K,V> referenceMapping
java.util.Map<K,V> referenceStore
java.util.Map<K,V> authorMapping
java.util.Map<K,V> authorStore
java.util.Map<K,V> languageMapping
boolean isDoMatchTaxa
java.util.UUID parentUUID
java.lang.String nameColumn
java.lang.String correctNameColumn
java.lang.Class<T> cdmClass
java.util.UUID uuidIdentifierType
boolean ignoreEmptyIdentifier
java.util.List<E> terms
java.util.List<E> termVocabularies
java.util.List<E> agents
java.util.List<E> collections
java.util.List<E> termTrees
java.util.List<E> polytomousKeys
java.util.List<E> classifications
java.util.List<E> taxonNodes
java.util.List<E> languageStrings
java.util.List<E> occurrences
java.util.List<E> eventBases
java.util.List<E> references
java.util.List<E> typeDesignations
java.util.List<E> taxonomicNames
java.util.List<E> taxonBases
java.util.List<E> media
java.util.List<E> homotypicalGroups
java.util.List<E> users
java.util.List<E> groups
java.util.List<E> grantedAuthorities
DataSet dataSet
int maxRows
boolean formattedOutput
java.lang.String encoding
boolean doUsers
boolean doAgentData
boolean doAuthors
boolean doLanguageData
boolean doFeatureData
boolean doDescriptions
boolean doMedia
boolean doOccurrence
IExportConfigurator.DO_REFERENCES doReferences
boolean doReferencedEntities
boolean doSynonyms
boolean doTaxonNames
boolean doTaxa
boolean doTerms
boolean doTermVocabularies
boolean doHomotypicalGroups
boolean doTypeDesignations
boolean doClassificationData
CdmDocumentBuilder cdmDocumentBuilder
int maxRows
boolean doUser
boolean doAgentData
boolean doLanguageData
boolean doFeatureData
boolean doDescriptions
boolean doMedia
boolean doOccurrence
boolean doReferencedEntities
boolean doSynonyms
boolean doTerms
boolean doTermVocabularies
boolean doHomotypicalGroups
boolean doTypeDesignations
boolean doClassificationData
boolean doAuthors
IImportConfigurator.DO_REFERENCES doReferences
boolean doTaxonNames
boolean doTaxa
UnmatchedLeads unmatchedLeads
IEditGeoService editGeoService
boolean replaceStandardKeyTitles
boolean doTaxa
boolean reuseExistingState
boolean allowCapitalSpeciesEpithet
boolean handlePagesAsDetailWhereNeeded
boolean useEditorAsInAuthorWhereNeeded
java.lang.String sourceReferenceTitle
java.util.UUID defaultLanguageUuid
java.util.List<E> knownCollections
boolean ignoreLocalityClass
boolean handleWriterManually
boolean doExtensionForTaxonTitle
java.util.UUID specimenNotSeenMarkerTypeUuid
java.lang.String specimenNotSeenMarkerTypeLabel
java.util.UUID lastTaxonUuid
boolean doPrintKeys
MarkupImportState state
boolean useFotGSpecimenTypeCollectionAndTypeOnly
ImportDeduplicationHelper<STATE extends ImportStateBase> deduplicationHelper
java.util.List<E> baseUrls
Language descriptionLanguage
Language titleLanguage
boolean readMediaData
MediaExcelImportConfigurator.MediaTitleEnum mediaTitle
boolean updateCacheStrategies
java.util.List<E> classList
boolean doReferences
boolean doAuthors
java.util.UUID subtreeUuid
boolean includeAcceptedTaxa
boolean includeSynonyms
boolean includeSharedTaxa
IProgressMonitor monitor
boolean publish
boolean doTaxonNode
boolean doFeatureNode
boolean doPolytomousKeyNode
PilotOutputDocumentBuilder pilotOutputDocumentBuilder
java.lang.String ioName
int maxRows
boolean doAgentData
boolean doLanguageData
boolean doFeatureData
boolean doDescriptions
boolean doMedia
boolean doOccurrence
boolean doReferencedEntities
boolean doSynonyms
boolean doTerms
boolean doTermVocabularies
boolean doHomotypicalGroups
boolean doAuthors
IExportConfigurator.DO_REFERENCES doReferences
boolean doTaxonNames
boolean doTaxa
boolean doRelTaxa
PilotOutputDocumentBuilder pilotOutputDocumentBuilder
boolean doOccurrence
org.jdom.Namespace endnoteNamespace
TermVocabulary<T extends DefinedTermBase> featureVoc
PolytomousKey cdmKey
java.util.Map<K,V> featureMap
java.util.Map<K,V> authors
java.util.Map<K,V> citations
java.util.Map<K,V> defaultUnitPrefixes
java.util.Map<K,V> editors
java.util.Map<K,V> featureNodes
java.util.Map<K,V> features
java.util.Map<K,V> locations
java.util.Map<K,V> mediaObject_ListCdmBase
java.util.Map<K,V> mediaObject_Role
java.util.Map<K,V> publications
java.util.Map<K,V> states
java.util.Map<K,V> taxonDescriptions
java.util.Map<K,V> taxonNameBases
java.util.Map<K,V> units
java.util.Map<K,V> taxonNodes
java.util.Map<K,V> namedAreas
java.util.Map<K,V> specimens
java.util.Map<K,V> modifiers
java.util.Set<E> markerTypes
java.util.Set<E> vocabularies
java.util.Set<E> descriptiveConcepts
java.util.Set<E> annotationTypes
java.util.Set<E> sources
Reference sec
Reference sourceReference
Language datasetLanguage
eu.etaxonomy.cdm.model.description.WorkingSet workingSet
org.jdom.Namespace xmlNamespace
java.lang.String generatorName
java.lang.String generatorVersion
java.util.Set<E> statisticalMeasures
java.util.Set<E> featureData
java.util.Set<E> featureTrees
java.util.Set<E> classifications
Rights copyright
int taxonNamesCount
java.lang.Class<T>[] ioClassList
java.util.Map<K,V> authors
java.util.Map<K,V> citations
java.util.Map<K,V> defaultUnitPrefixes
java.util.Map<K,V> editors
java.util.Map<K,V> termNodes
java.util.Map<K,V> features
java.util.Map<K,V> locations
java.util.Map<K,V> mediaObject_ListCdmBase
java.util.Map<K,V> mediaObject_Role
java.util.Map<K,V> publications
java.util.Map<K,V> states
java.util.Map<K,V> taxonDescriptions
java.util.Map<K,V> taxonNames
java.util.Map<K,V> units
java.util.Map<K,V> taxonNodes
java.util.Map<K,V> namedAreas
java.util.Map<K,V> specimens
java.util.Map<K,V> modifiers
java.util.Set<E> markerTypes
java.util.Set<E> vocabularies
java.util.Set<E> descriptiveConcepts
java.util.Set<E> annotationTypes
java.util.Set<E> sources
Reference sec
Reference sourceReference
Language datasetLanguage
DescriptiveDataSet descriptiveDataSet
org.jdom.Namespace xmlNamespace
java.lang.String generatorName
java.lang.String generatorVersion
java.util.Set<E> statisticalMeasures
java.util.Set<E> featureData
java.util.Set<E> featureTrees
java.util.Set<E> classifications
java.util.UUID uuidAnnotationTypeLocation
Rank defaultRank
Rights copyright
int taxonNamesCount
boolean doMatchTaxa
org.jdom.Namespace sddNamespace
SDDDocumentBuilder sddDocumentBuilder
int maxRows
boolean doAgentData
boolean doLanguageData
boolean doFeatureData
boolean doDescriptions
boolean doMedia
boolean doReferencedEntities
boolean doSynonyms
boolean doTerms
boolean doTermVocabularies
boolean doHomotypicalGroups
boolean doOccurrence
boolean doAuthors
IExportConfigurator.DO_REFERENCES doReferences
boolean doTaxonNames
boolean doTaxa
boolean doRelTaxa
java.util.Map<K,V> kindOfUnitsMap
boolean ignoreImportOfExistingSpecimen
boolean reuseExistingTaxaWhenPossible
java.util.Map<K,V> taxonToDescriptionMap
java.util.Map<K,V> titleCacheTeam
java.util.Map<K,V> titleCachePerson
boolean ignoreAuthorship
boolean removeCountryFromLocalityText
OccurenceQuery query
boolean addMediaAsMediaSpecimen
boolean reuseExistingMetaData
java.lang.String sourceReferenceTitle
java.lang.String taxonReference
boolean addIndividualsAssociationsSuchAsSpecimenAndObservations
boolean reuseExistingDescriptiveGroups
java.lang.String defaultAuthor
boolean allowReuseOtherClassifications
boolean deduplicateReferences
boolean deduplicateClassifications
boolean moveNewTaxaToDefaultClassification
boolean mapUnitIdToCatalogNumber
boolean mapUnitIdToAccessionNumber
boolean mapUnitIdToBarcode
boolean overwriteExistingSpecimens
boolean downloadSequenceData
SpecimenOrObservationType type
SpecimenUserInteraction specimenUserInteraction
java.util.Map<K,V> namedAreaDecisions
java.net.URI reportUri
java.util.List<E> sources
java.lang.String currentSource
java.net.URI sourceUri
boolean getSiblings
java.net.URI dnaSoure
boolean doParsing
boolean reuseMetadata
boolean reuseTaxon
java.lang.String taxonReference
boolean doSpecimen
boolean doAreaLevels
boolean doExtensionTypes
boolean useCountry
CdmImportBase.TermMatchMode areaMatchMode
PersonParserFormatEnum personParserFormat
boolean makeIndividualAssociations
boolean useMaterialsExaminedForIndividualsAssociations
boolean firstDeterminationIsStoredUnder
boolean determinationsAreDeterminationEvent
boolean preferNameCache
boolean createTaxonIfNotExists
boolean doParsing
boolean reuseMetadata
boolean reuseTaxon
java.lang.String taxonReference
boolean askForDate
java.util.Map<K,V> titleCacheTeam
java.util.Map<K,V> titleCachePerson
java.lang.String defaultAuthor
java.util.Map<K,V> namedAreaDecisions
Reference dataReference
boolean debugInstitutionOnly
java.lang.String fullScientificNameString
java.lang.String nomenclatureCode
java.lang.String institutionCode
java.lang.String collectionCode
java.lang.String unitID
java.lang.String recordBasis
java.lang.String accessionNumber
java.lang.String fieldNumber
java.lang.Double longitude
java.lang.Double latitude
java.lang.String locality
java.lang.String languageIso
java.lang.String country
java.lang.String isocountry
int depth
int altitude
java.lang.String gatheringYear
java.lang.String gatheringMonth
java.lang.String gatheringDay
java.lang.String gatheringDate
java.lang.String gatheringTeam
java.lang.String gatheringAgent
java.lang.String originalsource
java.lang.String identifier
java.lang.String gatheringNotes
DerivedUnit derivedUnitBase
Reference ref
org.springframework.transaction.TransactionStatus tx
Classification classification
java.util.ArrayList<E> identificationList
java.util.ArrayList<E> multimediaObjects
boolean keepAtomisedDate
boolean useTDWGarea
boolean DEBUG
au.com.bytecode.opencsv.CSVReader csvReader
ArchiveEntryBase archiveEntry
TermUri term
int line
StreamItem next
boolean usePartitions
int defaultPartitionSize
java.lang.String sourceReferenceTitle
IImportMapping.MappingType mappingType
java.lang.String databaseMappingFile
java.util.UUID stateUuid
java.util.List<E> innerStream
int index
TermUri termUri
java.lang.String streamLocation
java.io.InputStream stream
boolean doMods
boolean doFacts
boolean doTypes
boolean isPublishReferences
java.lang.String originalSourceTaxonNamespace
java.lang.String originalSourceId
Classification classification
Reference ref
TaxonXImportState taxonXstate
TaxonXDataHolder dataHolder
DerivedUnit derivedUnitBase
org.springframework.transaction.TransactionStatus tx
TaxonXXMLFieldGetter taxonXFieldGetter
java.util.Map<K,V> featuresMap
java.lang.String defaultImportClassification
boolean doMods
boolean doFacts
boolean doTypes
boolean alwaysUseDefaultClassification
boolean isUseOldUnparsedSynonymExtraction
boolean isPublishReferences
java.lang.String originalSourceTaxonNamespace
java.lang.String originalSourceId
java.util.Map<K,V> titleCachePerson
java.util.Map<K,V> namedAreaDecisions
Reference secundum
boolean keepOriginalSecundum
Rank maxRank
boolean askedForHRank
Reference sourceURL
boolean lastImport
boolean isPublishReferences
IImportConfigurator.DO_REFERENCES doReferences
boolean doTaxonNames
boolean doRelNames
boolean doTaxa
boolean doRelTaxa
boolean doFacts
java.util.Map<K,V> nsPrefixMap
IpniService service
boolean doMetaData
boolean doSpecimen
IImportConfigurator.DO_REFERENCES doReferences
boolean doTaxonNames
boolean doRelNames
boolean doTaxa
boolean doRelTaxa
boolean doGetMissingNames
java.lang.reflect.Method functionMetaDataDetailed
ITcsXmlPlaceholderClass placeholderClass
org.jdom.Namespace tcsXmlNamespace
TcsRdfTaxonNameImport rdfNameImport
TcsRdfImportConfigurator rdfConfig
TcsXmlExportState state
boolean doAuthors
boolean doTaxonNames
boolean overrideWithEmpty
java.util.UUID languageUuid
NonViralNameParserImpl parser
boolean createTaxa
java.util.UUID parentNodeUuid
java.lang.String classificationName
boolean unplaced
boolean allowTropicosDuplicates
boolean allowIpniDuplicates
boolean allowWfoDuplicates
boolean reportDuplicateIdentifier
boolean addAuthorsToReference
java.util.Map<K,V> nameMap
java.util.Map<K,V> pseudoParentMap
Classification classification
java.util.UUID parentNodeUuid
java.lang.String classificationName
boolean unplaced
boolean reportDuplicateIdentifier
boolean addAuthorsToReference
java.util.Map<K,V> nameMap
NonViralNameParserImpl parser
java.lang.Class<T> propertyItemType
java.lang.Class<T> beanClass
java.lang.String propertyName
java.lang.String addMethodName
java.lang.String removMethodName
Contact contact
java.util.List<E> emailAddresses
java.util.List<E> urls
java.util.List<E> phoneNumbers
java.util.List<E> faxNumbers
java.util.Set<E> addresses
java.lang.String code
java.lang.String name
java.util.Set<E> types
Institution isPartOf
TimePeriod period
java.lang.String department
java.lang.String role
Institution institute
Person person
java.lang.String baseNumber
java.lang.String checkSum
ORCID.checkDigit()
java.lang.String prefix
java.lang.String givenName
java.lang.String initials
java.lang.String familyName
java.lang.String suffix
TimePeriod lifespan
ORCID orcid
java.util.Set<E> institutionalMemberships
boolean protectedNomenclaturalTitleCache
boolean protectedCollectorTitleCache
java.util.List<E> teamMembers
boolean hasMoreMembers
java.lang.String nomenclaturalTitle
java.lang.String collectorTitle
boolean isGeneratingTitleCache
java.util.Set<E> markers
java.util.Set<E> annotations
java.util.Set<E> intextReferences
Person commentator
AnnotationType annotationType
java.net.URI linkbackUri
java.beans.PropertyChangeSupport propertyChangeSupport
int id
java.util.UUID uuid
org.joda.time.DateTime created
User createdBy
TaxonBase<S extends ITaxonCacheStrategy> taxon
AgentBase<S extends IIdentifiableEntityCacheStrategy<? extends AgentBase<S>>> agent
java.lang.String abbreviatedText
eu.etaxonomy.cdm.model.common.DefinedTermBase<T extends eu.etaxonomy.cdm.model.common.DefinedTermBase> kindOf
java.util.Set<E> generalizationOf
eu.etaxonomy.cdm.model.common.DefinedTermBase<T extends eu.etaxonomy.cdm.model.common.DefinedTermBase> partOf
java.util.Set<E> includes
java.util.Set<E> media
eu.etaxonomy.cdm.model.common.TermVocabulary<T extends eu.etaxonomy.cdm.model.common.DefinedTermBase> vocabulary
java.lang.String idInVocabulary
java.lang.String symbol
java.lang.String symbol2
TimePeriod timeperiod
AgentBase<S extends IIdentifiableEntityCacheStrategy<? extends AgentBase<S>>> actor
java.lang.String description
java.lang.String value
ExtensionType type
org.joda.time.DateTime lastRetrieved
java.lang.String externalId
java.net.URI externalLink
AuthorityType authorityType
ExternallyManagedImport importMethod
java.lang.String authority
java.lang.String name
java.util.Set<E> members
java.util.Set<E> grantedAuthorities
LSID lsid
java.lang.String titleCache
boolean protectedTitleCache
java.util.Set<E> rights
java.util.List<E> credits
java.util.Set<E> extensions
java.util.List<E> identifiers
IIdentifiableEntityCacheStrategy<T extends IIdentifiableEntity> cacheStrategy
java.lang.String identifier
DefinedTerm type
TaxonName taxonName
SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy<?>> occurrence
AgentBase<S extends IIdentifiableEntityCacheStrategy<? extends AgentBase<S>>> agent
Reference reference
OriginalSourceBase<T extends ISourceable> source
Media media
PolytomousKey key
LanguageString languageString
Annotation annotation
int startPos
int endPos
java.lang.String iso639_1
java.util.Set<E> intextReferences
java.lang.String text
Language language
java.lang.String lsid
java.lang.String authority
java.lang.String namespace
java.lang.String object
java.lang.String revision
java.lang.String authority
java.lang.String server
int port
java.lang.String url
javax.wsdl.Definition authorityWSDL
java.util.Map<K,V> namespaces
boolean flag
MarkerType markerType
boolean isTechnical
int orderIndex
eu.etaxonomy.cdm.model.common.OrderedTermBase<T extends eu.etaxonomy.cdm.model.common.OrderedTermBase<?>> toBeChangedByObject
eu.etaxonomy.cdm.model.common.OriginalSourceType type
java.lang.String idInSource
java.lang.String idNamespace
java.util.Set<E> links
Reference citation
java.lang.String citationMicroReference
java.lang.String originalNameString
boolean doubtful
boolean symmetric
boolean transitive
java.util.Set<E> inverseRepresentations
java.lang.String inverseSymbol
java.lang.String label
java.lang.String abbreviatedLabel
java.util.Set<E> sources
java.net.URI uri
eu.etaxonomy.cdm.model.common.TermType termType
java.util.Set<E> representations
java.net.URI termSourceUri
java.util.Set<E> terms
org.joda.time.Partial start
org.joda.time.Partial end
java.lang.String freeText
java.lang.String username
java.lang.String password
java.lang.String salt
java.lang.String emailAddress
java.util.Set<E> grantedAuthorities
java.util.Set<E> groups
boolean enabled
boolean accountNonExpired
boolean credentialsNonExpired
boolean accountNonLocked
Person person
java.util.Set<E> authorities
java.lang.String verbatimDate
org.joda.time.DateTime updated
User updatedBy
boolean orderRelevant
java.util.List<E> stateData
java.lang.Boolean unknownData
TermNode<T extends DefinedTermBase> structure
DefinedTerm structureModifier
TermNode<T extends DefinedTermBase> property
DefinedTerm propertyModifier
SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy<?>> describedSpecimenOrObservation
java.util.Set<E> descriptionSources
java.util.Set<E> descriptiveDataSets
java.util.Set<E> descriptionElements
boolean imageGallery
boolean isDefault
java.util.EnumSet<E extends java.lang.Enum<E>> types
Feature feature
java.util.Set<E> modifiers
java.util.Map<K,V> modifyingText
java.util.List<E> media
DescriptionBase<S extends IIdentifiableEntityCacheStrategy> inDescription
TimePeriod timeperiod
java.util.Set<E> sources
java.lang.Integer sortIndex
TaxonName nameUsedInSource
java.util.Set<E> representations
TermTree<T extends DefinedTermBase> descriptiveSystem
java.util.Set<E> descriptions
java.util.Set<E> taxonSubtreeFilter
java.util.Set<E> geoFilter
Rank minRank
Rank maxRank
NamedArea area
PresenceAbsenceTerm status
boolean supportsTextData
boolean supportsQuantitativeData
boolean supportsDistribution
boolean supportsIndividualAssociation
boolean supportsTaxonInteraction
boolean supportsCategoricalData
boolean supportsCommonTaxonName
java.util.Set<E> recommendedModifierEnumeration
java.util.Set<E> recommendedStatisticalMeasures
java.util.Set<E> supportedCategoricalEnumerations
java.util.Set<E> recommendedMeasurementUnits
java.util.Set<E> inverseRepresentations
eu.etaxonomy.cdm.model.description.FeatureTree featureTree
Feature feature
eu.etaxonomy.cdm.model.description.FeatureNode parent
java.lang.String treeIndex
java.util.List<E> children
java.lang.Integer sortIndex
java.util.Set<E> onlyApplicableIf
java.util.Set<E> inapplicableIf
eu.etaxonomy.cdm.model.description.FeatureNode root
java.util.Set<E> representations
java.util.Map<K,V> description
SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy<?>> associatedSpecimenOrObservation
java.util.Map<K,V> label
java.util.Set<E> coveredTaxa
java.util.Set<E> geographicalScope
java.util.Set<E> taxonomicScope
java.util.Set<E> scopeRestrictions
java.util.Set<E> keyRepresentations
java.util.Set<E> coveredTaxa
java.util.Set<E> taxonomicScope
java.util.Set<E> geographicalScope
java.util.Set<E> scopeRestrictions
java.util.Set<E> coveredTaxa
java.util.Set<E> taxonomicScope
java.util.Set<E> geographicalScope
java.util.Set<E> scopeRestrictions
PolytomousKeyNode root
int startNumber
PolytomousKey key
java.util.List<E> children
PolytomousKeyNode parent
java.lang.Integer sortIndex
KeyStatement statement
KeyStatement question
Feature feature
Taxon taxon
PolytomousKey subkey
PolytomousKeyNode otherNode
java.lang.Integer nodeNumber
java.util.Map<K,V> modifyingText
java.lang.String defaultColor
boolean absenceTerm
MeasurementUnit unit
java.util.Set<E> statisticalValues
java.lang.Boolean unknownData
CategoricalData categoricalData
State state
java.lang.Integer count
java.util.Set<E> modifiers
java.util.Map<K,V> modifyingText
float value
java.util.Set<E> modifiers
StatisticalMeasure type
QuantitativeData quantitativeData
java.util.Set<E> scopes
java.util.Set<E> geoScopes
Taxon taxon
java.util.Map<K,V> description
Taxon taxon2
TaxonName taxonName
java.util.Map<K,V> multilanguageText
TextFormat format
boolean isHashMapHibernateBugFixed
java.util.Set<E> representations
eu.etaxonomy.cdm.model.description.FeatureTree descriptiveSystem
java.util.Set<E> descriptions
java.util.Set<E> taxonSubtreeFilter
java.util.Set<E> geoFilter
Rank minRank
Rank maxRank
java.lang.String iso3166_A2
java.util.Set<E> continents
TimePeriod validPeriod
Media shape
Point pointApproximation
java.util.Set<E> countries
NamedAreaType type
NamedAreaLevel level
java.lang.Double longitude
java.lang.Double latitude
java.lang.Integer errorRadius
ReferenceSystem referenceSystem
int duration
ExternalLinkType linkType
type
of this link.java.net.URI uri
java.util.Map<K,V> description
java.lang.Integer size
java.util.Set<E> media
int height
int width
java.util.Map<K,V> title
TimePeriod mediaCreated
java.util.Map<K,V> description
java.util.Set<E> representations
AgentBase<S extends IIdentifiableEntityCacheStrategy<? extends AgentBase<S>>> artist
java.lang.String mimeType
java.lang.String suffix
Media media
java.util.List<E> mediaRepresentationParts
java.net.URI uri
java.lang.Integer size
MediaRepresentation mediaRepresentation
int duration
java.net.URI uri
java.lang.String abbreviatedText
RightsType type
AgentBase<S extends IIdentifiableEntityCacheStrategy<? extends AgentBase<S>>> agent
CdmMetaDataPropertyName propertyName
java.lang.String value
CdmPreference.PrefKey key
java.lang.String value
boolean allowOverride
java.lang.String subject
java.lang.String predicate
DefinedTerm dnaMarker
Amplification.getDnaMarker()
Primer forwardPrimer
Amplification.getForwardPrimer()
Primer reversePrimer
Amplification.getReversePrimer()
MaterialOrMethodEvent purification
Institution institution
java.lang.String ladderUsed
Amplification.getLadderUsed()
java.lang.Double electrophoresisVoltage
java.lang.Double gelRunningTime
Amplification.getGelRunningTime()
java.lang.Double gelConcentration
Amplification.getGelConcentration()
java.lang.String labelCache
DnaSample dnaSample
AmplificationResult.getDnaSample()
Amplification amplification
AmplificationResult.getAmplification()
java.util.Set<E> singleReads
Cloning cloning
java.lang.Boolean successful
AmplificationResult.getSuccessful()
java.lang.String successText
AmplificationResult.getSuccessText()
Media gelPhoto
java.lang.String strain
Cloning.getStrain()
Primer forwardPrimer
Cloning.getForwardPrimer()
Primer reversePrimer
Cloning.getReversePrimer()
MaterialOrMethodEvent typedPurificationMethod
java.lang.String purificationMethod
java.lang.Double ratioOfAbsorbance260_230
java.lang.Double ratioOfAbsorbance260_280
java.lang.Double concentration
MeasurementUnit concentrationUnit
OrderedTerm qualityTerm
org.joda.time.DateTime qualityCheckDate
java.util.Set<E> sequences
java.util.Set<E> amplificationResults
DnaQuality dnaQuality
java.util.Set<E> usedSequences
java.lang.String label
Primer.getLabel()
SequenceString sequence
Primer.getSequence()
DefinedTerm dnaMarker
Primer.getDnaMarker()
Reference publishedIn
Primer.getPublishedIn()
DnaSample dnaSample
Media contigFile
Sequence.getContigFile()
SequenceString consensusSequence
Sequence.getConsensusSequence()
java.lang.Boolean isBarcode
SequenceString barcodeSequencePart
#getBarcodeSequence()
java.lang.String geneticAccessionNumber
Sequence.getGeneticAccessionNumber()
java.lang.String boldProcessId
Sequence.getBoldProcessId()
java.util.Set<E> singleReadAlignments
DefinedTerm dnaMarker
Sequence.getDnaMarker()
java.lang.String haplotype
Sequence.getHaplotype()
java.util.Set<E> citations
Sequence.getCitations()
java.lang.String string
java.lang.Integer length
AmplificationResult amplificationResult
SingleRead.getAmplificationResult()
Primer primer
SingleRead.getPrimer()
SequenceString sequence
Media pherogram
SequenceDirection direction
SingleRead.getDirection()
MaterialOrMethodEvent materialOrMethod
Sequence consensusAlignment
#getDnaMarker()
SingleRead singleRead
#getDnaMarker()
SingleReadAlignment.Shift[] shifts
java.lang.Integer firstSeqPosition
java.lang.Integer leftCutPosition
java.lang.Integer rightCutPosition
java.lang.String editedSequence
boolean reverseComplement
int position
int shift
public java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
public java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
boolean anamorphic
java.util.Set<E> typifiedNames
TaxonName firstNameInGroup
boolean includeRanks
RuleConsidered ruleConsidered
TaxonName relatedFrom
TaxonName relatedTo
HybridRelationshipType type
RuleConsidered ruleConsidered
TaxonName relatedFrom
TaxonName relatedTo
NameRelationshipType type
boolean rejectedType
boolean conservedType
TaxonName typeName
RuleConsidered ruleConsidered
NomenclaturalStatusType type
public java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
RankClass rankClass
rank class
of a rank. It is usually needed for correct formatting of a
rank by using e.g. isSupraGeneric(). Prior to v3.3 this was computed by comparison of ranks.java.lang.String identifier
java.lang.String specificIdentifier
org.joda.time.DateTime registrationDate
RegistrationStatus status
Institution institution
TaxonName name
java.util.Set<E> typeDesignations
java.util.Set<E> blockedBy
User submitter
java.lang.String text
NomenclaturalCodeEdition codeEdition
code edition
for the rule considered.DerivedUnit typeSpecimen
NomenclaturalCode nameType
nomenclatural code
this taxon name is ruled by.java.lang.String fullTitleCache
boolean protectedFullTitleCache
java.util.Set<E> descriptions
java.lang.String appendedPhrase
java.lang.String nomenclaturalMicroReference
int parsingProblem
int problemStarts
int problemEnds
java.util.Set<E> typeDesignations
HomotypicalGroup homotypicalGroup
java.util.Set<E> relationsFromThisName
java.util.Set<E> relationsToThisName
java.util.Set<E> status
java.util.Set<E> taxonBases
Rank rank
Reference nomenclaturalReference
DescriptionElementSource nomenclaturalSource
java.util.Set<E> registrations
java.lang.String nameCache
boolean protectedNameCache
java.lang.String genusOrUninomial
java.lang.String infraGenericEpithet
java.lang.String specificEpithet
java.lang.String infraSpecificEpithet
TeamOrPersonBase<T extends TeamOrPersonBase<T>> combinationAuthorship
TeamOrPersonBase<T extends TeamOrPersonBase<T>> exCombinationAuthorship
TeamOrPersonBase<T extends TeamOrPersonBase<T>> inCombinationAuthorship
TeamOrPersonBase<T extends TeamOrPersonBase<T>> basionymAuthorship
TeamOrPersonBase<T extends TeamOrPersonBase<T>> exBasionymAuthorship
TeamOrPersonBase<T extends TeamOrPersonBase<T>> inBasionymAuthorship
java.lang.String authorshipCache
boolean protectedAuthorshipCache
java.util.Set<E> hybridParentRelations
java.util.Set<E> hybridChildRelations
boolean hybridFormula
boolean monomHybrid
boolean binomHybrid
boolean trinomHybrid
java.lang.String acronym
java.lang.String subGenusAuthorship
java.lang.String nameApprobation
java.lang.String breed
java.lang.Integer publicationYear
java.lang.Integer originalPublicationYear
java.lang.String cultivarName
boolean anamorphic
java.lang.String fullTitleCache
boolean protectedFullTitleCache
java.util.Set<E> descriptions
java.lang.String appendedPhrase
java.lang.String nomenclaturalMicroReference
int parsingProblem
int problemStarts
int problemEnds
java.util.Set<E> typeDesignations
HomotypicalGroup homotypicalGroup
java.util.Set<E> relationsFromThisName
java.util.Set<E> relationsToThisName
java.util.Set<E> status
java.util.Set<E> taxonBases
Rank rank
Reference nomenclaturalReference
java.lang.String nameCache
boolean protectedNameCache
java.lang.String genusOrUninomial
java.lang.String infraGenericEpithet
java.lang.String specificEpithet
java.lang.String infraSpecificEpithet
TeamOrPersonBase<T extends TeamOrPersonBase<T>> combinationAuthorship
TeamOrPersonBase<T extends TeamOrPersonBase<T>> exCombinationAuthorship
TeamOrPersonBase<T extends TeamOrPersonBase<T>> basionymAuthorship
TeamOrPersonBase<T extends TeamOrPersonBase<T>> exBasionymAuthorship
java.lang.String authorshipCache
boolean protectedAuthorshipCache
java.util.Set<E> hybridParentRelations
java.util.Set<E> hybridChildRelations
boolean hybridFormula
boolean monomHybrid
boolean binomHybrid
boolean trinomHybrid
java.lang.String acronym
java.lang.String subGenusAuthorship
java.lang.String nameApprobation
java.lang.String breed
java.lang.Integer publicationYear
java.lang.Integer originalPublicationYear
java.lang.String cultivarName
java.util.Map<K,V> text
boolean isVerbatim
boolean isHashMapHibernateBugFixed
boolean notDesignated
TypeDesignationStatusBase<T extends TypeDesignationStatusBase<T>> typeStatus
Reference citation
java.lang.String citationMicroReference
java.util.Set<E> typifiedNames
java.util.Set<E> registrations
public java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
public java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
java.lang.String code
java.lang.String codeStandard
java.lang.String name
java.lang.String townOrLocation
Institution institute
Collection superCollection
java.util.Set<E> originals
java.util.Set<E> derivatives
Institution institution
DerivationEventType type
Collection collection
java.lang.String catalogNumber
java.lang.String accessionNumber
java.lang.String collectorsNumber
java.lang.String barcode
TaxonName storedUnder
DerivationEvent derivedFrom
java.lang.String originalLabelInfo
java.util.Set<E> specimenTypeDesignations
PreservationMethod preservation
java.lang.String exsiccatum
SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy<?>> identifiedUnit
TaxonBase<S extends ITaxonCacheStrategy> taxon
TaxonName taxonName
DefinedTerm modifier
boolean preferredFlag
java.util.Set<E> references
java.lang.String fieldNumber
Person primaryCollector
java.lang.String fieldNotes
GatheringEvent gatheringEvent
LanguageString locality
Point exactLocation
NamedArea country
java.util.Set<E> collectingAreas
java.lang.String collectingMethod
java.lang.Integer absoluteElevation
java.lang.Integer absoluteElevationMax
java.lang.String absoluteElevationText
java.lang.Double distanceToGround
java.lang.Double distanceToGroundMax
java.lang.String distanceToGroundText
java.lang.Double distanceToWaterSurface
java.lang.Double distanceToWaterSurfaceMax
java.lang.String distanceToWaterSurfaceText
DefinedTerm definedMaterialOrMethod
Media mediaSpecimen
DefinedTerm medium
java.lang.Double temperature
SpecimenOrObservationType recordBasis
DataSets/DataSet/Units/Unit/RecordBasis
,
Core: http://wiki.tdwg.org/twiki/bin/view/DarwinCore/BasisOfRecord
java.util.Set<E> descriptions
java.util.Set<E> determinations
DefinedTerm sex
DefinedTerm lifeStage
DefinedTerm kindOfUnit
DataSets/DataSet/Units/Unit/KindOfUnit
,
TermType.KindOfUnit
java.lang.String individualCount
java.net.URI preferredStableUri
http://dev.e-taxonomy.eu/trac/ticket/5606
java.util.Map<K,V> definition
java.util.Set<E> derivationEvents
boolean publish
java.lang.String identityCache
boolean protectedIdentityCache
PermissionClass permissionClass
java.lang.String property
java.util.EnumSet<E extends java.lang.Enum<E>> operations
java.util.UUID targetUuid
java.lang.String authority
java.lang.String name
java.util.Set<E> members
java.util.Set<E> grantedAuthorities
java.util.Set<E> authorities
java.lang.String role
java.lang.String username
java.lang.String password
java.lang.String salt
https://dev.e-taxonomy.eu/redmine/issues/7210
,
https://code-bude.net/2015/03/30/grundlagen-sicheres-passwort-hashing-mit-salts/
java.lang.String emailAddress
java.util.Set<E> grantedAuthorities
java.util.Set<E> groups
boolean enabled
boolean accountNonExpired
boolean credentialsNonExpired
boolean accountNonLocked
Person person
java.util.Set<E> transientGrantedAuthorities
java.util.Set<E> authorities
java.util.Set<E> transientAuthorities
DescriptionBase<S extends IIdentifiableEntityCacheStrategy> description
OriginalSourceType type
type
of this source. According to PROV the type has to be thought as
an activity that leads from the source entity to the current entity. It is not a property of the
source itself.java.lang.String idInSource
java.lang.String idNamespace
CdmLinkSource cdmSource
java.util.Set<E> links
ReferenceType type
java.lang.String title
java.lang.String abbrevTitle
java.lang.String abbrevTitleCache
boolean protectedAbbrevTitleCache
java.lang.String editor
java.lang.String volume
java.lang.String pages
java.lang.String edition
java.lang.String isbn
DOI doi
java.lang.String issn
java.lang.String seriesPart
java.lang.String organization
java.lang.String publisher
java.lang.String placePublished
Institution institution
Institution school
Reference inReference
VerbatimTimePeriod datePublished
org.joda.time.DateTime accessed
java.lang.String referenceAbstract
java.net.URI uri
boolean nomenclaturallyRelevant
TeamOrPersonBase<T extends TeamOrPersonBase<T>> authorship
ExternallyManaged externallyManaged
int parsingProblem
int problemStarts
int problemEnds
TaxonNode replacedTaxonNode
LanguageString name
TaxonNode rootNode
Reference reference
java.lang.String microReference
TimePeriod timeperiod
java.util.Set<E> geoScopes
java.util.Map<K,V> description
TaxonBase<S extends ITaxonCacheStrategy> firstTaxonInGroup
TaxonName firstNameInGroup
Taxon acceptedTaxon
SynonymType type
java.util.Set<E> descriptions
java.util.Set<E> synonyms
java.util.Set<E> relationsFromThisTaxon
java.util.Set<E> relationsToThisTaxon
boolean taxonStatusUnknown
java.util.Set<E> taxonNodes
boolean includeRanks
Taxon taxon
TaxonNode parent
java.lang.String treeIndex
Classification classification
java.util.List<E> childNodes
java.lang.Integer sortIndex
Reference referenceForParentChildRelation
java.lang.String microReferenceForParentChildRelation
int countChildren
java.util.Set<E> agentRelations
boolean unplaced
boolean doubtful
boolean excluded
java.util.Map<K,V> excludedNote
Synonym synonymToBeUsed
TaxonNode taxonNode
TeamOrPersonBase<T extends TeamOrPersonBase<T>> agent
DefinedTerm type
Taxon relatedFrom
Taxon relatedTo
TaxonRelationshipType type
DefinedTermBase<T extends DefinedTermBase> kindOf
java.util.Set<E> generalizationOf
DefinedTermBase<T extends DefinedTermBase> partOf
java.util.Set<E> includes
java.util.Set<E> media
TermVocabulary<T extends DefinedTermBase> vocabulary
java.lang.String idInVocabulary
java.lang.String symbol
java.lang.String symbol2
ExternallyManaged externallyManaged
eu.etaxonomy.cdm.model.term.FeatureTree<T extends DefinedTermBase> featureTree
TermType termType
DefinedTermBase<T extends DefinedTermBase> feature
eu.etaxonomy.cdm.model.term.FeatureNode<T extends DefinedTermBase> parent
java.lang.String treeIndex
java.util.List<E> children
java.lang.Integer sortIndex
java.util.Set<E> onlyApplicableIf
java.util.Set<E> inapplicableIf
eu.etaxonomy.cdm.model.term.FeatureNode<T extends DefinedTermBase> root
TermType termType
java.util.Set<E> representations
boolean allowDuplicates
int orderIndex
OrderedTermBase<T extends OrderedTermBase<?>> toBeChangedByObject
java.lang.String label
java.lang.String abbreviatedLabel
java.lang.String plural
java.net.URI uri
TermType termType
java.util.Set<E> representations
java.util.Set<E> termRelations
boolean allowDuplicates
boolean orderRelevant
boolean isFlat
TermNode<T extends DefinedTermBase> parent
java.lang.String treeIndex
java.util.List<E> children
java.lang.Integer sortIndex
java.util.Set<E> onlyApplicableIf
java.util.Set<E> inapplicableIf
DefinedTermBase<T extends DefinedTermBase> toTerm
TermGraphBase<TERM extends DefinedTermBase,REL extends TermRelationBase> graph
TermType termType
type
of this term relation.
Must be the same type as for the term collection
this node belongs to and as the term type of the term this node links to.DefinedTermBase<T extends DefinedTermBase> term
TermNode<T extends DefinedTermBase> root
java.net.URI termSourceUri
java.util.Set<E> terms
ExternallyManaged externallyManaged
java.lang.String propertyPath
java.lang.String userFriendlyFieldName
java.lang.String invalidValue
Severity severity
java.lang.String message
java.lang.String validator
java.lang.String validationGroup
EntityValidation entityValidation
int validatedEntityId
java.util.UUID validatedEntityUuid
java.lang.String validatedEntityClass
int validationCount
org.joda.time.DateTime updated
java.lang.String userFriendlyDescription
java.lang.String userFriendlyTypeName
CRUDEventType crudEventType
EntityValidationStatus status
java.util.Set<E> entityConstraintViolations
java.util.UUID uuid
java.lang.Integer revisionNumber
org.joda.time.DateTime date
java.lang.Long timestamp
AuditEvent auditEvent
java.util.UUID uuid
java.net.URI uri
TermType termType
java.util.Set<E> representations
java.lang.String representation_L10n
java.lang.String representation_L10n_abbreviatedLabel
java.lang.String representation_L10n_text
ICdmBase mergedEntity
java.util.Set<E> newEntities
UuidAndTitleCache<T extends ICdmBase> uuidAndTitleCache
SpecimenOrObservationType type
TaxonNode taxonNode
java.util.UUID taxonDescriptionUuid
int taxonomicChildrenCount
java.util.UUID secUuid
java.util.UUID taxonUuid
java.util.List<E> taggedTitle
boolean unplaced
boolean excluded
boolean doubtful
java.lang.String rankLabel
java.lang.Integer rankOrderIndex
TaxonStatus status
java.util.UUID classificationUUID
java.util.UUID parentUUID
java.lang.String treeIndex
java.lang.Integer sortIndex
boolean ignoreHybridSign
boolean sortInfraGenericFirst
java.util.Set<E> terms
java.util.UUID kindOfUuid
java.util.UUID partOfUuid
java.util.UUID vocabularyUuid
TermDto kindOfDto
TermDto partOfDto
TermVocabularyDto vocabularyDto
java.lang.Integer orderIndex
java.lang.String idInVocabulary
java.util.Collection<E> includes
java.util.Collection<E> generalizationOf
java.util.Set<E> vocRepresentations
java.lang.String vocRepresentation_L10n
java.lang.String vocRepresentation_L10n_abbreviatedLabel
java.util.Collection<E> media
NamedAreaLevel level
java.lang.Class<T> type
java.util.UUID uuid
java.lang.Integer id
java.lang.String titleCache
java.lang.String abbrevTitleCache
boolean isOrphaned
CdmBase entity
org.hibernate.persister.entity.EntityPersister persister
java.util.Set<E> affectedObjects
java.lang.Object[] state
java.lang.Object[] oldState
java.io.Serializable id
CdmDataChangeEvent.EventType eventType
int updates
int creates
int loads
boolean delayed
CdmPostDataChangeObservableListener.delayedNotify()
. All events until then will be stored in CdmPostDataChangeObservableListener.changeEvents
boolean propagateLoads
boolean propagateInserts
boolean propagateUpdates
boolean propagateDeletes
CdmDataChangeMap changeEvents
java.util.Set<E> observers
ICdmPermissionEvaluator permissionEvaluator
java.lang.Boolean showSql
java.lang.Boolean formatSql
java.lang.Boolean registerSearch
java.lang.Boolean registerEnvers
java.lang.Class<T> cacheProviderClass
java.util.Map<K,V> beforeTransactionCompletionProcessTypes
ValidationExecutor validationExecutor
IEntityValidationCrud dao
boolean enabled
PermissionClass permissionClass
java.lang.String property
java.util.EnumSet<E extends java.lang.Enum<E>> operation
java.util.UUID targetUuid
java.util.UUID uuid
java.lang.String authority
java.lang.String function
java.lang.String propertyName
boolean ascending
java.lang.String nativeSQL
java.lang.String nativeSQL
java.lang.Boolean ascending
java.lang.String propertyName
OrderHint.SortOrder sortOrder
java.lang.String LUCENE_SCORE
ICdmRepository applicationConfiguration
java.net.URL webserviceUrl
java.util.List<E> selectedTaxonNodeElements
boolean doSynonymy
boolean doDescriptions
boolean doPolytomousKey
java.util.UUID featureTreeUuid
boolean doImages
boolean doPublishEntireBranches
java.io.File exportFolder
java.util.List<E> outputModules
boolean remote
IProgressMonitor progressMonitor
java.util.UUID uuid
java.lang.String label
java.lang.Class<T> type
java.lang.String value
org.joda.time.DateTime expirationDate
java.math.BigInteger completeListSize
java.math.BigInteger cursor
MetadataPrefix metadataPrefix
org.joda.time.DateTime from
org.joda.time.DateTime until
SetSpec set
java.lang.Class<T> enumTermClass
java.lang.String text
TagEnum type
TypedEntityReference<T> entityReference
java.lang.String initialsSeparator
int etAlPosition
java.lang.String nameAuthorSeperator
java.lang.String basionymStart
java.lang.String basionymEnd
java.lang.String exAuthorSeperator
java.lang.CharSequence basionymAuthorCombinationAuthorSeperator
java.lang.String zooAuthorYearSeperator
java.lang.String nameAuthorSeperator
java.lang.String basionymStart
java.lang.String basionymEnd
java.lang.String exAuthorSeperator
java.lang.CharSequence basionymAuthorCombinationAuthorSeperator
java.lang.String zooAuthorYearSeperator
java.lang.String AuthorYearSeperator
java.lang.String afterSectionAuthor
java.lang.String inSeparator
java.util.UUID uuid
java.util.Map<K,V> strategies
java.lang.Class<T> baseClass
Matching matching
boolean deleteSecondObject
java.util.List<E> elements
boolean expandElements
java.lang.String[] params
java.lang.String text
boolean nullObject
java.util.Map<K,V> properties
org.hibernate.boot.spi.MetadataBuildingContext buildingContext
org.hibernate.mapping.Collection collection
java.util.Map<K,V> localInheritedMetas
java.lang.String referencedEntityName
org.hibernate.mapping.Component component
org.hibernate.boot.spi.MetadataBuildingContext buildingContext
org.hibernate.cfg.Ejb3JoinColumn[] joinColumns
org.hibernate.mapping.RootClass rootClass
org.hibernate.mapping.JoinedSubclass joinedSubClass
boolean resolved
org.hibernate.mapping.SimpleValue value
org.hibernate.cfg.Ejb3JoinColumn[] columns
int uniqueCounter
org.hibernate.mapping.Table table
java.lang.String indexName
java.lang.String[] columns
org.hibernate.boot.spi.MetadataBuildingContext buildingContext
org.hibernate.cfg.Ejb3Column column
boolean unique
org.hibernate.mapping.JoinedSubclass entity
org.hibernate.boot.spi.MetadataBuildingContext buildingContext
org.hibernate.boot.spi.MetadataBuildingContext buildingContext
java.lang.String mappedBy
java.lang.String ownerEntity
java.lang.String ownerProperty
org.hibernate.cfg.PropertyHolder propertyHolder
boolean ignoreNotFound
org.hibernate.cfg.PropertyData inferredData
org.hibernate.annotations.common.reflection.XClass targetEntity
boolean cascadeOnDelete
boolean optional
java.lang.String cascadeStrategy
org.hibernate.cfg.Ejb3JoinColumn[] joinColumns
java.lang.String referencedEntityName
org.hibernate.cfg.Ejb3JoinColumn[] columns
org.hibernate.mapping.SimpleValue value
org.hibernate.cfg.annotations.EntityBinder entityBinder
org.hibernate.cfg.PropertyHolder propertyHolder
org.hibernate.annotations.common.reflection.XAnnotatedElement annotatedClass
org.hibernate.cfg.annotations.SimpleValueBinder binder
org.hibernate.boot.spi.MetadataBuildingContext buildingContext
boolean unique
java.lang.String path
java.lang.String entityClassName
java.lang.String fetchProfileName
org.hibernate.annotations.FetchProfile.FetchOverride fetch
org.hibernate.boot.spi.MetadataBuildingContext buildingContext
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