Modifier and Type | Method and Description |
---|---|
java.util.List<UuidAndTitleCache<Classification>> |
ClassificationServiceImpl.getUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern) |
java.util.List<Classification> |
IClassificationService.listClassifications(java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<Classification> |
ClassificationServiceImpl.listClassifications(java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<Classification> |
TaxonServiceImpl.listClassifications(TaxonBase taxonBase,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<Classification> |
ITaxonService.listClassifications(TaxonBase taxonBase,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths)
Lists all classifications the given taxon/synonym is used in
Synonym |
Modifier and Type | Method and Description |
---|---|
ClassificationLookupDTO |
IClassificationService.classificationLookup(Classification classification) |
ClassificationLookupDTO |
ClassificationServiceImpl.classificationLookup(Classification classification) |
int |
TaxonNodeServiceImpl.countAllNodesForClassification(Classification classification) |
int |
ITaxonNodeService.countAllNodesForClassification(Classification classification)
Counts all TaxonNodes for a given Classification
|
java.util.List<Synonym> |
TaxonServiceImpl.createAllInferredSynonyms(Taxon taxon,
Classification tree,
boolean doWithMisappliedNames) |
java.util.List<Synonym> |
ITaxonService.createAllInferredSynonyms(Taxon taxon,
Classification tree,
boolean doWithMisappliedNames)
Creates all inferred synonyms for the taxon in the classification, but do not insert it to the database
|
UpdateResult |
IClassificationService.createHierarchyInClassification(Classification classification,
CreateHierarchyForClassificationConfigurator configurator) |
UpdateResult |
ClassificationServiceImpl.createHierarchyInClassification(Classification classification,
CreateHierarchyForClassificationConfigurator configurator)
creates new Classification and parent TaxonNodes at genus level
|
java.util.List<Synonym> |
TaxonServiceImpl.createInferredSynonyms(Taxon taxon,
Classification classification,
SynonymType type,
boolean doWithMisappliedNames) |
java.util.List<Synonym> |
ITaxonService.createInferredSynonyms(Taxon taxon,
Classification tree,
SynonymType type,
boolean doWithMisappliedNames)
Creates the specified inferred synonyms for the taxon in the classification, but do not insert it to the database
|
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findByDescriptionElementFullText(java.lang.Class<? extends DescriptionElementBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.util.List<Feature> features,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findByDescriptionElementFullText(java.lang.Class<? extends DescriptionElementBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.util.List<Feature> features,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Searches for TaxonBase instances by using the DescriptionElement free text index.
|
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findByDistribution(java.util.List<NamedArea> areaFilter,
java.util.List<PresenceAbsenceTerm> statusFilter,
Classification classification,
TaxonNode subtree,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findByDistribution(java.util.List<NamedArea> areaFilter,
java.util.List<PresenceAbsenceTerm> statusFilter,
Classification classification,
TaxonNode subtree,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findByEverythingFullText(java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findByEverythingFullText(java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Deprecated.
this search should fully be covered by the new method
#findTaxaAndNamesByFullText(EnumSet, String, Classification, Set, List, boolean, Integer, Integer, List, List)
, maybe we should rename this latter method to give it a more meaningful name |
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findByFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findByFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Searches for TaxonBase instances using the TaxonBase free text index.
|
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findTaxaAndNamesByFullText(java.util.EnumSet<TaxaAndNamesSearchMode> searchModes,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.util.Set<NamedArea> namedAreas,
java.util.Set<PresenceAbsenceTerm> distributionStatus,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findTaxaAndNamesByFullText(java.util.EnumSet<TaxaAndNamesSearchMode> searchModes,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.util.Set<NamedArea> namedAreas,
java.util.Set<PresenceAbsenceTerm> distributionStatus,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Searches for TaxonBase instances using the TaxonBase free text index.
|
java.util.List<UuidAndTitleCache<TaxonNode>> |
IClassificationService.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification) |
java.util.List<UuidAndTitleCache<TaxonNode>> |
ClassificationServiceImpl.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification) |
java.util.List<UuidAndTitleCache<TaxonNode>> |
IClassificationService.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,
boolean searchForClassifications) |
java.util.List<UuidAndTitleCache<TaxonNode>> |
ClassificationServiceImpl.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,
boolean searchForClassifications) |
java.util.List<UuidAndTitleCache<TaxonNode>> |
IClassificationService.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,
java.lang.Integer limit,
java.lang.String pattern) |
java.util.List<UuidAndTitleCache<TaxonNode>> |
ClassificationServiceImpl.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,
java.lang.Integer limit,
java.lang.String pattern) |
java.util.List<UuidAndTitleCache<TaxonNode>> |
IClassificationService.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,
java.lang.Integer limit,
java.lang.String pattern,
boolean searchForClassifications) |
java.util.List<UuidAndTitleCache<TaxonNode>> |
ClassificationServiceImpl.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,
java.lang.Integer limit,
java.lang.String pattern,
boolean searchForClassifications) |
java.util.List<TaxonNode> |
TaxonNodeServiceImpl.listAllNodesForClassification(Classification classification,
java.lang.Integer start,
java.lang.Integer end) |
java.util.List<TaxonNode> |
ITaxonNodeService.listAllNodesForClassification(Classification classification,
java.lang.Integer start,
java.lang.Integer end) |
java.util.List<TaxonNode> |
IClassificationService.listRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths)
Loads all TaxonNodes of the specified classification for a given Rank or lower.
|
java.util.List<TaxonNode> |
ClassificationServiceImpl.listRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
IClassificationService.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
ClassificationServiceImpl.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
IClassificationService.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
TaxonNode subtree,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths)
Although this method seems to be a redundant alternative to
IClassificationService.loadChildNodesOfTaxonNode(TaxonNode, List) it is an important
alternative from which web services benefit. |
java.util.List<TaxonNode> |
ClassificationServiceImpl.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
TaxonNode subtree,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonNode> |
IClassificationService.pageRankSpecificRootNodes(Classification classification,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths)
Deprecated.
keep this for compatibility to older versions, might be removed in versions >5.3
|
Pager<TaxonNode> |
ClassificationServiceImpl.pageRankSpecificRootNodes(Classification classification,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonNode> |
IClassificationService.pageRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths)
Loads all TaxonNodes of the specified classification for a given Rank or lower.
|
Pager<TaxonNode> |
ClassificationServiceImpl.pageRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
protected LuceneSearch |
TaxonServiceImpl.prepareByDescriptionElementFullTextSearch(java.lang.Class<? extends CdmBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.util.List<Feature> features,
java.util.List<Language> languages,
boolean highlightFragments) |
protected LuceneSearch |
TaxonServiceImpl.prepareByDistributionSearch(java.util.List<NamedArea> namedAreaList,
java.util.List<PresenceAbsenceTerm> distributionStatusList,
Classification classification,
TaxonNode subtree)
This method has been primarily created for testing the area join query but might
also be useful in other situations
|
protected LuceneSearch |
TaxonServiceImpl.prepareFindByFullTextSearch(java.lang.Class<? extends CdmBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.lang.String className,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
org.apache.lucene.search.SortField[] sortFields) |
protected LuceneSearch |
TaxonServiceImpl.prepareFindByTaxonRelationFullTextSearch(TaxonRelationshipEdge edge,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
org.apache.lucene.search.SortField[] sortFields)
Uses org.apache.lucene.search.join.JoinUtil for query time joining, alternatively
the BlockJoinQuery could be used.
|
java.util.UUID |
IClassificationService.saveClassification(Classification classification) |
java.util.UUID |
ClassificationServiceImpl.saveClassification(Classification classification) |
java.util.List<TaxonNodeDto> |
TaxonNodeServiceImpl.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
java.util.List<TaxonNodeDto> |
ITaxonNodeService.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
java.util.List<TaxonNodeDto> |
TaxonNodeServiceImpl.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonName name) |
java.util.List<TaxonNodeDto> |
ITaxonNodeService.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonName name) |
Modifier and Type | Method and Description |
---|---|
UpdateResult |
ClassificationServiceImpl.updateCaches(java.lang.Class<? extends Classification> clazz,
java.lang.Integer stepSize,
IIdentifiableEntityCacheStrategy<Classification> cacheStrategy,
IProgressMonitor monitor) |
UpdateResult |
ClassificationServiceImpl.updateCaches(java.lang.Class<? extends Classification> clazz,
java.lang.Integer stepSize,
IIdentifiableEntityCacheStrategy<Classification> cacheStrategy,
IProgressMonitor monitor) |
Modifier and Type | Method and Description |
---|---|
Classification |
FindTaxaAndNamesConfiguratorImpl.getClassification() |
Classification |
IFindTaxaAndNamesConfigurator.getClassification() |
Modifier and Type | Method and Description |
---|---|
void |
FindTaxaAndNamesConfiguratorImpl.setClassification(Classification classification) |
void |
IFindTaxaAndNamesConfigurator.setClassification(Classification classification) |
Modifier and Type | Method and Description |
---|---|
java.util.List<LogicFilter<Classification>> |
TaxonNodeFilter.getClassificationFilter() |
Modifier and Type | Method and Description |
---|---|
static TaxonNodeFilter |
TaxonNodeFilter.NewClassificationInstance(Classification classification) |
TaxonNodeFilter |
TaxonNodeFilter.orClassification(Classification classification) |
Constructor and Description |
---|
TaxonNodeFilter(Classification classification) |
Modifier and Type | Method and Description |
---|---|
protected Classification |
Cdm2CdmImportBase.handlePersistedClassification(Classification classification) |
Modifier and Type | Method and Description |
---|---|
protected Classification |
Cdm2CdmImportBase.handlePersistedClassification(Classification classification) |
Modifier and Type | Method and Description |
---|---|
Classification |
ImportStateBase.getTree(java.lang.Object ref) |
protected Classification |
CdmImportBase.makeTree(STATE state,
Reference reference) |
protected Classification |
CdmImportBase.makeTreeMemSave(STATE state,
Reference ref)
Alternative memory saving method variant of
#makeTree(STATE state, Reference ref) which stores only the
UUID instead of the full tree in the ImportStateBase by
using state.putTreeUuid(ref, tree); |
Modifier and Type | Method and Description |
---|---|
void |
ImportStateBase.putClassificationUuid(java.lang.String treeKey,
Classification tree) |
void |
ImportStateBase.putClassificationUuidInt(int classificationKeyId,
Classification classification)
Adds a classification uuid to the classification uuid map,
which maps a key for the classification to its UUID in the CDM
|
void |
ImportStateBase.putTree(java.lang.Object ref,
Classification tree) |
void |
ImportStateBase.putTreeUuid(Reference ref,
Classification tree) |
Modifier and Type | Method and Description |
---|---|
protected java.util.Set<Classification> |
CsvDemoExport.assembleClassificationSet(CsvDemoExportConfigurator config) |
Modifier and Type | Method and Description |
---|---|
void |
CsvDemoRecord.setDatasetId(Classification classification) |
Modifier and Type | Method and Description |
---|---|
protected java.util.List<TaxonNode> |
CsvDemoBase.getAllNodes(java.util.Set<Classification> classificationList)
Returns the list of
taxon nodes that are part in one of the given classifications
and do have a Taxon attached (empty taxon nodes should not but do exist in CDM databases). |
Modifier and Type | Method and Description |
---|---|
void |
CsvTaxRecordRedlist.setDatasetId(Classification classification) |
Modifier and Type | Method and Description |
---|---|
void |
DwcaTaxonRecord.setDatasetId(Classification classification) |
Modifier and Type | Method and Description |
---|---|
Classification |
TaxonExcelImportState.getClassification() |
Modifier and Type | Method and Description |
---|---|
void |
TaxonExcelImportState.setClassification(Classification classification) |
Modifier and Type | Field and Description |
---|---|
protected java.util.List<Classification> |
DataSet.classifications |
Modifier and Type | Method and Description |
---|---|
java.util.List<Classification> |
DataSet.getClassifications() |
Modifier and Type | Method and Description |
---|---|
void |
DataSet.setClassifications(java.util.List<Classification> value) |
Modifier and Type | Method and Description |
---|---|
Classification |
SpecimenUserInteraction.askForClassification(java.util.Map<java.lang.String,Classification> classMap) |
Classification |
SpecimenImportStateBase.getClassification() |
Classification |
SpecimenImportStateBase.getDefaultClassification(boolean createIfNotExist) |
Modifier and Type | Method and Description |
---|---|
protected void |
SpecimenImportBase.addParentTaxon(Taxon taxon,
STATE state,
boolean preferredFlag,
Classification classification)
Add the hierarchy for a Taxon(add higher taxa)
|
Taxon |
SpecimenUserInteraction.askWhereToFixData(java.lang.String scientificName,
java.util.List<TaxonBase> taxonList,
Classification classification)
Look if the same name already exists in the ALL classifications and ask the user to select one or none.
|
protected Taxon |
SpecimenImportBase.linkParentChildNode(Taxon parent,
Taxon child,
Classification classification,
STATE state)
Link a parent to a child and save it in the current classification
|
Taxon |
SpecimenUserInteraction.lookForTaxaIntoCurrentClassification(java.util.List<TaxonBase> taxonBaseList,
Classification classification)
Look if the same TaxonBase already exists in the SAME classification
|
void |
SpecimenImportStateBase.setClassification(Classification classification) |
void |
SpecimenImportStateBase.setDefaultClassification(Classification defaultClassification) |
Modifier and Type | Method and Description |
---|---|
Classification |
SpecimenUserInteraction.askForClassification(java.util.Map<java.lang.String,Classification> classMap) |
Modifier and Type | Method and Description |
---|---|
Classification |
GbifImportState.getClassification() |
Classification |
GbifImportState.getDefaultClassification(boolean createIfNotExist) |
Modifier and Type | Method and Description |
---|---|
void |
GbifImportState.setClassification(Classification classification) |
void |
GbifImportState.setDefaultClassification(Classification defaultClassification) |
Modifier and Type | Method and Description |
---|---|
protected Taxon |
TaxonXExtractor.askParent(Taxon taxon,
Classification classification)
asks for the hierarchical parent, based on the current classification
|
void |
TaxonXTreatmentExtractor.updateClassification(Classification classification2) |
void |
TaxonXXMLFieldGetter.updateClassification(Classification classification2)
updates the classification in the treatment extractor
|
Constructor and Description |
---|
TaxonXTreatmentExtractor(NomenclaturalCode nomenclaturalCode,
Classification classification,
TaxonXImport importer,
TaxonXImportState configState,
java.util.Map<java.lang.String,Feature> featuresMap,
Reference urlSource) |
TaxonXXMLFieldGetter(TaxonXDataHolder dataholder,
java.lang.String prefix,
org.w3c.dom.Document document,
TaxonXImport taxonXImport,
TaxonXImportState taxonXstate,
Classification classif,
java.util.Map<java.lang.String,Feature> featuresMap) |
Modifier and Type | Method and Description |
---|---|
protected Classification |
TropicosNameImport.makeClassification(STATE state) |
Modifier and Type | Method and Description |
---|---|
protected Classification |
WfoAccessTaxonImport.makeClassification(STATE state) |
Modifier and Type | Method and Description |
---|---|
static PreferenceSubject |
PreferenceSubject.NewInstance(Classification classification) |
Modifier and Type | Method and Description |
---|---|
Classification |
TaxonNode.getClassification() |
static Classification |
Classification.NewInstance(java.lang.String name) |
static Classification |
Classification.NewInstance(java.lang.String name,
Language language) |
static Classification |
Classification.NewInstance(java.lang.String name,
Reference reference) |
static Classification |
Classification.NewInstance(java.lang.String name,
Reference reference,
Language language) |
Modifier and Type | Method and Description |
---|---|
TaxonNode |
Taxon.getTaxonNode(Classification classification) |
protected void |
TaxonNode.setClassification(Classification classification)
Deprecated.
for internal use only
|
Constructor and Description |
---|
TaxonNode(Taxon taxon,
Classification classification)
Deprecated.
setting of classification is handled in the addTaxonNode() method,
use TaxonNode(taxon) instead
|
Modifier and Type | Method and Description |
---|---|
java.lang.Long |
StatisticsDaoHibernateImpl.countDescriptive(java.lang.Boolean sourceRef,
Classification classification) |
java.lang.Long |
StatisticsDaoHibernateImpl.countNomenclaturalReferences(Classification classification) |
java.lang.Long |
StatisticsDaoHibernateImpl.countReferencesInClassification(Classification classification) |
java.lang.Long |
StatisticsDaoHibernateImpl.countReferencesInClassificationWithUuids(Classification classification) |
java.lang.Long |
StatisticsDaoHibernateImpl.countTaxaInClassification(java.lang.Class<? extends TaxonBase> clazz,
Classification classification) |
java.lang.Long |
StatisticsDaoHibernateImpl.countTaxonNames(Classification classification) |
Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonDaoHibernateImpl.acceptedTaxonFor(Synonym synonym,
Classification classificationFilter,
java.util.List<java.lang.String> propertyPaths) |
protected void |
TaxonDaoHibernateImpl.addRestrictions(boolean doAreaRestriction,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.Set<java.util.UUID> namedAreasUuids,
org.hibernate.Query query) |
ClassificationLookupDTO |
ClassificationDaoHibernateImpl.classificationLookup(Classification classification) |
long |
TaxonDaoHibernateImpl.countAcceptedTaxonFor(Synonym synonym,
Classification classificationFilter) |
java.lang.Long |
ClassificationDaoHibernateImpl.countChildrenOf(Taxon taxon,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished) |
java.lang.Long |
TaxonNodeDaoHibernateImpl.countChildrenOf(TaxonNode node,
Classification classification,
boolean recursive,
boolean includeUnpublished) |
long[] |
ClassificationDaoHibernateImpl.countRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
Rank rank) |
java.lang.Long |
ClassificationDaoHibernateImpl.countSiblingsOf(Taxon taxon,
Classification classification,
boolean includeUnpublished) |
long |
TaxonDaoHibernateImpl.countTaxaByCommonName(java.lang.String searchString,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas) |
long |
TaxonDaoHibernateImpl.countTaxaByName(boolean doTaxa,
boolean doSynonyms,
boolean doMisappliedNames,
boolean doCommonNames,
boolean doIncludeAuthors,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
boolean includeUnpublished) |
int |
TaxonNodeDaoHibernateImpl.countTaxonOfAcceptedTaxaByClassification(Classification classification) |
java.util.UUID |
ClassificationDaoHibernateImpl.delete(Classification persistentObject) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.findByNameTitleCache(boolean doTaxa,
boolean doSynonyms,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNodeDto> |
TaxonNodeDaoHibernateImpl.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
java.util.List<TaxonNodeDto> |
TaxonNodeDaoHibernateImpl.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonName name) |
java.util.List<Taxon> |
TaxonDaoHibernateImpl.getTaxaByCommonName(java.lang.String queryString,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<UuidAndTitleCache<Taxon>> |
TaxonDaoHibernateImpl.getTaxaByCommonNameForEditor(java.lang.String titleSearchStringSqlized,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.getTaxaByName(boolean doTaxa,
boolean doSynonyms,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeAuthors,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
boolean includeUnpublished,
NameSearchOrder order,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>> |
TaxonDaoHibernateImpl.getTaxaByNameForEditor(boolean doTaxa,
boolean doSynonyms,
boolean doNamesWithoutTaxa,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order) |
java.util.List<UuidAndTitleCache<TaxonNode>> |
TaxonNodeDaoHibernateImpl.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,
java.lang.Integer limit,
java.lang.String pattern,
boolean searchForClassifications) |
java.util.List<TaxonNode> |
TaxonNodeDaoHibernateImpl.getTaxonOfAcceptedTaxaByClassification(Classification classification,
java.lang.Integer start,
java.lang.Integer end) |
java.util.List<TaxonNode> |
ClassificationDaoHibernateImpl.listChildrenOf(Taxon taxon,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
ClassificationDaoHibernateImpl.listRankSpecificRootNodes(Classification classification,
TaxonNode taxonNode,
Rank rank,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths,
int queryIndex) |
java.util.List<TaxonNode> |
ClassificationDaoHibernateImpl.listSiblingsOf(Taxon taxon,
Classification classification,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
java.lang.Long |
IStatisticsDao.countDescriptive(java.lang.Boolean sourceRef,
Classification classification)
count all references that are attached to any description in the given classification
|
java.lang.Long |
IStatisticsDao.countNomenclaturalReferences(Classification classification)
counts all NomenclaturalReference items attached to the given classification
|
java.lang.Long |
IStatisticsDao.countReferencesInClassification(Classification classification)
count all Reference items attached to the given classification
but not nomenclatural references
|
java.lang.Long |
IStatisticsDao.countReferencesInClassificationWithUuids(Classification classification) |
java.lang.Long |
IStatisticsDao.countTaxaInClassification(java.lang.Class<? extends TaxonBase> clazz,
Classification classification)
counts items of the type Taxon, Synonym or TaxonBase (Taxon & Synonym)
|
java.lang.Long |
IStatisticsDao.countTaxonNames(Classification classification)
counts all TaxonNames that are attached to the given classification
|
Modifier and Type | Method and Description |
---|---|
Taxon |
ITaxonDao.acceptedTaxonFor(Synonym synonym,
Classification classificationFilter,
java.util.List<java.lang.String> propertyPaths)
This method was originally required when synonyms still had a synonym relationship
to taxa and could belong to multiple taxa.
|
ClassificationLookupDTO |
IClassificationDao.classificationLookup(Classification classification) |
long |
ITaxonDao.countAcceptedTaxonFor(Synonym synonym,
Classification classificationFilter)
This method was originally required when synonyms still had a synonym relationship
to taxa and could belong to multiple taxa.
|
java.lang.Long |
IClassificationDao.countChildrenOf(Taxon taxon,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished) |
java.lang.Long |
ITaxonNodeDao.countChildrenOf(TaxonNode node,
Classification classification,
boolean recursive,
boolean includeUnpublished) |
long[] |
IClassificationDao.countRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
Rank rank) |
java.lang.Long |
IClassificationDao.countSiblingsOf(Taxon taxon,
Classification classification,
boolean includeUnpublished) |
long |
ITaxonDao.countTaxaByCommonName(java.lang.String searchString,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas) |
long |
ITaxonDao.countTaxaByName(boolean doTaxa,
boolean doSynonyms,
boolean doMisappliedNames,
boolean doCommonNames,
boolean doIncludeAuthors,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
boolean includeUnpublished) |
int |
ITaxonNodeDao.countTaxonOfAcceptedTaxaByClassification(Classification classification) |
java.util.List<TaxonBase> |
ITaxonDao.findByNameTitleCache(boolean doTaxa,
boolean doSynonyms,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
java.util.List<java.lang.String> propertyPaths)
Find taxa by searching for Taxa and Synonyms where the
TaxonName .titleCache matches
the name specified as queryString taxonName |
java.util.List<TaxonNodeDto> |
ITaxonNodeDao.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
java.util.List<TaxonNodeDto> |
ITaxonNodeDao.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonName name) |
java.util.List<Taxon> |
ITaxonDao.getTaxaByCommonName(java.lang.String queryString,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<UuidAndTitleCache<Taxon>> |
ITaxonDao.getTaxaByCommonNameForEditor(java.lang.String titleSearchStringSqlized,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas) |
java.util.List<TaxonBase> |
ITaxonDao.getTaxaByName(boolean doTaxa,
boolean doSynonyms,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeAuthors,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
boolean includeUnpublished,
NameSearchOrder order,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
where the taxonBase.name.nameCache property matches the String queryString.
|
java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>> |
ITaxonDao.getTaxaByNameForEditor(boolean doTaxa,
boolean doSynonyms,
boolean doNamesWithoutTaxa,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order) |
java.util.List<UuidAndTitleCache<TaxonNode>> |
ITaxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,
java.lang.Integer limit,
java.lang.String pattern,
boolean searchForClassifications) |
java.util.List<TaxonNode> |
ITaxonNodeDao.getTaxonOfAcceptedTaxaByClassification(Classification classification,
java.lang.Integer start,
java.lang.Integer end) |
java.util.List<TaxonNode> |
IClassificationDao.listChildrenOf(Taxon taxon,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
IClassificationDao.listRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths,
int queryIndex)
Lists all TaxonNodes of the specified tree for a given Rank.
|
java.util.List<TaxonNode> |
IClassificationDao.listSiblingsOf(Taxon taxon,
Classification classification,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
Classification |
ClassificationLookupDTO.getClassification() |
Constructor and Description |
---|
ClassificationLookupDTO(Classification classification) |
Modifier and Type | Method and Description |
---|---|
protected Classification |
BaseListController.getClassificationOrError(java.util.UUID classificationUuid,
IClassificationService classificationService,
javax.servlet.http.HttpServletResponse response) |
protected Classification |
BaseController.getClassificationOrError(java.util.UUID classificationUuid,
IClassificationService classificationService,
javax.servlet.http.HttpServletResponse response) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Classification> |
TaxonController.doGetClassifications(java.util.UUID uuid,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response) |
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