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- added javadoc
[cdmlib.git] / .gitattributes
diff --git a/.gitattributes b/.gitattributes
index 53e3b913de6042d9a4b07277d61bf90f893a2229..e4eda34c20d4a49e4b1b8a8a8c0a4579fcda7e77 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -4,8 +4,10 @@
 cdmlib-commons/LICENSE.TXT -text
 cdmlib-commons/README.TXT -text
 cdmlib-commons/pom.xml -text
+cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/AbstractStringComparator.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/AccountStore.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/CdmUtils.java -text
+cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/DOI.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/DocUtils.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/DoubleResult.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/ExcelUtils.java -text
@@ -17,6 +19,7 @@ cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/Tree.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/TreeNode.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/UTF8.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/UriUtils.java -text
+cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/UrlUtf8Coder.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/XmlHelp.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/media/AudioInfo.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/media/ImageInfo.java -text
@@ -32,6 +35,7 @@ cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/monitor/SubProgressMonitor.
 cdmlib-commons/src/main/resources/MUST-EXIST.txt -text
 cdmlib-commons/src/main/resources/log4j.properties -text
 cdmlib-commons/src/test/java/eu/etaxonomy/cdm/common/CdmUtilsTest.java -text
+cdmlib-commons/src/test/java/eu/etaxonomy/cdm/common/DoiTest.java -text
 cdmlib-commons/src/test/java/eu/etaxonomy/cdm/common/GeneralParserTest.java -text
 cdmlib-commons/src/test/java/eu/etaxonomy/cdm/common/UriUtilsTest.java -text
 cdmlib-commons/src/test/java/eu/etaxonomy/cdm/common/UuidGenerator.java -text
@@ -47,6 +51,10 @@ cdmlib-ext/pom.xml -text
 cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/bci/BciSchemaAdapter.java -text
 cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/bci/BciServiceWrapper.java -text
 cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/bci/IBciServiceWrapper.java -text
+cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/biocase/BioCaseQuery.java -text
+cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/biocase/BioCaseQueryGenerator.java -text
+cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/biocase/BioCaseQueryServiceWrapper.java -text
+cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/biocase/BioCaseResponseSchemaAdapter.java -text
 cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/common/SchemaAdapterBase.java -text
 cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/common/ServiceWrapperBase.java -text
 cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/dc/DublinCoreSchemaAdapter.java -text
@@ -71,6 +79,7 @@ cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/scratchpads/ScratchpadsService.jav
 cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/sru/SruServiceWrapper.java -text
 cdmlib-ext/src/main/resources/eu/etaxonomy/cdm/ext/geo/mapServices_v10.xsd -text
 cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/bci/BciServiceTest.java -text
+cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/biocase/BioCaseQueryServiceWrapperTest.java -text
 cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/geo/EditGeoServiceTest.java -text
 cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/geo/GeoServiceAreaTest.java -text
 cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/ipni/IpniServiceTest.java -text
@@ -681,6 +690,7 @@ cdmlib-model/LICENSE.TXT -text
 cdmlib-model/README.TXT -text
 cdmlib-model/pom.xml -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/aspectj/PropertyChangeAspect.aj -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/DOIUserType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/EnumUserType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/HibernateProxyHelper.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/PartialUserType.java -text
@@ -693,6 +703,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/ClassInfoBridge.jav
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/DateTimeBridge.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/DefinedTermBaseClassBridge.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/DescriptionBaseClassBridge.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/DoiBridge.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/GroupByTaxonClassBridge.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/IdFieldOptions.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/MultilanguageTextFieldBridge.java -text
@@ -700,6 +711,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/NotNullAwareIdBridg
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/PartialBridge.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/SortFieldOptions.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/StripHtmlBridge.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/TaxonRelationshipClassBridge.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/UuidBridge.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/CdmAccessor.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/CdmAccessorFactoryImpl.java -text
@@ -729,13 +741,10 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/Team.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/TeamOrPersonBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/package-info.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/package.html -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/AbstractStringComparator.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/AnnotatableEntity.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Annotation.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/AnnotationType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/CdmBase.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/CdmMetaData.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/CdmPreferences.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Credit.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefaultTermInitializer.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTerm.java -text
@@ -752,6 +761,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IDefinedTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IEnumTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IEvent.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IIdentifiableEntity.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IKeyTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ILoadableTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IMultiLanguageText.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IMultiLanguageTextHolder.java -text
@@ -773,7 +783,6 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/LanguageString.java -te
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/LanguageStringBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Marker.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MarkerType.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MaterialAndMethod.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MultilanguageText.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MultilanguageTextHelper.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/NoDefinedTermClassException.java -text
@@ -840,13 +849,13 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/TextFormat.java -t
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/WorkingSet.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/package-info.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/package.html -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/Country.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/NamedArea.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaLevel.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/Point.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/ReferenceSystem.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/TdwgArea_Old.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/WaterbodyOrCountry.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/package-info.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/package.html -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/AudioFile.java -text
@@ -862,6 +871,10 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/MovieFile.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/Rights.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/RightsType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/package-info.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/metadata/CdmMetaData.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/metadata/CdmPreference.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/metadata/PreferencePredicate.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/metadata/PreferenceSubject.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Amplification.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Cloning.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java -text
@@ -907,6 +920,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DerivedUnit.java -t
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DeterminationEvent.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/FieldUnit.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/GatheringEvent.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/MaterialOrMethodEvent.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/MediaSpecimen.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/PreservationMethod.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/SpecimenOrObservationBase.java -text
@@ -932,7 +946,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/IProceedings.java -t
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/IPublicationBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/IReference.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/IReport.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/ISectionBase.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/ISection.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/IThesis.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/IVolumeReference.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/IWebPage.java -text
@@ -1073,9 +1087,11 @@ cdmlib-model/src/main/resources/log4j.properties -text
 cdmlib-model/src/main/resources/terms/AbsenceTerm.csv -text
 cdmlib-model/src/main/resources/terms/AnnotationType.csv -text
 cdmlib-model/src/main/resources/terms/Continent.csv -text
+cdmlib-model/src/main/resources/terms/Country.csv -text
 cdmlib-model/src/main/resources/terms/DerivationEventType.csv -text
 cdmlib-model/src/main/resources/terms/DeterminationModifier.csv -text
-cdmlib-model/src/main/resources/terms/DnaMarker.csv -text
+cdmlib-model/src/main/resources/terms/DnaMarkerChloroplast.csv -text
+cdmlib-model/src/main/resources/terms/DnaMarkerEukaryote.csv -text
 cdmlib-model/src/main/resources/terms/ExtensionType.csv -text
 cdmlib-model/src/main/resources/terms/Feature.csv -text
 cdmlib-model/src/main/resources/terms/HybridRelationshipType.csv -text
@@ -1112,7 +1128,7 @@ cdmlib-model/src/main/resources/terms/TaxonRelationshipType.csv -text
 cdmlib-model/src/main/resources/terms/TdwgArea.csv -text
 cdmlib-model/src/main/resources/terms/TextFormat.csv -text
 cdmlib-model/src/main/resources/terms/UndefinedLanguage.csv -text
-cdmlib-model/src/main/resources/terms/WaterbodyOrCountry.csv -text
+cdmlib-model/src/main/resources/terms/Waterbody.csv -text
 cdmlib-model/src/main/resources/update/update_for_security.sql -text
 cdmlib-model/src/main/resources/update/update_r2.1.2.2_r2.4.1.2.mysql.sql -text
 cdmlib-model/src/main/resources/update/update_term_r2.4.2.1-r2.4.2.2.mysql.sql -text
@@ -1124,8 +1140,6 @@ cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/agent/InstitutionalMembershipT
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/agent/TeamTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/common/AnnotationTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/common/CdmBaseTest.java -text
-cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/common/CdmMetaDataTest.java -text
-cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/common/CdmPreferencesTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/common/DefaultTermInitializerTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/common/DefinedTermBaseTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/common/ExtensionTypeTest.java -text
@@ -1155,6 +1169,9 @@ cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/PointTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/TdwgAreaTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/media/MediaTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/media/MediaUtilsTest.java -text
+cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/metadata/CdmMetaDataTest.java -text
+cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/metadata/CdmPreferenceTest.java -text
+cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/metadata/PreferenceSubjectTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/molecular/MolecularTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/BacterialNameTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/BotanicalNameTest.java -text
@@ -1254,7 +1271,9 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/SqlServer2000Da
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/SqlServer2005DatabaseType.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/SqlServer2008DatabaseType.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/SybaseDatabaseType.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/AuditedSchemaUpdaterStepBase.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/CdmUpdater.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/ClassChanger.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/ColumnAdder.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/ColumnNameChanger.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/ColumnRemover.java -text
@@ -1270,10 +1289,13 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/MnTableCreator
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SchemaUpdaterBase.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SchemaUpdaterStepBase.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SimpleSchemaUpdaterStep.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SingleTermRemover.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SingleTermUpdater.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SortIndexUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TableCreator.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TableDroper.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TableNameChanger.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TermMover.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TermRepresentationUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TermUpdaterBase.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TreeIndexUpdater.java -text
@@ -1282,7 +1304,6 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/UpdaterBase.ja
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/VocabularyCreator.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/permissions/PermissionsUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v24_25/SchemaUpdater_24_25.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v24_25/SortIndexUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v24_25/TermUpdater_24_25.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v25_30/FeatureNodeTreeColumnUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v25_30/PolytomousKeyDataMover.java -text
@@ -1299,21 +1320,13 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v30_31/TermUpd
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v30_31/TermUpdater_31_311.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v31_33/RankClassUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v31_33/SchemaUpdater_31_33.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v31_33/SpecimenMediaMoverUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v31_33/TermUpdater_31_33.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/AbstractBeanInitializer.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/AnnotationTypeAutoInitializer.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/AutoPropertyInitializer.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/GatheringEventLocationAutoInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v31_33/TermVocabularyRepresentationUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/IAlternativeSpellingSuggestionParser.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/IBeanInitializer.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/IMethodCache.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/MarkerTypeAutoInitializer.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/MediaAutoInitializer.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/MethodCacheImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/QueryParseException.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/TermBaseAutoInitializer.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/TitleCacheAutoInitializer.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/TypeDesignationAutoInitializer.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/agent/IAgentDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/AuditEventSort.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IAnnotatableDao.java -text
@@ -1331,6 +1344,7 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/ILsidAu
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IMarkerDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IOrderedTermVocabularyDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IOriginalSourceDao.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IPreferenceDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IReferencedEntityDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IRepresentationDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/ISearchableDao.java -text
@@ -1369,6 +1383,7 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/comm
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/MarkerDaoImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/OrderedTermVocabularyDaoImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/OriginalSourceDaoImpl.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/PreferenceDaoImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/ReferencedEntityDaoImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/RepresentationDaoImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/TermVocabularyDaoImpl.java -text
@@ -1394,11 +1409,22 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/name
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/CollectionDaoHibernateImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/OccurrenceDaoHibernateImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/reference/ReferenceDaoHibernateImpl.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/statistics/StatisticsDaoHibernateImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/ClassificationDaoHibernateImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonAlternativeSpellingSuggestionParser.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonNodeDaoHibernateImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/view/AuditEventDao.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/AbstractBeanInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/AnnotationTypeAutoInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/AutoPropertyInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/GatheringEventLocationAutoInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/IBeanInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/MarkerTypeAutoInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/MediaAutoInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/TermBaseAutoInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/TitleAndNameCacheAutoInitializer.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/TypeDesignationAutoInitializer.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/media/IMediaDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/media/IMediaRepresentationDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/media/IMediaRepresentationPartDao.java -text
@@ -1409,6 +1435,7 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/name/ITypeDesi
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/occurrence/ICollectionDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/occurrence/IOccurrenceDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/reference/IReferenceDao.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/statistics/IStatisticsDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/IClassificationDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonNodeDao.java -text
@@ -1499,6 +1526,7 @@ cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/comm
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/DefinedTermDaoImplTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/GroupDaoHibernateImplTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/IdentifiableDaoBaseTest.java -text
+cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/PreferenceDaoTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/TermVocabularyDaoImplTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/UserDaoHibernateImplTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/description/DescriptionDaoHibernateImplTest.java -text
@@ -1515,6 +1543,7 @@ cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/name
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/name/TypeDesignationDaoHibernateImplTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/OccurrenceDaoHibernateImplTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/reference/ReferenceDaoHibernateImplTest.java -text
+cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/statistics/StatisticsDaoHibernateImplTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImplBenchmark.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImplTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonNodeDaoHibernateImplTest.java -text
@@ -1574,6 +1603,7 @@ cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/common/DefinedTermDaoImplTest.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/common/GroupDaoHibernateImplTest.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/common/IdentifiableDaoBaseTest.xml -text
+cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/common/PreferenceDaoTest.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/common/TermVocabularyDaoImplTest.testListVocabularyEmpty.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/common/TermVocabularyDaoImplTest.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/common/UserDaoHibernateImplTest.xml -text
@@ -1638,6 +1668,7 @@ cdmlib-print/src/main/java/eu/etaxonomy/cdm/print/XMLHelper.java -text
 cdmlib-print/src/main/java/eu/etaxonomy/cdm/print/XmlEntityFactoryBase.java -text
 cdmlib-print/src/main/java/eu/etaxonomy/cdm/print/out/IPublishOutputModule.java -text
 cdmlib-print/src/main/java/eu/etaxonomy/cdm/print/out/PublishOutputModuleBase.java -text
+cdmlib-print/src/main/java/eu/etaxonomy/cdm/print/out/mediawiki/MediawikiOutputModule.java -text
 cdmlib-print/src/main/java/eu/etaxonomy/cdm/print/out/odf/DocumentCreator.java -text
 cdmlib-print/src/main/java/eu/etaxonomy/cdm/print/out/odf/IStyleNames.java -text
 cdmlib-print/src/main/java/eu/etaxonomy/cdm/print/out/odf/OdfOutputModule.java -text
@@ -1650,6 +1681,8 @@ cdmlib-print/src/main/resources/log4j.properties -text
 cdmlib-print/src/main/resources/stylesheets/mediawiki/functx-1.0-doc-2007-01.xsl -text
 cdmlib-print/src/main/resources/stylesheets/mediawiki/multipages.xsl -text
 cdmlib-print/src/main/resources/stylesheets/odf/cdmToOdfText.xsl -text
+cdmlib-print/src/main/resources/stylesheets/pdf/Untitled21212.xml -text
+cdmlib-print/src/main/resources/stylesheets/pdf/caryophyllales.xsl -text
 cdmlib-print/src/main/resources/stylesheets/pdf/flora-malesiana.xsl -text
 cdmlib-print/src/main/resources/stylesheets/pdf/flore-afrique-centrale.xsl -text
 cdmlib-print/src/site/apt/download.apt -text
@@ -2053,6 +2086,7 @@ cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/INaturalLanguageTextD
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IOccurrenceService.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IPolytomousKeyNodeService.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IPolytomousKeyService.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IPreferenceService.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IReferenceService.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IService.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IStatisticsService.java -text
@@ -2075,10 +2109,12 @@ cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/NaturalLanguageGenera
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/PolytomousKeyNodeServiceImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/PolytomousKeyServiceImpl.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/PreferenceServiceImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ReferenceServiceImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ServiceBase.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ServiceImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/StatisticsServiceImpl.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxaAndNamesSearchMode.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TermServiceImpl.java -text
@@ -2123,10 +2159,14 @@ cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/pager/impl/AbstractPa
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/pager/impl/DefaultPagerImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/pager/impl/StringLabelPagerImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/CdmMassIndexer.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/DocIdBitSetPrinter.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/DocumentSearchResult.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/ICdmMassIndexer.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/ILuceneIndexToolProvider.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/ISearchResultBuilder.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/LuceneIndexToolProviderImpl.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/LuceneMultiSearch.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/LuceneMultiSearchException.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/LuceneSearch.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/QueryFactory.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/search/SearchResult.java -text
@@ -2162,11 +2202,13 @@ cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/facade/DerivedUnitFacadeTest.
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/ClassificationServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/CommonServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/DescriptionServiceImplTest.java -text
+cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/FeatureNodeServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/IdentifiableServiceBaseTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/IdentificationKeyGeneratorTTT.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/NameServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/NaturalLanguageGeneratorTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/PolytomousKeyServiceImplTest.java -text
+cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/PreferenceServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/SecurityTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/SecurityWithTransaction.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/StatisticsServiceImplTest.java -text
@@ -2214,6 +2256,7 @@ cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/facade/DerivedUnitFacade
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/BlankDataSet.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/ClassificationServiceImplTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/CommonServiceImplTest.xml -text
+cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/FeatureNodeServiceImplTest-indexing.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/IdentifiableServiceBaseTest.testUpdateTitleCache-result.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/IdentifiableServiceBaseTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/MediaDaoImplTest.xml -text
@@ -2221,6 +2264,7 @@ cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/NameServiceImplT
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/OregonScientificDS6639-DSC_0307-small.jpg -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/OregonScientificDS6639-DSC_0307-small.tif -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/PolytomousKeyServiceImplTest.xml -text
+cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/PreferenceServiceImplTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/SecurityTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImplTest-indexing.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImplTest.xml -text