- added context menu option to DerivateEditor to open sequence in AlignmentEditor
[taxeditor.git] / .gitattributes
index 4e918641b49f455e88a3a53c6d60f3c9ba43b53f..af4393860bd2b159652b9801a0b0c5ee5e77820c 100644 (file)
@@ -82,7 +82,6 @@ eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkedito
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/BulkEditorViewerConfiguration.java -text
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/IBulkEditorConstants.java -text
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/IBulkEditorSortProvider.java -text
-eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/PropertyTester.java -text
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/command/BulkEditorPropertyTester.java -text
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/command/DeleteObjectContributionItem.java -text
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/command/DynamicMarkerTypeEditingMenu.java -text
@@ -367,11 +366,17 @@ eu.etaxonomy.taxeditor.editor/icons/emblem-photos.png -text
 eu.etaxonomy.taxeditor.editor/icons/leaf_detail.png -text
 eu.etaxonomy.taxeditor.editor/icons/link_obj.gif -text
 eu.etaxonomy.taxeditor.editor/icons/xper64.png -text
+eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar -text
+eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar -text
+eu.etaxonomy.taxeditor.editor/lib/commons-lang3-3.1.jar -text
+eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar -text
+eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar -text
 eu.etaxonomy.taxeditor.editor/p2.inf -text
 eu.etaxonomy.taxeditor.editor/plugin.xml -text
 eu.etaxonomy.taxeditor.editor/pom.xml -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/CdmDataTransfer.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/ChooseFromMultipleTaxonNodesDialog.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/EditorCdmViewer.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/EditorStateManager.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/EditorUtil.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/IDropTargetable.java -text
@@ -391,13 +396,19 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditorInput.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/handler/EditCdmAuthoritiesHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditNewTaxonHandler.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditSequenceHandler.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenAlignmentEditor.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenChecklistEditorHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenDerivateViewHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenParentHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenTaxonEditorHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SaveAllHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SaveTaxonHandler.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SpecimenPropertyTester.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/TaxonParameterConverter.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ToggleInsertOverwriteHandler.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ToggleLeftRightInsertionHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewNameHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewPersonHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewReferenceHandler.java -text
@@ -425,6 +436,12 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/po
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/CreateNodeOperation.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/DeleteNodeOperation.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/RefreshNodeNumberingOperation.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CDMAlignmentObjectPlaceholder.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroup.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java -text
@@ -542,7 +559,6 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/d
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientReferenceService.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientTaxonService.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientTermService.java -text
-eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/DerivateContentProvider.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/DerivateDragListener.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/DerivateDropListener.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/DerivateView.java -text
@@ -614,7 +630,10 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/v
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidationProblemsView.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidatorClassMarkerField.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidatorMessageMarkerField.java -text
+eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1 -text
+eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1 -text
 eu.etaxonomy.taxeditor.editor/src/main/resources/TaonDescriptionEditor.screen -text
+eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf -text
 eu.etaxonomy.taxeditor.editor/src/main/resources/log4j.properties -text
 eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/Application.java -text
 eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/ApplicationActionBarAdvisor.java -text
@@ -1208,6 +1227,7 @@ eu.etaxonomy.taxeditor.store/icons/web.gif -text
 eu.etaxonomy.taxeditor.store/p2.inf -text
 eu.etaxonomy.taxeditor.store/plugin.xml -text
 eu.etaxonomy.taxeditor.store/pom.xml -text
+eu.etaxonomy.taxeditor.store/schema/eu.etaxonomy.taxeditor.store.cdmViewer.exsd -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/datasource/CdmDataSourceRepository.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/datasource/wizard/CdmDataSourceCredentialsWizardPage.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/datasource/wizard/CdmDataSourceH2WizardPage.java -text
@@ -1410,11 +1430,12 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/bar/Authent
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/combo/EnumComboElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/combo/TermComboElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/DefaultLanguageDialog.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/DeleteConfiguratorComposite.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/DeleteConfiguratorDialog.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/DeleteTaxonConfiguratorDialog.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/LoginDialog.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/UriDialog.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/deleteConfigurator/DeleteConfiguratorComposite.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/deleteConfigurator/DeleteConfiguratorDialog.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/deleteConfigurator/DeleteSpecimenConfiguratorComposite.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/deleteConfigurator/DeleteTaxonConfiguratorComposite.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/AbstractFilteredCdmEnumSelectionDialog.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/AbstractFilteredCdmResourceSelectionDialog.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/AgentSelectionDialog.java -text
@@ -1491,7 +1512,6 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/group/grant
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/AbstractCdmComposite.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/DerivedUnitGeneralDetailElementMVC.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/GeographicPointElement.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/OriginalLabelDataField.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/combo/EnumTermCombo.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/combo/EnumTermComboController.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/element/DateElement.java -text
@@ -1584,6 +1604,8 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/gro
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/group/GroupSelectionElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/group/MemberDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/group/MemberDetailSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/identifier/IdentifierDetailElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/identifier/IdentifierDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/key/GeographicalScopeDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/key/PolytomousKeyDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/key/PolytomousKeyDetailSection.java -text
@@ -1633,8 +1655,6 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occ
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitBaseDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitBaseDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitBaseWizardPage.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitFacadeDetailElement.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitFacadeDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitGeneralDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitGeneralDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitGeneralWizardPage.java -text
@@ -1658,6 +1678,8 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occ
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/SourceCollectionDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/SpecimenCollectionDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/SpecimenCollectionDetailSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/SpecimenHierarchyDetailElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/SpecimenHierarchyDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/association/TaxonAssociationDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/association/TaxonAssociationDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/derivedUnit/PreservedSpecimenAbstractDeterminationEventDetailSection.java -text
@@ -1764,6 +1786,8 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/AbstractC
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/AbstractCdmEditorViewPart.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/AbstractCdmViewPart.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/AbstractSplitableViewPart.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/CdmViewerChooser.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/ICdmViewer.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/CdmDataSourceContentProvider.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/CdmDataSourceLabelProvider.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/CdmDataSourceViewPart.java -text
@@ -1779,6 +1803,7 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasourc
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/handler/DeleteDataSourceHandler.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/handler/EditDataSourceHandler.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/handler/UpdateDataSourceHandler.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/derivateSearch/DerivateContentProvider.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/derivateSearch/DerivateLabelProvider.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/derivateSearch/DerivateSearchComposite.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/derivateSearch/DerivateSearchCompositeController.java -text