BGBM BDI Projects / taxeditor.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
Fix menu contributions
[taxeditor.git] / .gitattributes
diff --git a/.gitattributes b/.gitattributes
index 1f8c325ff4b9e402f4f318c596dcefc2b5b33320..f8680ab3327f935c405ca6a4fed9d1d84d3c2974 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -369,16 +369,7 @@ eu.etaxonomy.taxeditor.editor/icons/edit_16x16.gif -text
 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/pherogram-insert-left-16x16.png -text
-eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-left-disabled-16x16.png -text
-eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-right-16x16.png -text
-eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-right-disabled-16x16.png -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
@@ -404,23 +395,13 @@ 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/OpenAlignmentEditorHandler.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/ShowPherogramHandler.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/alignmenteditor/CreateConsensusSequenceHandler.java -text
-eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ReverseComplementHandler.java -text
-eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ToggleInsertOverwriteHandler.java -text
-eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ToggleLeftRightInsertionHandler.java -text
-eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/UpdateConsensusSequenceHandler.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
@@ -448,12 +429,6 @@ 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
@@ -643,10 +618,7 @@ 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
@@ -961,6 +933,46 @@ eu.etaxonomy.taxeditor.help/src/eu/etaxonomy/taxeditor/help/Activator.java -text
 eu.etaxonomy.taxeditor.help/toc.xml -text
 eu.etaxonomy.taxeditor.help/tocgettingstarted.xml -text
 eu.etaxonomy.taxeditor.help/tocnameparser.xml -text
+eu.etaxonomy.taxeditor.molecular.aggregator/.project -text
+eu.etaxonomy.taxeditor.molecular.aggregator/pom.xml -text
+eu.etaxonomy.taxeditor.molecular/.classpath -text
+eu.etaxonomy.taxeditor.molecular/.project -text
+eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF -text
+eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin.properties -text
+eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin_de.properties -text
+eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin_en.properties -text
+eu.etaxonomy.taxeditor.molecular/build.properties -text
+eu.etaxonomy.taxeditor.molecular/icons/insert-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/overwrite-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-left-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-left-disabled-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-right-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-right-disabled-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/plugin.xml -text
+eu.etaxonomy.taxeditor.molecular/pom.xml -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/TaxeditorMolecularPlugin.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditorInput.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/PherogramMouseListener.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/PherogramViewPart.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AbstractAlignmentEditorHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AbstractPherogramComponentHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ChangePherogramQualityOutputType.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/CreateConsensusSequenceHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramLeftHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramRightHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/EditSequenceHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/HandlerTools.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/LoadPherogramHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ReverseComplementHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ShowPherogramHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/SpecimenPropertyTester.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleInsertOverwriteHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleLeftRightInsertionHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramBaseCallLinesHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramProbabilitiesHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/UpdateConsensusSequenceHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/package-info.java -text
 eu.etaxonomy.taxeditor.navigation/.classpath -text
 eu.etaxonomy.taxeditor.navigation/.project -text
 eu.etaxonomy.taxeditor.navigation/META-INF/MANIFEST.MF -text
@@ -977,6 +989,7 @@ eu.etaxonomy.taxeditor.navigation/icons/tree_icon.jpg -text
 eu.etaxonomy.taxeditor.navigation/p2.inf -text
 eu.etaxonomy.taxeditor.navigation/plugin.xml -text
 eu.etaxonomy.taxeditor.navigation/pom.xml -text
+eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/NavigationCdmViewer.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/NavigationUtil.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/NavigatorStateManager.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/RecentNamesContributionItem.java -text
@@ -1003,7 +1016,6 @@ eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigatio
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonLinkHelper.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNavigator.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNavigatorDataChangeBehavior.java -text
-eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNodeComparator.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNodeContentProvider.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNodeLabelProvider.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNodePropertyTester.java -text
@@ -1219,6 +1231,7 @@ eu.etaxonomy.taxeditor.store/icons/specimen_scan_derivate_data-16x16-32.png -tex
 eu.etaxonomy.taxeditor.store/icons/step_done.gif -text
 eu.etaxonomy.taxeditor.store/icons/swap.gif -text
 eu.etaxonomy.taxeditor.store/icons/swap2.gif -text
+eu.etaxonomy.taxeditor.store/icons/switch_view_type-16x16-32.png -text
 eu.etaxonomy.taxeditor.store/icons/synced.gif -text
 eu.etaxonomy.taxeditor.store/icons/system-file-manager.png -text
 eu.etaxonomy.taxeditor.store/icons/system-users.png -text
@@ -1289,6 +1302,7 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/featuretree/Op
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/featuretree/SelectFeatureTreeWizard.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/featuretree/SelectFeatureTreeWizardPage.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/handler/OpenDistributionEditorWizardHandler.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/handler/OpenHandler.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/handler/OpenPasswordWizzardHandler.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/handler/ShowLoginWindowHandler.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/identificationkey/AbstractIdentificaitonKeyWizard.java -text
@@ -1363,6 +1377,7 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/model/TimeHelp
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/AbstractNewEntityWizard.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/AmplificationGeneralWizardPage.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/ExternalReferenceServiceWizardPage.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/IWizardPageListener.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/NewAmplificationWizard.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/NewClassificationWizard.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/NewCollectionWizard.java -text
@@ -1608,7 +1623,6 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/des
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/ScopeSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StateDataElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StateDataSection.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StateModifierElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StatisticalMeasurementValueElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StatisticalMeasurementValueSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/detail/AbstractDetailedDescriptionDetailElement.java -text
@@ -1800,7 +1814,8 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/voc
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/NamedAreaDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/NamedAreaDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/NamedAreaLevelDetailSection.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/StateModifierCollectionSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/RecommendedModifierVocabulariesCollectionSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/RecommendedModifierVocabulariesElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/StateVocabularyCollectionElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/StateVocabularyCollectionSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/StatisticalMeasureCollectionElement.java -text