merge-update from trunk

[taxeditor.git] / .gitattributes

diff --git a/.gitattributes b/.gitattributes
index 77114bc1e5f153e621220ce34e56b46d6e1fa851..1f8c325ff4b9e402f4f318c596dcefc2b5b33320 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -82,11 +82,14 @@ 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/command/BulkEditorMenuPropertyTester.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
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/command/DynamicNewObjectMenu.java -text
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/command/OpenBulkEditorContributionItem.java -text
+eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/handler/ConvertPerson2TeamHandler.java -text
+eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/handler/ConvertTeam2PersonHandler.java -text
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/handler/DeleteHandler.java -text
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/handler/MergeGroupHandler.java -text
 eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/handler/OpenBulkEditorHandler.java -text
@@ -355,6 +358,7 @@ eu.etaxonomy.taxeditor.editor/.project -text
 eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF -text
 eu.etaxonomy.taxeditor.editor/OSGI-INF/l10n/plugin.properties -text
 eu.etaxonomy.taxeditor.editor/OSGI-INF/l10n/plugin_de.properties -text
+eu.etaxonomy.taxeditor.editor/OSGI-INF/l10n/plugin_en.properties -text
 eu.etaxonomy.taxeditor.editor/build.properties -text
 eu.etaxonomy.taxeditor.editor/icons/address-book-new.png -text
 eu.etaxonomy.taxeditor.editor/icons/camera-photo.png -text
@@ -365,7 +369,16 @@ 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
@@ -391,13 +404,23 @@ 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
@@ -425,6 +448,12 @@ 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
@@ -460,6 +489,7 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/h
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/DeleteAllEmptyNamesHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/DeleteTaxonBaseHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/GroupBasionymContributionItem.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/MoveSynonymToAnotherAcceptedTaxonHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/NameEditorMenuPropertyTester.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/RemoveBasionymHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/SetBasionymHandler.java -text
@@ -613,7 +643,10 @@ 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
@@ -1356,6 +1389,7 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/operation/IPos
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/parser/MatchStrategyConfigurator.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/parser/ParseHandler.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/CdmPreferences.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/CdmStorePropertyTester.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/ChecklistEditorGeneralPreference.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/DefaultFeatureTreePreferenecs.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/DescriptionPreferences.java -text
@@ -1368,6 +1402,7 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/Mat
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/MediaPreferences.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/MobotOpenUrlPreferences.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/NomenclaturalCodePreferences.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/OrderPreferences.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/PreferencePropertyTester.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/PreferencesUtil.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/Resources.java -text
@@ -1454,6 +1489,7 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/sele
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/SpecimenOrObservationTypeSelectionDialog.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/TaxonBaseSelectionDialog.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/TaxonNodeSelectionDialog.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/TaxonNodeSelectionNaturalOrderDialog.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/TeamSelectionDialog.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/UserSelectionDialog.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/AbstractCdmEntityWizardPage.java -text