merge-update from trunk

[taxeditor.git] / .gitattributes

diff --git a/.gitattributes b/.gitattributes
index 57b4b4aee5fdc98b98a55a2254e00074c9ffaff5..b784f78f8a5a880c0f409c51759c8a9355a7591c 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -358,6 +358,11 @@ 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/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
@@ -381,7 +386,10 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/Viewer
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditor.java -text
 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/AddAHandler.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/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
@@ -414,6 +422,10 @@ 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/CMDAlignmentObjectPlaceholder.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/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
@@ -536,6 +548,8 @@ 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/derivate/contextMenu/CreateDerivateContextMenu.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/contextMenu/DerivateViewContextMenu.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/contextMenu/SingleReadSequenceContextMenu.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/handler/DeleteDerivateHandler.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/operation/DeleteDerivateOperation.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/DescriptionElementDragListener.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/DescriptionElementDropAdapter.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/DescriptionElementTransfer.java -text
@@ -583,7 +597,10 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/u
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateTaxonUseOperation.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseRecordOperation.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseSummaryOperation.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
@@ -1042,6 +1059,7 @@ eu.etaxonomy.taxeditor.store/icons/binary.gif -text
 eu.etaxonomy.taxeditor.store/icons/bookmark.gif -text
 eu.etaxonomy.taxeditor.store/icons/category.gif -text
 eu.etaxonomy.taxeditor.store/icons/change.gif -text
+eu.etaxonomy.taxeditor.store/icons/character_data_derivate-16x16-32.png -text
 eu.etaxonomy.taxeditor.store/icons/clear.gif -text
 eu.etaxonomy.taxeditor.store/icons/close.gif -text
 eu.etaxonomy.taxeditor.store/icons/close_view.gif -text
@@ -1435,6 +1453,7 @@ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/Lay
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/MinMaxTextSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/MultilanguageTextElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/NumberWithLabelElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/OriginalLabelDataElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/PartialElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/PointElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/RootElement.java -text
@@ -1452,8 +1471,7 @@ 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/OriginalLabelDataController.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/OriginalLabelDataElement.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
@@ -1630,6 +1648,7 @@ 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/derivedUnit/PreservedSpecimenGeneralDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/derivedUnit/PreservedSpecimenGeneralDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/derivedUnit/PreservedSpecimenSourceCollectionDetailSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AbstractSampleDesignationDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AbstractUnboundEntityCollectionSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationCloningDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationCloningDetailSection.java -text
@@ -1639,11 +1658,16 @@ 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/dna/AmplificationGeneralDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationPrimerDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationPrimerDetailSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/CurrentSampleDesignationDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaQualityDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaQualityDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaSampleGeneralDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaSampleGeneralDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/PrimerGeneralDetailElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SampleDesignationDetailElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SampleDesignationDetailSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SampleDesignationHistoryDetailSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SampleDesignationTextDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceContigFileCollectionDetailSection.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceGeneralDetailElement.java -text
 eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceGeneralDetailSection.java -text