merge-update from trunk

diff --combined .gitattributes
index d0ba8c7653d9041bd565f6518ebe40ef0c719e0c,b4b448120d47c5e96b07eb0470e108dee3515f2a..3bdd135049398bdcf3b04cf8971e7bb1097f70e5
--- 1/.gitattributes
--- 2/.gitattributes
+++ b/.gitattributes
@@@ -222,6 -222,8 +222,8 @@@ eu.etaxonomy.taxeditor.cdmlib/lib/jboss
  eu.etaxonomy.taxeditor.cdmlib/lib/jboss-transaction-api_1.1_spec-1.0.0.Final.jar -text
  eu.etaxonomy.taxeditor.cdmlib/lib/jdbc4-2.0.jar -text
  eu.etaxonomy.taxeditor.cdmlib/lib/jdom-1.1.3.jar -text
+ eu.etaxonomy.taxeditor.cdmlib/lib/jena-core-2.12.1-SNAPSHOT.jar -text
+ eu.etaxonomy.taxeditor.cdmlib/lib/jena-iri-1.1.1-SNAPSHOT.jar -text
  eu.etaxonomy.taxeditor.cdmlib/lib/joda-time-2.1.jar -text
  eu.etaxonomy.taxeditor.cdmlib/lib/json-lib-2.4-jdk15.jar -text
  eu.etaxonomy.taxeditor.cdmlib/lib/jsr250-api-1.0.jar -text
@@@ -341,14 -343,6 +343,6 @@@ eu.etaxonomy.taxeditor.cdmlib/src/main/
  eu.etaxonomy.taxeditor.cdmlib/src/main/resources/eu/etaxonomy/cdm/remotingApplicationContext.xml -text
  eu.etaxonomy.taxeditor.cdmlib/src/main/resources/eu/etaxonomy/cdm/remoting_persistence_security.xml -text
  eu.etaxonomy.taxeditor.cdmlib/src/main/resources/eu/etaxonomy/cdm/remoting_services_security.xml -text
- eu.etaxonomy.taxeditor.cdmlib/src/test/java/eu/etaxonomy/taxeditor/remoting/CdmApplicationRemoteControllerTest.java -text
- eu.etaxonomy.taxeditor.cdmlib/src/test/java/eu/etaxonomy/taxeditor/remoting/CdmPersistentRemoteSourceTest.java -text
- eu.etaxonomy.taxeditor.cdmlib/src/test/java/eu/etaxonomy/taxeditor/remoting/CdmRemoteSourceTest.java -text
- eu.etaxonomy.taxeditor.cdmlib/src/test/java/eu/etaxonomy/taxeditor/remoting/CdmServiceCacherTest.java -text
- eu.etaxonomy.taxeditor.cdmlib/src/test/java/eu/etaxonomy/taxeditor/remoting/HttpInvokerServicesTest.java -text
- eu.etaxonomy.taxeditor.cdmlib/src/test/java/eu/etaxonomy/taxeditor/remoting/RemoteApplicationConfigurationTest.java -text
- eu.etaxonomy.taxeditor.cdmlib/src/test/java/eu/etaxonomy/taxeditor/remoting/RemoteLazyLoadingTest.java -text
- eu.etaxonomy.taxeditor.cdmlib/src/test/java/eu/etaxonomy/taxeditor/remoting/RemotePersistentCollectionTest.java -text
  eu.etaxonomy.taxeditor.cdmlib/src/test/resources/eu/etaxonomy/cdm/cdm.datasources.xml -text
  eu.etaxonomy.taxeditor.editor/.classpath -text
  eu.etaxonomy.taxeditor.editor/.project -text
@@@ -364,11 -358,6 +358,11 @@@ eu.etaxonomy.taxeditor.editor/icons/edi
  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
@@@ -393,7 -382,6 +387,7 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  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/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
@@@ -426,10 -414,6 +420,10 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  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
@@@ -599,10 -583,7 +593,10 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  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
@@@ -1019,6 -1000,50 +1013,50 @@@ eu.etaxonomy.taxeditor.printpublisher/s
  eu.etaxonomy.taxeditor.printpublisher/src/main/java/eu/etaxonomy/taxeditor/printpublisher/wizard/SelectServiceWizardPage.java -text
  eu.etaxonomy.taxeditor.printpublisher/src/main/java/eu/etaxonomy/taxeditor/printpublisher/wizard/SelectStylesheetWizardPage.java -text
  eu.etaxonomy.taxeditor.printpublisher/src/main/java/eu/etaxonomy/taxeditor/printpublisher/wizard/SelectTaxaWizardPage.java -text
+ eu.etaxonomy.taxeditor.remoting/.classpath -text
+ eu.etaxonomy.taxeditor.remoting/.project -text
+ eu.etaxonomy.taxeditor.remoting/.settings/org.eclipse.jdt.core.prefs -text
+ eu.etaxonomy.taxeditor.remoting/.settings/org.eclipse.pde.core.prefs -text
+ eu.etaxonomy.taxeditor.remoting/META-INF/MANIFEST.MF -text
+ eu.etaxonomy.taxeditor.remoting/build.properties -text
+ eu.etaxonomy.taxeditor.remoting/pom.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationRemoteConfiguration.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationRemoteController.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/api/cache/CdmServiceCacher.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/CdmPersistentRemoteSource.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/CdmRemoteSource.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/CdmRemoteSourceBase.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/CdmRemoteSourceException.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/ICdmRemoteSource.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/taxeditor/remoting/RemotingTestPluginActivator.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/org/hibernate/collection/internal/AbstractPersistentCollection.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/java/org/hibernate/proxy/AbstractLazyInitializer.java -text
+ eu.etaxonomy.taxeditor.remoting/src/main/resources/etc/jetty/jetty-runner-9.2.3.v20140905.jar -text
+ eu.etaxonomy.taxeditor.remoting/src/main/resources/etc/jetty/start-9.2.3.v20140905.jar -text
+ eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/config.properties -text
+ eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/httpInvokerServiceClients.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/localApplicationContext.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/remotingApplicationContext.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/remoting_persistence_security.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/remoting_services_security.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/exception/CDMServerException.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/BaseRemotingTest.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/CDMServer.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/CdmPersistentRemoteSourceTest.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/CdmRemoteSourceTest.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/CdmServerTest.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/HttpInvokerServicesTest.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/lazyloading/AbstractLazyInitializerTest.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/lazyloading/CdmServiceCacherTest.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/lazyloading/RemoteLazyLoadingTest.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/lazyloading/RemotePersistentCollectionTest.java -text
+ eu.etaxonomy.taxeditor.remoting/src/test/resources/datasources.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/test/resources/eu/etaxonomy/cdm/cdm.datasources.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/test/resources/eu/etaxonomy/cdm/testRemotingApplicationContext.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/test/resources/eu/etaxonomy/taxeditor/lazyloading/AbstractLazyInitializerTest.xml -text
+ eu.etaxonomy.taxeditor.remoting/src/test/resources/h2/cdmTest.h2.db -text
+ eu.etaxonomy.taxeditor.remoting/src/test/resources/h2/cdmTest.trace.db -text
+ eu.etaxonomy.taxeditor.remoting/src/test/resources/unitils.properties -text
  eu.etaxonomy.taxeditor.store/.classpath -text
  eu.etaxonomy.taxeditor.store/.project -text
  eu.etaxonomy.taxeditor.store/META-INF/MANIFEST.MF -text
@@@ -1277,7 -1302,7 +1315,7 @@@ eu.etaxonomy.taxeditor.store/src/main/j
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/model/ICdmEditorHandle.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/model/IContextListener.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/model/IDataChangeBehavior.java -text
- eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/model/IDirtyMarkableSelectionProvider.java -text
+ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/model/IDirtyMarkable.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/model/IElementHasDetails.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/model/IPartChangeListener.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/model/IPartContentHasDetails.java -text

diff --combined eu.etaxonomy.taxeditor.editor/plugin.xml
index a31ca6d0b03d99c6aef772c16c7554c66204eb98,5617ce118fc762b669b027f669b09d55e3b75687..5ac42f04eae6039484627739a02a3e0ba7f65551
--- 1/eu.etaxonomy.taxeditor.editor/plugin.xml
--- 2/eu.etaxonomy.taxeditor.editor/plugin.xml
+++ b/eu.etaxonomy.taxeditor.editor/plugin.xml
@@@ -83,12 -83,6 +83,12 @@@
              id="eu.etaxonomy.taxeditor.editor.view.checklist.ChecklistEditor"
              name="%editor.name.8">
        </editor>
 +      <editor
 +            class="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor"
 +            default="false"
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor"
 +            name="Alignment Editor">
 +      </editor>
     </extension>
        <extension
              point="org.eclipse.ui.views">
@@@ -249,11 -243,6 +249,11 @@@
                 </reference>
              </visibleWhen>
           </command>
 +         <command
 +               commandId="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
 +               label="Alignment Editor"
 +               style="push">
 +         </command>
        </menuContribution>
        <menuContribution
              locationURI="menu:org.eclipse.ui.main.menu.navigate">
@@@ -616,6 -605,11 +616,11 @@@
                 class="eu.etaxonomy.taxeditor.editor.view.derivate.contextMenu.DerivateViewContextMenu"
                 id="eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
           </dynamic>
+          <command
+                commandId="org.eclipse.ui.edit.delete"
+                label="Delete"
+                style="push">
+          </command>
        </menuContribution>
        <menuContribution
              locationURI="popup:eu.etaxonomy.taxeditor.editor.view.dataimport.SpecimenImportEditor">
@@@ -878,6 -872,9 +883,9 @@@
                     <equals
                           value="eu.etaxonomy.taxeditor.editor.view.media">
                     </equals>
+                    <equals
+                          value="eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView">
+                    </equals>
                  </or>
               </with>
            </activeWhen>
@@@ -1194,19 -1191,13 +1202,19 @@@
               defaultHandler="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler"
               id="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistViewHandler"
               name="%command.name.38">
 -       </command>
 +      </command>
        <command
              categoryId="eu.etaxonomy.taxeditor.editor.new.category"
              defaultHandler="eu.etaxonomy.taxeditor.view.datasource.handler.CreateDataSourceHandler"
              id="eu.etaxonomy.taxeditor.editor.command.new.datasource"
              name="%command.name.39">
        </command>
 +      <command
 +            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
 +            id="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
 +            name="Open Alignment Editor">
 +      </command>
 +
     </extension>
     <extension
           point="org.eclipse.core.expressions.definitions">