merge-update from trunk

diff --cc .gitattributes
index 8674896df85fea719f9b3c424423335447c78c53,292f101cf9512954698985d661e6b37aee591019..f62d61671fdb7c2b97cd9e393a16e5b151602bf7
--- 1/.gitattributes
--- 2/.gitattributes
+++ b/.gitattributes
@@@ -397,10 -394,10 +401,12 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  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/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
@@@ -608,10 -604,16 +619,19 @@@ 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/java/eu/etaxonomy/taxeditor/editor/view/validation/EntityClassMarkerField.java -text
+ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/EntityIdMarkerField.java -text
+ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/InvalidValueMarkerField.java -text
+ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/UserFriendlyDescriptionMarkerField.java -text
+ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/UserFriendlyFieldNameMarkerField.java -text
+ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/UserFriendlyTypeNameMarkerField.java -text
+ 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

diff --cc eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
Simple merge

diff --cc eu.etaxonomy.taxeditor.editor/build.properties
index 91b72a915f0fd3b88450f0d7c20155a94c86664a,df9378660517f9cd598aab37f9da0413890e85c1..8486515b2a719bb63c86aba7ec0bedd557e03de8
--- 1/eu.etaxonomy.taxeditor.editor/build.properties
--- 2/eu.etaxonomy.taxeditor.editor/build.properties
+++ b/eu.etaxonomy.taxeditor.editor/build.properties
@@@ -3,15 -3,8 +3,15 @@@ source.. = src/main/java/,
  bin.includes = META-INF/,\
                 .,\
                 plugin.xml,\
-                OSGI-INF/l10n/plugin.properties,\
                 icons/,\
                 p2.inf,\
+                OSGI-INF/l10n/plugin.properties,\
                 OSGI-INF/l10n/plugin_de.properties,\
 -               OSGI-INF/l10n/plugin_en.properties
 +               OSGI-INF/l10n/plugin_en.properties,\
 +               lib/biojava3-alignment-3.0.7.jar,\
 +               lib/biojava3-core-3.0.7.jar,\
 +               lib/core-1.8.5.jar,\
 +               lib/sequencing-1.8.5.jar,\
 +               lib/bioinfweb.commons/,\
 +               lib/LibrAlign/,\
 +               lib/commons-lang3-3.1.jar

diff --cc eu.etaxonomy.taxeditor.editor/plugin.xml
index 03d06d1ad565161771ac4752f995383fb298ce60,53080cc47d69177e2a1509e581dcb603f1e19765..99f70453118a991826507087998fcafb714460ba
--- 1/eu.etaxonomy.taxeditor.editor/plugin.xml
--- 2/eu.etaxonomy.taxeditor.editor/plugin.xml
+++ b/eu.etaxonomy.taxeditor.editor/plugin.xml
@@@ -152,14 -145,89 +152,86 @@@
                 name="%view.name.5">
           </view>
           <view
 -               allowMultiple="false"
 -               category="eu.etaxonomy.taxeditor.editor.category"
 -               class="eu.etaxonomy.taxeditor.editor.view.validation.ValidationProblemsView"
 -               icon="icons/edit_16x16.gif"
 -               id="eu.etaxonomy.taxeditor.editor.view.validation.problems"
 -               name="%view.name.6">
 +               allowMultiple="true"
 +               class="eu.etaxonomy.taxeditor.editor.molecular.PherogramViewPart"
 +               id="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
 +               name="PherogramView"
 +               restorable="true">
           </view>
        </extension>
 -      
 -      <!-- VALIDATION RELATED STUFF -->
++      <!-- VALIDATION RELATED STUFF -->
+       <extension point="org.eclipse.core.resources.markers" name="Validation Error" id="eu.etaxonomy.taxeditor.markers.validationerror">
+               <super type="org.eclipse.core.resources.problemmarker"/>
+               <attribute name="databaseId"/>
+               <attribute name="userFriendlyTypeName"/>
+               <attribute name="userFriendlyDescription"/>
+               <attribute name="userFriendlyFieldName"/>
+               <attribute name="validatorMessage"/>
+               <attribute name="invalidValue"/>
+               <attribute name="validatorClass"/>
+               <attribute name="entityClass"/>
+               <attribute name="entityId"/>
+               <persistent value="false"/>
+       </extension>
+ 
+       <extension point="org.eclipse.ui.ide.markerSupport">
+           <markerContentGenerator
+                   id="eu.etaxonomy.taxeditor.editor.validation.ValidationProblemsMarkerGenerator" 
+                   name="Validation Problems Marker Generator">  
+               <markerTypeReference id="eu.etaxonomy.taxeditor.markers.validationerror" />
+               
+               <markerFieldReference id="eu.etaxonomy.taxeditor.markers.validation.userFriendlyTypeName" visible="true" />
+               <markerFieldReference id="eu.etaxonomy.taxeditor.markers.validation.userFriendlyDescription" visible="true" />
+               <markerFieldReference id="eu.etaxonomy.taxeditor.markers.validation.userFriendlyFieldName" visible="true" />
+               <markerFieldReference id="eu.etaxonomy.taxeditor.markers.validation.validatorMessage" visible="true" />
+               <markerFieldReference id="eu.etaxonomy.taxeditor.markers.validation.invalidValue" visible="true" />
+               <markerFieldReference id="eu.etaxonomy.taxeditor.markers.validation.validatorClass" visible="false" />
+               <markerFieldReference id="eu.etaxonomy.taxeditor.markers.validation.entityClass" visible="false" />
+               <markerFieldReference id="eu.etaxonomy.taxeditor.markers.validation.entityId" visible="false" />
+           </markerContentGenerator>
+           
+               <markerField
+                       class="eu.etaxonomy.taxeditor.editor.view.validation.UserFriendlyTypeNameMarkerField"
+                       id="eu.etaxonomy.taxeditor.markers.validation.userFriendlyTypeName"
+                       name="%marker.field.0">
+               </markerField>
+               <markerField
+                       class="eu.etaxonomy.taxeditor.editor.view.validation.UserFriendlyDescriptionMarkerField"
+                       id="eu.etaxonomy.taxeditor.markers.validation.userFriendlyDescription"
+                       name="%marker.field.1">
+               </markerField>
+               <markerField
+                       class="eu.etaxonomy.taxeditor.editor.view.validation.UserFriendlyFieldNameMarkerField"
+                       id="eu.etaxonomy.taxeditor.markers.validation.userFriendlyFieldName"
+                       name="%marker.field.2 = Attribute">
+               </markerField>
+               <markerField
+                       class="eu.etaxonomy.taxeditor.editor.view.validation.InvalidValueMarkerField"
+                       id="eu.etaxonomy.taxeditor.markers.validation.invalidValue"
+                       name="%marker.field.3 = Problematic Value">
+               </markerField>
+               <markerField
+                       class="eu.etaxonomy.taxeditor.editor.view.validation.ValidatorMessageMarkerField"
+                       id="eu.etaxonomy.taxeditor.markers.validation.validatorMessage"
+                       name="%marker.field.4 = Problem description">
+               </markerField>
+               <markerField
+                       class="eu.etaxonomy.taxeditor.editor.view.validation.ValidatorClassMarkerField"
+                       id="eu.etaxonomy.taxeditor.markers.validation.validatorClass"
+                       name="%marker.field.5">
+               </markerField>
+               <markerField
+                       class="eu.etaxonomy.taxeditor.editor.view.validation.EntityClassMarkerField"
+                       id="eu.etaxonomy.taxeditor.markers.validation.entityClass"
+                       name="%marker.field.6">
+               </markerField>
+               <markerField
+                       class="eu.etaxonomy.taxeditor.editor.view.validation.EntityIdMarkerField"
+                       id="eu.etaxonomy.taxeditor.markers.validation.entityId"
+                       name="%marker.field.7">
+               </markerField>
+       </extension>
 -      
 -  <extension
 +   <extension
           point="org.eclipse.ui.elementFactories">
        <factory
              class="eu.etaxonomy.taxeditor.editor.TaxonEditorInputFactory"
@@@ -1353,15 -1386,32 +1480,41 @@@
              id="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations"
              name="Show Only Individual Associations">
        </command>
 +      <command
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite"
 +            name="Toggle insert/overwrite">
 +      </command>
 +      <command
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion"
 +            name="Toggle left/right insertion in base call sequence">
 +      </command>
+       <command
+             defaultHandler="eu.etaxonomy.taxeditor.editor.handler.OpenTaxonEditorHandler"
+             id="eu.etaxonomy.taxeditor.editor.openTaxonEditor"
+             name="Open Taxon Editor">
+          <commandParameter
+                id="eu.etaxonomy.taxeditor.editor.taxonParameter"
+                name="taxonUUID"
+                optional="false"
+                typeId="eu.etaxonomy.taxeditor.editor.taxonParameterType">
+          </commandParameter>
+       </command>
+       <commandParameterType
+             converter="eu.etaxonomy.taxeditor.editor.handler.TaxonParameterConverter"
+             id="eu.etaxonomy.taxeditor.editor.taxonParameterType"
+             type="eu.etaxonomy.cdm.model.taxon.TaxonBase">
+       </commandParameterType>
+       <command
+             defaultHandler="eu.etaxonomy.taxeditor.editor.view.derivate.handler.CreateFieldUnitHandler"
+             id="eu.etaxonomy.taxeditor.editor.derivate.createFieldUnit"
+             name="Create Field Unit">
+       </command>
+       <command
+             defaultHandler="eu.etaxonomy.taxeditor.editor.view.derivate.handler.DeleteDerivateHandler"
+             id="eu.etaxonomy.taxeditor.editor.derivate.deepDelete"
+             name="Deep Delete">
+       </command>
 +
     </extension>
     <extension
           point="org.eclipse.core.expressions.definitions">

diff --cc eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/EditorUtil.java
index 4ed9313d32cf8063e44cccad67ca856f13df9eb9,c9350145261000221c842ae1127f8c5d96779a32..d923dd9b8a7dcb49424471312505a5f04c9853e9
--- 1/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/EditorUtil.java
--- 2/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/EditorUtil.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/EditorUtil.java
@@@ -35,10 -37,8 +37,10 @@@ import eu.etaxonomy.taxeditor.editor.gr
  import eu.etaxonomy.taxeditor.editor.internal.TaxeditorEditorPlugin;
  import eu.etaxonomy.taxeditor.editor.key.KeyEditor;
  import eu.etaxonomy.taxeditor.editor.key.polytomous.PolytomousKeyEditorInput;
- import eu.etaxonomy.taxeditor.editor.view.checklist.ChecklistEditorInput;
 +import eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor;
 +import eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditorInput;
  import eu.etaxonomy.taxeditor.editor.view.checklist.ChecklistEditor;
+ import eu.etaxonomy.taxeditor.editor.view.checklist.ChecklistEditorInput;
  import eu.etaxonomy.taxeditor.editor.view.dataimport.BioCaseEditorInput;
  import eu.etaxonomy.taxeditor.editor.view.dataimport.DataImportEditor;
  import eu.etaxonomy.taxeditor.editor.view.dataimport.DataImportEditorInput;