merge-update from trunk

[taxeditor.git] / eu.etaxonomy.taxeditor.editor / plugin.xml

diff --git a/eu.etaxonomy.taxeditor.editor/plugin.xml b/eu.etaxonomy.taxeditor.editor/plugin.xml
index 83b8d25e3ccb2ddc25bbb73242bd2ae515a7cfd4..9c171a2137d2e1a25755a48885d8bf1b87fc6a66 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/plugin.xml
+++ b/eu.etaxonomy.taxeditor.editor/plugin.xml
@@ -83,8 +83,15 @@
             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
+            id="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
             point="org.eclipse.ui.views">
          <view
                allowMultiple="false"
@@ -152,10 +159,16 @@
                id="eu.etaxonomy.taxeditor.editor.view.validation.problems"
                name="%view.name.6">
          </view>
+         <view
+               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 -->
-       <extension point="org.eclipse.core.resources.markers" name="Validation Error" id="eu.etaxonomy.taxeditor.markers.validationerror">
+      <!-- VALIDATION RELATED STUFF -->
+       <extension point="org.eclipse.core.resources.markers" name="%extension.name.0" id="eu.etaxonomy.taxeditor.markers.validationerror">
                <super type="org.eclipse.core.resources.problemmarker"/>
                <attribute name="databaseId"/>
                <attribute name="userFriendlyTypeName"/>
@@ -172,7 +185,7 @@
        <extension point="org.eclipse.ui.ide.markerSupport">
            <markerContentGenerator
                    id="eu.etaxonomy.taxeditor.editor.validation.ValidationProblemsMarkerGenerator" 
-                   name="Validation Problems Marker Generator">  
+                   name="%markerContentGenerator.name">  
                <markerTypeReference id="eu.etaxonomy.taxeditor.markers.validationerror" />
                
                <markerFieldReference id="eu.etaxonomy.taxeditor.markers.validation.userFriendlyTypeName" visible="true" />
@@ -226,8 +239,7 @@
                        name="%marker.field.7">
                </markerField>
        </extension>
-       
-  <extension
+   <extension
          point="org.eclipse.ui.elementFactories">
       <factory
             class="eu.etaxonomy.taxeditor.editor.TaxonEditorInputFactory"
@@ -325,6 +337,11 @@
                </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">
@@ -468,7 +485,7 @@
                visible="true">
          </separator>
          <command
-               commandId="org.eclipse.ui.edit.delete"
+               commandId="eu.etaxonomy.taxeditor.editor.name.delete"
                label="%command.label.15"
                style="push">
             <visibleWhen>
@@ -523,6 +540,16 @@
                </reference>
             </visibleWhen>
          </command>
+         <command
+                  commandId="eu.etaxonomy.taxeditor.editor.name.moveSynonymToAnotherAcceptedTaxon"
+                  label="%command.label.56"
+                  style="push">
+               <visibleWhen>
+                   <reference
+                         definitionId="isSynonym">
+                   </reference>
+                </visibleWhen>
+          </command>
          <separator
                name="taxeditor-editor.separator3"
                visible="true">
@@ -558,7 +585,7 @@
                visible="true">
          </separator>
          <command
-               commandId="org.eclipse.ui.edit.delete"
+               commandId="eu.etaxonomy.taxeditor.key.polytomous.delete"
                label="%command.label.21"
                style="push">
          </command>
@@ -594,7 +621,7 @@
                style="push">
          </command>
          <command
-               commandId="org.eclipse.ui.edit.delete"
+               commandId="eu.etaxonomy.taxeditor.key.polytomous.command.delete"
                label="%command.label.26"
                style="push">
          </command>
@@ -602,7 +629,7 @@
       <menuContribution
             locationURI="popup:eu.etaxonomy.taxeditor.editor.view.descriptive">
          <command
-               commandId="eu.etaxonomy.taxeditor.description.commands.adddescription"
+               commandId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.adddescription"
                label="%command.label.27"
                style="push">
          </command>
@@ -637,20 +664,25 @@
          </separator>
          <command
                commandId="eu.etaxonomy.taxeditor.editor.handler.openDerivateView"
-               label="Open in Derivate Editor"
+               label="%command.label.51"
                style="push">
             <visibleWhen
                   checkEnabled="true">
+               <and>
                <with
                      variable="selection">
                   <count
                         value="+">
                   </count>
                </with>
+                  <reference
+                        definitionId="isIndividualsAssociation">
+                  </reference>
+               </and>
             </visibleWhen>
          </command>
          <command
-               commandId="eu.etaxonomy.taxeditor.editor.commands.description.moveDescriptionToTaxon"
+               commandId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.moveDescriptionToTaxon"
                label="%command.label.28"
                style="push">
             <visibleWhen
@@ -661,7 +693,7 @@
             </visibleWhen>
          </command>
          <command
-               commandId="eu.etaxonomy.taxeditor.description.commands.moveDescriptionElements"
+               commandId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.moveDescriptionElements"
                label="%command.label.29"
                style="push">
             <visibleWhen
@@ -681,7 +713,7 @@
                visible="true">
          </separator>
          <command
-               commandId="org.eclipse.ui.edit.delete"
+               commandId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.delete"
                label="%command.label.30"
                style="push">
          </command>
@@ -701,21 +733,43 @@
       <menuContribution
             locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView">
          <command
-               commandId="org.eclipse.ui.edit.delete"
-               label="Delete"
+               commandId="eu.etaxonomy.taxeditor.editor.derivate.delete"
+               label="%command.label.52"
                style="push">
          </command>
          <command
                commandId="eu.etaxonomy.taxeditor.editor.derivate.createFieldUnit"
-               label="Create Field Unit"
+               label="%command.label.53"
                style="push">
          </command>
          <command
                commandId="eu.etaxonomy.taxeditor.editor.derivate.deepDelete"
                icon="icons/deep-delete-16x16-32.png"
-               label="Delete (with children)"
+               label="%command.label.54"
                style="push">
          </command>
+         <command
+               commandId="eu.etaxonomy.taxeditor.editor.editSequence"
+               label="Edit Sequence"
+               style="push">
+            <visibleWhen
+                  checkEnabled="true">
+               <reference
+                     definitionId="isSequence">
+               </reference>
+            </visibleWhen>
+         </command>
+         <command
+               commandId="eu.etaxonomy.taxeditor.editor.showPherogram"
+               label="Show Pherogram"
+               style="push">
+            <visibleWhen
+                  checkEnabled="true">
+               <reference
+                     definitionId="isSingleRead">
+               </reference>
+            </visibleWhen>
+         </command>
          <dynamic
                class="eu.etaxonomy.taxeditor.editor.view.derivate.contextMenu.DerivateViewContextMenu"
                id="eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
@@ -797,7 +851,7 @@
                visible="true">
          </separator>
          <command
-               commandId="org.eclipse.ui.edit.delete"
+               commandId="eu.etaxonomy.taxeditor.editor.use.command.delete"
                label="%command.label.35"
                style="push">
          </command>
@@ -819,7 +873,7 @@
       <menuContribution
             locationURI="popup:eu.etaxonomy.taxeditor.editor.view.media">
          <command
-               commandId="taxeditor-editor.command.newimagegallery"
+               commandId="eu.etaxonomy.taxeditor.editor.media.command.newimagegallery"
                label="%command.label.37"
                style="push">
             <visibleWhen>
@@ -841,7 +895,7 @@
                visible="true">
          </separator>
          <command
-               commandId="taxeditor-editor.newimage"
+               commandId="eu.etaxonomy.taxeditor.editor.media.command.newimage"
                label="%command.label.38"
                style="push">
             <visibleWhen>
@@ -851,7 +905,7 @@
             </visibleWhen>
          </command>
          <command
-               commandId="taxeditor-editor.useExistingImage"
+               commandId="eu.etaxonomy.taxeditor.editor.media.command.useExistingImage"
                label="%command.label.50"
                style="push">
             <visibleWhen>
@@ -861,7 +915,7 @@
             </visibleWhen>
          </command>
          <command
-               commandId="taxeditor-editor.command.moveimgdown"
+               commandId="eu.etaxonomy.taxeditor.editor.media.command.moveimgdown"
                label="%command.label.39"
                style="push">
             <visibleWhen>
@@ -871,7 +925,7 @@
             </visibleWhen>
          </command>
          <command
-               commandId="taxeditor-editor.command.moveimgup"
+               commandId="eu.etaxonomy.taxeditor.editor.media.command.moveimgup"
                label="%command.label.40"
                style="push">
             <visibleWhen>
@@ -885,7 +939,7 @@
                visible="true">
          </separator>
          <command
-               commandId="org.eclipse.ui.edit.delete"
+               commandId="eu.etaxonomy.taxeditor.editor.media.command.delete"
                label="%command.label.41"
                style="push">
          </command>
@@ -914,7 +968,7 @@
                visible="true">
          </separator>
          <command
-               commandId="org.eclipse.ui.edit.delete"
+               commandId="eu.etaxonomy.taxeditor.editor.view.concept.command.delete"
                label="%command.label.44"
                style="push">
          </command>
@@ -933,6 +987,62 @@
             </visibleWhen>
          </command>
       </menuContribution>
+      <menuContribution
+            allPopups="false"
+            locationURI="menu:org.eclipse.ui.main.menu">
+         <menu
+               label="Alignment Editor">
+            <command
+                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram"
+                  label="Load Pherogram"
+                  style="push">
+            </command>
+            <visibleWhen
+                  checkEnabled="true">
+               <with
+                     variable="activePartId">
+                  <equals
+                        value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
+                  </equals>
+               </with>
+            </visibleWhen>
+         </menu>
+      </menuContribution>
+      <menuContribution
+            locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
+         <toolbar
+               id="eu.etaxonomy.taxeditor.editor.alignmentToolbar">
+            <command
+                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite"
+                  label="Toggle insert/overwrite"
+                  style="push">
+               <visibleWhen
+                     checkEnabled="true">
+                  <with
+                        variable="activePartId">
+                     <equals
+                           value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
+                     </equals>
+                  </with>
+               </visibleWhen>
+            </command>
+            <command
+                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion"
+                  icon="icons/pherogram-insert-left-16x16.png"
+                  style="push">
+               <visibleWhen
+                     checkEnabled="true">
+                  <with
+                        variable="activePartId">
+                     <equals
+                           value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
+                     </equals>
+                  </with>
+               </visibleWhen>
+            </command>
+         </toolbar>
+      </menuContribution>
+      
       <menuContribution
             allPopups="false"
             locationURI="toolbar:eu.etaxonomy.taxeditor.editor.view.descriptive">
@@ -940,7 +1050,7 @@
                commandId="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations"
                icon="icons/link_obj.gif"
                style="toggle"
-               tooltip="Show Only Individuals Associations">
+               tooltip="%command.tooltip">
          </command>
       </menuContribution>
       <menuContribution
@@ -948,7 +1058,7 @@
             locationURI="popup:eu.etaxonomy.taxeditor.navigation.navigatorpopup?after=taxeditor-navigation.separator2">
          <command
                commandId="eu.etaxonomy.taxeditor.editor.handler.openDerivateView"
-               label="Open Associated Derivates"
+               label="%command.label.55"
                style="push">
             <visibleWhen
                   checkEnabled="false">
@@ -1004,7 +1114,7 @@
       </handler>
       <handler
             class="eu.etaxonomy.taxeditor.editor.name.handler.DeleteTaxonBaseHandler"
-            commandId="org.eclipse.ui.edit.delete">
+            commandId="eu.etaxonomy.taxeditor.editor.name.command.delete">
          <activeWhen>
             <and>
                <reference
@@ -1020,7 +1130,7 @@
       </handler>
       <handler
             class="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.DeleteHandler"
-            commandId="org.eclipse.ui.edit.delete">
+            commandId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.delete">
           <activeWhen>
              <with
                    variable="activePartId">
@@ -1031,13 +1141,16 @@
                    <equals
                          value="eu.etaxonomy.taxeditor.editor.view.media">
                    </equals>
+                   <equals
+                       value="eu.etaxonomy.taxeditor.editor.view.uses">
+                               </equals>
                 </or>
              </with>
           </activeWhen>
       </handler>
       <handler
             class="eu.etaxonomy.taxeditor.editor.key.polytomous.handler.DeleteNodeHandler"
-            commandId="org.eclipse.ui.edit.delete">
+            commandId="eu.etaxonomy.taxeditor.editor.key.polytomous.command.delete">
          <activeWhen>
             <with
                   variable="activePartId">
@@ -1049,7 +1162,7 @@
       </handler>
       <handler
             class="eu.etaxonomy.taxeditor.editor.view.concept.handler.DeleteConceptRelationHandler"
-            commandId="org.eclipse.ui.edit.delete">
+            commandId="eu.etaxonomy.taxeditor.editor.view.concept.command.delete">
          <activeWhen>
             <with
                   variable="activePartId">
@@ -1060,24 +1173,24 @@
          </activeWhen>
       </handler>
       <handler
-            class="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.DeleteHandler"
-            commandId="org.eclipse.ui.edit.delete">
+            class="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler"
+            commandId="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler">
+      </handler>
+      <handler
+            class="eu.etaxonomy.taxeditor.editor.handler.LoadPherogramHandler"
+            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram">
          <activeWhen>
             <with
                   variable="activePartId">
                <equals
-                     value="eu.etaxonomy.taxeditor.editor.view.uses">
+                     value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
                </equals>
             </with>
          </activeWhen>
       </handler>
-      <handler
-            class="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler"
-            commandId="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler">
-      </handler>
       <handler
             class="eu.etaxonomy.taxeditor.editor.view.derivate.handler.DeleteDerivateHandler"
-            commandId="org.eclipse.ui.edit.delete">
+            commandId="eu.etaxonomy.taxeditor.editor.view.derivate.command.delete">
          <activeWhen>
             <with
                   variable="activePartId">
@@ -1104,8 +1217,12 @@
             commandId="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations">
       </handler>
       <handler
-            class="eu.etaxonomy.taxeditor.editor.handler.FixClassificationHierarchyHandler"
-            commandId="eu.etaxonomy.taxeditor.editor.handler.FixClassificationHierarchyHandler">
+            class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleInsertOverwriteHandler"
+            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite">
+      </handler>
+      <handler
+            class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleLeftRightInsertionHandler"
+            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion">
       </handler>
    </extension>
    <extension
@@ -1173,6 +1290,12 @@
             defaultHandler="eu.etaxonomy.taxeditor.editor.name.handler.SwapSynonymAndAcceptedHandler"
             id="eu.etaxonomy.taxeditor.editor.name.swapSynonymAndAccepted"
             name="%command.name.6">
+      </command>
+       <command
+            categoryId="eu.etaxonomy.taxeditor.editor.taxon.name.command.category"
+            defaultHandler="eu.etaxonomy.taxeditor.editor.name.handler.MoveSynonymToAnotherAcceptedTaxonHandler"
+            id="eu.etaxonomy.taxeditor.editor.name.moveSynonymToAnotherAcceptedTaxon"
+            name="%command.name.46">
       </command>
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.taxon.name.command.category"
@@ -1192,6 +1315,12 @@
             id="eu.etaxonomy.taxeditor.editor.name.changeAcceptedToSynonym"
             name="Change Accepted Taxon to Synonym">
       </command>-->
+      <command
+            categoryId="eu.etaxonomy.taxeditor.editor.taxon.name.command.category"
+            defaultHandler="eu.etaxonomy.taxeditor.editor.name.handler.DeleteTaxonBaseHandler"
+            id="eu.etaxonomy.taxeditor.editor.name.delete"
+            name="%command.name.45">
+      </command>
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.taxon.name.command.category"
             defaultHandler="eu.etaxonomy.taxeditor.editor.name.handler.DeleteAllEmptyNamesHandler"
@@ -1205,26 +1334,20 @@
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.CreateDescriptionElementHandler"
-            id="eu.etaxonomy.taxeditor.editor.description.createDescriptionElement"
+            id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.createDescriptionElement"
             name="%command.name.10">
       </command>
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.CreateDescriptionHandler"
-            id="eu.etaxonomy.taxeditor.description.commands.adddescription"
+            id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.adddescription"
             name="%command.name.11">
       </command>
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
-            defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.MoveDescriptionElementsHandler"
-            id="eu.etaxonomy.taxeditor.description.commands.moveDescriptionElements"
-            name="%command.name.12">
-      </command>
-      <command
-            categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
-            defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.MoveDescriptionToOtherTaxonHandler"
-            id="eu.etaxonomy.taxeditor.editor.commands.description.moveDescriptionToTaxon"
-            name="%command.name.13">
+             defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.DeleteHandler"
+             id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.delete"
+             name="%command.name.48">
       </command>
       <category
             id="eu.etaxonomy.taxeditor.editor.view.uses.command.category"
@@ -1236,6 +1359,12 @@
             id="eu.etaxonomy.taxeditor.use.commands.adduse"
             name="%command.name.14">
       </command>
+      <command
+            categoryId="eu.etaxonomy.taxeditor.editor.view.uses.command.category"
+            defaultHandler="eu.etaxonomy.taxeditor.editor.view.uses.handler.CreateUseRecordHandler"
+            id="eu.etaxonomy.taxeditor.editor.use.createUseRecord"
+            name="%command.name.16">
+      </command>
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.view.uses.command.category"
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.uses.handler.CreateUseSummaryHandler"
@@ -1243,10 +1372,8 @@
             name="%command.name.15">
       </command>
       <command
-            categoryId="eu.etaxonomy.taxeditor.editor.view.uses.command.category"
-            defaultHandler="eu.etaxonomy.taxeditor.editor.view.uses.handler.CreateUseRecordHandler"
-            id="eu.etaxonomy.taxeditor.editor.use.createUseRecord"
-            name="%command.name.16">
+            id="eu.etaxonomy.taxeditor.editor.use.command.delete"
+            name="%command.name.47">
       </command>
       <category
             id="eu.etaxonomy.taxeditor.editor.media.category"
@@ -1255,32 +1382,38 @@
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.media.category"
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.media.handler.MoveImageDownInListHandler"
-            id="taxeditor-editor.command.moveimgdown"
+            id="eu.etaxonomy.taxeditor.editor.media.command.moveimgdown"
             name="%command.name.19">
       </command>
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.media.category"
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.media.handler.AddImageGalleryHandler"
-            id="taxeditor-editor.command.newimagegallery"
+            id="eu.etaxonomy.taxeditor.editor.media.command.newimagegallery"
             name="%command.name.20">
       </command>
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.media.category"
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.media.handler.CreateMediaHandler"
-            id="taxeditor-editor.newimage"
+            id="eu.etaxonomy.taxeditor.editor.media.command.newimage"
             name="%command.name.21">
       </command>
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.media.category"
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.media.handler.AddExistingMediaHandler"
-            id="taxeditor-editor.useExistingImage"
+            id="eu.etaxonomy.taxeditor.editor.media.command.useExistingImage"
             name="%command.name.37">
       </command>
       <command
             categoryId="eu.etaxonomy.taxeditor.editor.media.category"
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.media.handler.MoveImageUpInListHandler"
-            id="taxeditor-editor.command.moveimgup"
+            id="eu.etaxonomy.taxeditor.editor.media.command.moveimgup"
             name="%command.name.22">
+      </command>
+       <command
+            categoryId="eu.etaxonomy.taxeditor.editor.media.category"
+            defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.DeleteHandler"
+            id="eu.etaxonomy.taxeditor.editor.media.command.delete"
+            name="%command.name.49">
       </command>
       <category
             id="eu.etaxonomy.taxeditor.editor.new.category"
@@ -1344,6 +1477,11 @@
             id="eu.etaxonomy.taxeditor.key.command.applyLayout"
             name="%command.name.31">
       </command>
+      <command
+            defaultHandler="eu.etaxonomy.taxeditor.editor.key.polytomous.handler.DeleteNodeHandler"
+            id="eu.etaxonomy.taxeditor.key.polytomous.command.delete"
+            name="%command.name.50">
+      </command>
       <category
             id="eu.etaxonomy.taxeditor.editor.view.concept.category"
             name="%category.name.6">
@@ -1379,24 +1517,41 @@
              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.OpenAlignmentEditorHandler"
+            id="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
+            name="Open Alignment Editor">
+      </command>
+      <command
+            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram"
+            name="Load Pherogram">
+      </command>
       <command
             id="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations"
-            name="Show Only Individual Associations">
+            name="%command.name.41">
+      </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">
+            name="%command.name.42">
          <commandParameter
                id="eu.etaxonomy.taxeditor.editor.taxonParameter"
-               name="taxonUUID"
+               name="%commandParameter.name"
                optional="false"
                typeId="eu.etaxonomy.taxeditor.editor.taxonParameterType">
          </commandParameter>
@@ -1409,17 +1564,34 @@
       <command
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.derivate.handler.CreateFieldUnitHandler"
             id="eu.etaxonomy.taxeditor.editor.derivate.createFieldUnit"
-            name="Create Field Unit">
+            name="%command.name.43">
       </command>
       <command
             defaultHandler="eu.etaxonomy.taxeditor.editor.view.derivate.handler.DeleteDerivateHandler"
             id="eu.etaxonomy.taxeditor.editor.derivate.deepDelete"
-            name="Deep Delete">
+            name="%command.name.44">
+      </command>
+      <command
+            categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
+            defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.MoveDescriptionToOtherTaxonHandler"
+            id="eu.etaxonomy.taxeditor.editor.commands.description.moveDescriptionToTaxon"
+            name="%command.name.13">
       </command>
       <command
-            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.FixClassificationHierarchyHandler"
-            id="eu.etaxonomy.taxeditor.editor.handler.OpenFixClassificationHierarchyHandler"
-            name="Fix Classification Hierarchy">
+            categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
+            defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.MoveDescriptionElementsHandler"
+            id="eu.etaxonomy.taxeditor.description.commands.moveDescriptionElements"
+            name="%command.name.12">
+      </command>
+      <command
+            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.EditSequenceHandler"
+            id="eu.etaxonomy.taxeditor.editor.editSequence"
+            name="Edit Sequence">
+      </command>
+      <command
+            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.ShowPherogramHandler"
+            id="eu.etaxonomy.taxeditor.editor.showPherogram"
+            name="Show Pherogram">
       </command>
    </extension>
    <extension
@@ -1577,6 +1749,33 @@
             </test>
          </with>
       </definition>
+      <definition
+            id="isIndividualsAssociation">
+         <with
+               variable="selection">
+            <test
+                  property="eu.etaxonomy.taxeditor.descriptions.propertyTester.isIndividualsAssociation">
+            </test>
+         </with>
+      </definition>
+      <definition
+            id="isSequence">
+         <with
+               variable="selection">
+            <test
+                  property="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester.isSequence">
+            </test>
+         </with>
+      </definition>
+      <definition
+            id="isSingleRead">
+         <with
+               variable="selection">
+            <test
+                  property="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester.isSingleRead">
+            </test>
+         </with>
+      </definition>
    </extension>
    <extension
          point="org.eclipse.core.expressions.propertyTesters">
@@ -1591,7 +1790,7 @@
             class="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.DescriptionsMenuPropertyTester"
             id="eu.etaxonomy.taxeditor.descriptions.PropertyTester"
             namespace="eu.etaxonomy.taxeditor.descriptions.propertyTester"
-            properties="isMedia,isDescription,isDescriptionElement,isDeletable,isFeatureNodeContainer,isImageGallery,isTaxonEditor,isBulkEditor,isDerivateEditor"
+            properties="isMedia,isDescription,isDescriptionElement,isDeletable,isFeatureNodeContainer,isImageGallery,isTaxonEditor,isBulkEditor,isDerivateEditor, isIndividualsAssociation"
             type="org.eclipse.jface.viewers.TreeSelection">
       </propertyTester>
       <propertyTester
@@ -1601,6 +1800,13 @@
             properties="isGroup"
             type="eu.etaxonomy.taxeditor.bulkeditor.BulkEditor">
       </propertyTester>
+      <propertyTester
+            class="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester"
+            id="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester"
+            namespace="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester"
+            properties="isSequence,isSingleRead"
+            type="org.eclipse.jface.viewers.IStructuredSelection">
+      </propertyTester>
    </extension>
    <extension
          point="org.eclipse.ui.bindings">   
@@ -1609,6 +1815,11 @@
             id="eu.etaxonomy.taxeditor.bindings.scheme.default"
             name="%scheme.name">
       </scheme>
+      <key
+            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram"
+            schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
+            sequence="M1+O">
+      </key>
    </extension>
     <extension
          point="org.eclipse.ui.importWizards">