fixing #5150

[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 9b1edc9bb89d269001f9e07dae7f6cfcec3e8c62..66def47309837982fcbfaea4fa1efb79fc917fc0 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/plugin.xml
+++ b/eu.etaxonomy.taxeditor.editor/plugin.xml
@@ -83,15 +83,8 @@
             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"
@@ -159,15 +152,9 @@
                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 -->
+      
+       <!-- 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"/>
@@ -239,7 +226,8 @@
                        name="%marker.field.7">
                </markerField>
        </extension>
-   <extension
+       
+  <extension
          point="org.eclipse.ui.elementFactories">
       <factory
             class="eu.etaxonomy.taxeditor.editor.TaxonEditorInputFactory"
@@ -337,11 +325,6 @@
                </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">
@@ -669,12 +652,12 @@
             <visibleWhen
                   checkEnabled="true">
                <and>
-               <with
-                     variable="selection">
-                  <count
-                        value="+">
-                  </count>
-               </with>
+                  <with
+                        variable="selection">
+                     <count
+                           value="+">
+                     </count>
+                  </with>
                   <reference
                         definitionId="isIndividualsAssociation">
                   </reference>
@@ -699,20 +682,20 @@
             <visibleWhen
                   checkEnabled="true">
                <or>
-                  <reference
-                        definitionId="isDescriptionElement">
-                  </reference>
                   <reference
                         definitionId="isFeatureNodeContainer">
                   </reference>
-               </or>
+                   <reference
+                        definitionId="isDescriptionElement">
+                  </reference>
+              </or>
             </visibleWhen>
          </command>
          <separator
                name="eu.etaxonomy.taxeditor.taxonDescriptionEditor.separator.afterNew"
                visible="true">
          </separator>
-         <command
+                  <command
                commandId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.delete"
                label="%command.label.30"
                style="push">
@@ -748,28 +731,6 @@
                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">
@@ -987,84 +948,6 @@
             </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"
-                  style="push">
-            </command>
-            <command
-                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.cutPherogramLeft"
-                  id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.cutPherogramLeft"
-                  name="Cut pherogram left">
-            </command>
-            <command
-                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.cutPherogramRight"
-                  id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.cutPherogramRight"
-                  style="push">
-            </command>
-            <command
-                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.reverseComplementRows"
-                  mnemonic="r"
-                  style="push">
-            </command>
-            <command
-                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.createConsensus"
-                  style="push">
-            </command>
-            <command
-                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.updateConsensus"
-                  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="false">
-                  <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">
@@ -1167,8 +1050,8 @@
                        value="eu.etaxonomy.taxeditor.editor.view.uses">
                                </equals>
                 </or>
-             </with>
-          </activeWhen>
+                </with>
+         </activeWhen>
       </handler>
       <handler
             class="eu.etaxonomy.taxeditor.editor.key.polytomous.handler.DeleteNodeHandler"
@@ -1198,18 +1081,6 @@
             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.molecular.AlignmentEditor">
-               </equals>
-            </with>
-         </activeWhen>
-      </handler>
       <handler
             class="eu.etaxonomy.taxeditor.editor.view.derivate.handler.DeleteDerivateHandler"
             commandId="eu.etaxonomy.taxeditor.editor.view.derivate.command.delete">
@@ -1238,34 +1109,6 @@
             class="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.ToggleShowOnlyIndividualAssociationsHandler"
             commandId="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations">
       </handler>
-      <handler
-            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>
-      <handler
-            class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.CutPherogramLeftHandler"
-            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.cutPherogramLeft">
-      </handler>
-      <handler
-            class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.CutPherogramRightHandler"
-            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.cutPherogramRight">
-      </handler>
-      <handler
-            class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ReverseComplementHandler"
-            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.reverseComplementRows">
-      </handler>
-      <handler
-            class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.CreateConsensusSequenceHandler"
-            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.createConsensus">
-      </handler>
-      <handler
-            class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.UpdateConsensusSequenceHandler"
-            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.updateConsensus">
-      </handler>
    </extension>
    <extension
          name="%extension.name"
@@ -1333,7 +1176,7 @@
             id="eu.etaxonomy.taxeditor.editor.name.swapSynonymAndAccepted"
             name="%command.name.6">
       </command>
-       <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"
@@ -1385,8 +1228,8 @@
             id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.adddescription"
             name="%command.name.11">
       </command>
-      <command
-            categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
+       <command
+             categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
              defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.DeleteHandler"
              id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.delete"
              name="%command.name.48">
@@ -1457,6 +1300,7 @@
             id="eu.etaxonomy.taxeditor.editor.media.command.delete"
             name="%command.name.49">
       </command>
+      
       <category
             id="eu.etaxonomy.taxeditor.editor.new.category"
             name="%category.name.4">
@@ -1559,34 +1403,17 @@
              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="%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"
@@ -1616,45 +1443,17 @@
       <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"
+            id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.moveDescriptionToTaxon"
             name="%command.name.13">
       </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"
+            id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.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>
-      <command
-            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.cutPherogramLeft"
-            name="Cut pherogram left">
-      </command>
-      <command
-            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.cutPherogramRight"
-            name="Cut pherogram right">
-      </command>
-      <command
-            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.reverseComplementRows"
-            name="Reverse complement selected rows">
-      </command>
-      <command
-            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.createConsensus"
-            name="(Re)create consensus sequence">
-      </command>
-      <command
-            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.updateConsensus"
-            name="Update consensus sequence">
-      </command>
+        
    </extension>
    <extension
          point="org.eclipse.core.expressions.definitions">
@@ -1877,11 +1676,6 @@
             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">