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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 d06b782aa811d6b29e2875ed6f37b4a6d63f1d12..ed687ff8531d18b08f56b8ad3e58cc0ccf77fd65 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"
@@ -152,9 +159,15 @@
                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"/>
@@ -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">
@@ -652,12 +669,12 @@
             <visibleWhen
                   checkEnabled="true">
                <and>
-                  <with
-                        variable="selection">
-                     <count
-                           value="+">
-                     </count>
-                  </with>
+               <with
+                     variable="selection">
+                  <count
+                        value="+">
+                  </count>
+               </with>
                   <reference
                         definitionId="isIndividualsAssociation">
                   </reference>
@@ -695,7 +712,7 @@
                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">
@@ -731,6 +748,28 @@
                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">
@@ -948,6 +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">
@@ -1050,8 +1145,8 @@
                        value="eu.etaxonomy.taxeditor.editor.view.uses">
                                </equals>
                 </or>
-                </with>
-         </activeWhen>
+             </with>
+          </activeWhen>
       </handler>
       <handler
             class="eu.etaxonomy.taxeditor.editor.key.polytomous.handler.DeleteNodeHandler"
@@ -1081,6 +1176,18 @@
             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">
@@ -1109,6 +1216,14 @@
             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>
    </extension>
    <extension
          name="%extension.name"
@@ -1176,7 +1291,7 @@
             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"
@@ -1228,8 +1343,8 @@
             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">
@@ -1402,17 +1517,34 @@
              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"
@@ -1451,7 +1583,16 @@
             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
          point="org.eclipse.core.expressions.definitions">
@@ -1617,6 +1758,24 @@
             </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">
@@ -1641,6 +1800,13 @@
             properties="isGroupEditor"
             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">   
@@ -1649,6 +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">