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 53080cc47d69177e2a1509e581dcb603f1e19765..99f70453118a991826507087998fcafb714460ba 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"
@@ -145,16 +152,14 @@
                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"/>
@@ -226,8 +231,7 @@
                        name="%marker.field.7">
                </markerField>
        </extension>
-       
-  <extension
+   <extension
          point="org.eclipse.ui.elementFactories">
       <factory
             class="eu.etaxonomy.taxeditor.editor.TaxonEditorInputFactory"
@@ -325,6 +329,11 @@
                </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">
@@ -933,6 +942,62 @@
             </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"
+                  label="Toggle left/right insertion"
+                  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">
@@ -1074,6 +1139,18 @@
       <handler
             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"
@@ -1103,6 +1180,14 @@
             class="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.ToggleShowOnlyIndividualAssociationsHandler"
             commandId="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations">
       </handler>
+      <handler
+            class="eu.etaxonomy.taxeditor.editor.handler.ToggleInsertOverwriteHandler"
+            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite">
+      </handler>
+      <handler
+            class="eu.etaxonomy.taxeditor.editor.handler.ToggleLeftRightInsertionHandler"
+            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion">
+      </handler>
    </extension>
    <extension
          name="%extension.name"
@@ -1375,17 +1460,34 @@
              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.OpenAlignmentEditor"
+            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">
       </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"
@@ -1412,6 +1514,7 @@
             id="eu.etaxonomy.taxeditor.editor.derivate.deepDelete"
             name="Deep Delete">
       </command>
+
    </extension>
    <extension
          point="org.eclipse.core.expressions.definitions">
@@ -1600,6 +1703,11 @@
             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">