X-Git-Url: https://dev.e-taxonomy.eu/gitweb/taxeditor.git/blobdiff_plain/13c5d3f034d13a7ffa2d9e7a8e3d7bb0d2f0cc2a..405fc70fc578a7c8a5d6d31b8a4d22edd42d2fd7:/eu.etaxonomy.taxeditor.editor/plugin.xml

diff --git a/eu.etaxonomy.taxeditor.editor/plugin.xml b/eu.etaxonomy.taxeditor.editor/plugin.xml
index 23f66c05e..975db0d6a 100644
--- 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"
@@ -144,7 +151,94 @@
                id="eu.etaxonomy.taxeditor.editor.view.dataimport.GbifResponseImportView"
                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">
+         </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">
+		<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
          point="org.eclipse.ui.elementFactories">
       <factory
@@ -243,6 +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">
@@ -553,6 +652,20 @@
                name="taxeditor-editor.separator1"
                visible="true">
          </separator>
+         <command
+               commandId="eu.etaxonomy.taxeditor.editor.handler.openDerivateView"
+               label="Open in Derivate Editor"
+               style="push">
+            <visibleWhen
+                  checkEnabled="true">
+               <with
+                     variable="selection">
+                  <count
+                        value="+">
+                  </count>
+               </with>
+            </visibleWhen>
+         </command>
          <command
                commandId="eu.etaxonomy.taxeditor.editor.commands.description.moveDescriptionToTaxon"
                label="%command.label.28"
@@ -598,6 +711,9 @@
                label="%command.label.31"
                style="push">
          </command>
+         <separator
+               name="eu.etaxonomy.taxeditor.editor.separator1">
+         </separator>
       </menuContribution>
       <menuContribution
             locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView">
@@ -610,6 +726,28 @@
                label="Delete"
                style="push">
          </command>
+         <command
+               commandId="eu.etaxonomy.taxeditor.editor.derivate.createFieldUnit"
+               label="Create Field Unit"
+               style="push">
+         </command>
+         <command
+               commandId="eu.etaxonomy.taxeditor.editor.derivate.deepDelete"
+               icon="icons/deep-delete-16x16-32.png"
+               label="Delete (with children)"
+               style="push">
+         </command>
+         <command
+               commandId="eu.etaxonomy.taxeditor.editor.editSequence"
+               label="Edit Sequence"
+               style="push">
+            <visibleWhen
+                  checkEnabled="true">
+               <reference
+                     definitionId="isSequence">
+               </reference>
+            </visibleWhen>
+         </command>
       </menuContribution>
       <menuContribution
             locationURI="popup:eu.etaxonomy.taxeditor.editor.view.dataimport.SpecimenImportEditor">
@@ -823,6 +961,62 @@
             </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">
@@ -840,12 +1034,39 @@
                commandId="eu.etaxonomy.taxeditor.editor.handler.openDerivateView"
                label="Open Associated Derivates"
                style="push">
+            <visibleWhen
+                  checkEnabled="false">
+               <and>
+                  <reference
+                        definitionId="isCdmStoreConnected">
+                  </reference>
+                  <reference
+                        definitionId="isTaxonNode">
+                  </reference>
+               </and>
+            </visibleWhen>
          </command>
          <separator
                name="eu.etaxonomy.taxeditor.editor.separator1"
                visible="true">
          </separator>
       </menuContribution>
+      <menuContribution
+            locationURI="menu:eu.etaxonomy.taxeditor.menu.showView?after=org.eclipse.ui.views.showView.supplemental">
+         <separator
+               name="eu.etaxonomy.taxeditor.store.showViewMenu.validation.separator"
+               visible="true">
+         </separator>
+         <command
+               commandId="org.eclipse.ui.views.showView"
+               label="%command.name.40"
+               style="push">
+            <parameter
+                  name="org.eclipse.ui.views.showView.viewId"
+                  value="eu.etaxonomy.taxeditor.editor.view.validation.problems">
+            </parameter>
+         </command>
+      </menuContribution>
    </extension>
    <extension
          point="org.eclipse.ui.handlers">
@@ -937,6 +1158,18 @@
       <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"
@@ -966,6 +1199,14 @@
             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"
@@ -1238,17 +1479,34 @@
              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"
@@ -1265,6 +1523,21 @@
             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>
+      <command
+            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.EditSequenceHandler"
+            id="eu.etaxonomy.taxeditor.editor.editSequence"
+            name="Edit Sequence">
+      </command>
    </extension>
    <extension
          point="org.eclipse.core.expressions.definitions">
@@ -1421,6 +1694,15 @@
             </test>
          </with>
       </definition>
+      <definition
+            id="isSequence">
+         <with
+               variable="selection">
+            <test
+                  property="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester.isSequence">
+            </test>
+         </with>
+      </definition>
    </extension>
    <extension
          point="org.eclipse.core.expressions.propertyTesters">
@@ -1445,6 +1727,13 @@
             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"
+            type="org.eclipse.jface.viewers.IStructuredSelection">
+      </propertyTester>
    </extension>
    <extension
          point="org.eclipse.ui.bindings">   
@@ -1453,6 +1742,11 @@
             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">
@@ -1466,4 +1760,10 @@
          </description>
       </wizard>
    </extension>
+    <extension
+          point="eu.etaxonomy.taxeditor.store.cdmViewer">
+       <cdmViewer
+             class="eu.etaxonomy.taxeditor.editor.EditorCdmViewer">
+       </cdmViewer>
+    </extension>
 </plugin>