merge-update from trunk
authorPatric Plitzner <p.plitzner@bgbm.org>
Tue, 24 Mar 2015 13:26:52 +0000 (13:26 +0000)
committerPatric Plitzner <p.plitzner@bgbm.org>
Tue, 24 Mar 2015 13:26:52 +0000 (13:26 +0000)
1  2 
.gitattributes
eu.etaxonomy.taxeditor.editor/plugin.xml

diff --combined .gitattributes
index f1d27f0f893a5808727b1b961cd6117e71d4b4ea,09a07e4cab3567495cd151e216a804dd00459fb7..fb3688ef79bc9d66665c09988cefeba1a85249f4
@@@ -366,11 -366,6 +366,11 @@@ eu.etaxonomy.taxeditor.editor/icons/emb
  eu.etaxonomy.taxeditor.editor/icons/leaf_detail.png -text
  eu.etaxonomy.taxeditor.editor/icons/link_obj.gif -text
  eu.etaxonomy.taxeditor.editor/icons/xper64.png -text
 +eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/commons-lang3-3.1.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar -text
  eu.etaxonomy.taxeditor.editor/p2.inf -text
  eu.etaxonomy.taxeditor.editor/plugin.xml -text
  eu.etaxonomy.taxeditor.editor/pom.xml -text
@@@ -396,21 -391,14 +396,21 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditorInput.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/handler/EditCdmAuthoritiesHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditNewTaxonHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditSequenceHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/FixClassificationHierarchyHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenAlignmentEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenChecklistEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenDerivateViewHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenParentHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenTaxonEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SaveAllHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SaveTaxonHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ShowPherogramHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SpecimenPropertyTester.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/TaxonParameterConverter.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ToggleInsertOverwriteHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ToggleLeftRightInsertionHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewNameHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewPersonHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewReferenceHandler.java -text
@@@ -438,12 -426,6 +438,12 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/CreateNodeOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/DeleteNodeOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/RefreshNodeNumberingOperation.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CDMAlignmentObjectPlaceholder.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroup.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java -text
@@@ -632,10 -614,7 +632,10 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidationProblemsView.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidatorClassMarkerField.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidatorMessageMarkerField.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1 -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1 -text
  eu.etaxonomy.taxeditor.editor/src/main/resources/TaonDescriptionEditor.screen -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf -text
  eu.etaxonomy.taxeditor.editor/src/main/resources/log4j.properties -text
  eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/Application.java -text
  eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/ApplicationActionBarAdvisor.java -text
@@@ -666,7 -645,10 +666,10 @@@ eu.etaxonomy.taxeditor.feature.platform
  eu.etaxonomy.taxeditor.feature.platform/pom.xml -text
  eu.etaxonomy.taxeditor.feature/.project -text
  eu.etaxonomy.taxeditor.feature/LICENSE.TXT -text
+ eu.etaxonomy.taxeditor.feature/README.txt -text
  eu.etaxonomy.taxeditor.feature/build.properties -text
+ eu.etaxonomy.taxeditor.feature/build.properties.with.jre -text
+ eu.etaxonomy.taxeditor.feature/build.properties.wo.jre -text
  eu.etaxonomy.taxeditor.feature/feature.xml -text
  eu.etaxonomy.taxeditor.feature/pom.xml -text
  eu.etaxonomy.taxeditor.help/.classpath -text
@@@ -1863,8 -1845,11 +1866,11 @@@ eu.etaxonomy.taxeditor.test/src/test/ja
  eu.etaxonomy.taxeditor.test/src/test/java/eu/etaxonomy/taxeditor/ui/selection/TaxonSelectionElementTest.java -text
  eu.etaxonomy.taxeditor/.classpath -text
  eu.etaxonomy.taxeditor/.project -text
+ eu.etaxonomy.taxeditor/README.txt -text
  eu.etaxonomy.taxeditor/deploy_nightly.sh -text
  eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product -text
+ eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product.with.jre -text
+ eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product.wo.jre -text
  eu.etaxonomy.taxeditor/plugin_customization.ini -text
  eu.etaxonomy.taxeditor/pom.xml -text
  eu.etaxonomy.taxeditor/rcp.target -text
index 5775ab4f5454f4e3388492e3e735ad6e8a2cb88c,20254cc3e0b0d1eda74a9dc932be46df55c82e56..3aca8a587514ecd4a6f57a1508dc37109f8cb02f
              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"
                 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="Validation Error" id="eu.etaxonomy.taxeditor.markers.validationerror">
+       <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"/>
                        name="%marker.field.7">
                </markerField>
        </extension>
 -      
 -  <extension
 +   <extension
           point="org.eclipse.ui.elementFactories">
        <factory
              class="eu.etaxonomy.taxeditor.editor.TaxonEditorInputFactory"
                 </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">
           </separator>
           <command
                 commandId="eu.etaxonomy.taxeditor.editor.handler.openDerivateView"
-                label="Open in Derivate Editor"
+                label="%command.label.51"
                 style="push">
              <visibleWhen
                    checkEnabled="true">
              locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView">
           <command
                 commandId="org.eclipse.ui.edit.delete"
-                label="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">
              </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">
                 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
              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">
        <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"
              class="eu.etaxonomy.taxeditor.editor.handler.FixClassificationHierarchyHandler"
              commandId="eu.etaxonomy.taxeditor.editor.handler.FixClassificationHierarchyHandler">
        </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"
               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"
        <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
              defaultHandler="eu.etaxonomy.taxeditor.editor.handler.FixClassificationHierarchyHandler"
              id="eu.etaxonomy.taxeditor.editor.handler.OpenFixClassificationHierarchyHandler"
-             name="Fix Classification Hierarchy">
+             name="%command.name.45">
        </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">
              </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">
              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">   
              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">