X-Git-Url: https://dev.e-taxonomy.eu/gitweb/taxeditor.git/blobdiff_plain/cca70f19901a30eecbbe1f63f74a7f9cebecc5ba..12e620bc6d34d4d10d026b4fdb653303d3db3923:/eu.etaxonomy.taxeditor.molecular/plugin.xml

diff --git a/eu.etaxonomy.taxeditor.molecular/plugin.xml b/eu.etaxonomy.taxeditor.molecular/plugin.xml
index 78b734fd1..ff56c7c4b 100644
--- a/eu.etaxonomy.taxeditor.molecular/plugin.xml
+++ b/eu.etaxonomy.taxeditor.molecular/plugin.xml
@@ -1,82 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <?eclipse version="3.4"?>
 <plugin>
-   <extension
-         point="org.eclipse.ui.editors">
-      <editor
-            class="eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor"
-            default="false"
-            id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"
-            name="%editor.ALIGNMENT_EDITOR">
-      </editor>
-   </extension>
-      <extension
-            point="org.eclipse.ui.views">
-         <view
-               allowMultiple="true"
-               class="eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart"
-               id="eu.etaxonomy.taxeditor.molecular.PherogramView"
-               name="%view.PHEROGRAM_VIEW"
-               restorable="true">
-         </view>
-      </extension>
-      <extension
-            point="org.eclipse.ui.commands">
-         <command
-               defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler"
-               id="eu.etaxonomy.taxeditor.molecular.editSequence"
-               name="%command.EDIT_SEQUENCE">
-         </command>
-         <command
-               defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler"
-               id="eu.etaxonomy.taxeditor.molecular.showPherogram"
-               name="%command.name.SHOW_PHEROGRAM">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
-               name="%command.name.CUT_PHEROGRAM_LEFT">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
-               name="%command.name.CUT_PHEROGRAM_RIGHT">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
-               name="%command.name.REVERSE_COMPLEMENT_SELECTED_ROWS">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
-               name="%command.name.CREATE_CONSENUS_SEQUENCE">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
-               name="%command.name.UPDATE_CONSENSUS_SEQUENCE">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
-               name="%command.name.TOGGLE_SHOW_PROBABILITY_VALUES">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
-               name="%command.name.TOGGLE_SHOW_BASE_CALL_LINES">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
-               name="%command.name.CHANGE_QUALITY_OUTPUT">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
-               name="%command.name.LOAD_PHEROGRAM">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
-               name="%command.name.TOGGLE_INSERT_OVERWRITE">
-         </command>
-         <command
-               id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
-               name="%command.name.TOGGLE_LEFT_RIGHT_INSERTION">
-         </command>
-      </extension>
       <extension
             point="org.eclipse.ui.menus">
          <menuContribution
@@ -113,206 +37,35 @@
                </command>
             </toolbar>
          </menuContribution>
-         <menuContribution
-               allPopups="false"
-               locationURI="menu:org.eclipse.ui.main.menu">
-            <menu
-                  label="%menu.ALIGNMENT_EDITOR">
-               <command
-                     commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
-                     style="push">
-               </command>
-               <command
-                     commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
-                     id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
-                     name="Cut pherogram left">
-               </command>
-               <command
-                     commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
-                     id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
-                     style="push">
-               </command>
-               <command
-                     commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
-                     mnemonic="r"
-                     style="push">
-               </command>
-               <command
-                     commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
-                     style="push">
-               </command>
-               <command
-                     commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
-                     style="push">
-               </command>
-               <visibleWhen
-                     checkEnabled="true">
-                  <with
-                        variable="activePartId">
-                     <equals
-                           value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
-                     </equals>
-                  </with>
-               </visibleWhen>
-            </menu>
-            <menu
-                  label="%menu.label.PHEROGRAM_VIEW">
-               <command
-                     commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
-                     style="push">
-               </command>
-               <command
-                     commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
-                     style="push">
-               </command>
-               <command
-                     commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
-                     style="push">
-               </command>
-               <visibleWhen
-                     checkEnabled="true">
-                  <with
-                        variable="activePartId">
-                     <equals
-                           value="eu.etaxonomy.taxeditor.molecular.PherogramView">
-                     </equals>
-                  </with>
-               </visibleWhen>
-            </menu>
-         </menuContribution>
-         <menuContribution
-               locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView?before=eu.etaxonomy.taxeditor.editor.derivative.reuseSingleReadMenuItem">
-            <separator
-                  name="eu.etaxonomy.taxeditor.molecular.separator5"
-                  visible="true">
-            </separator>
-            <command
-                  commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
-                  label="%command.label.EDIT_SEQUENCE"
-                  style="push">
-               <visibleWhen
-                     checkEnabled="true">
-                  <reference
-                        definitionId="isSequence">
-                  </reference>
-               </visibleWhen>
-            </command>
-            <command
-                  commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
-                  label="%command.label.SHOW_PHEROGRAM"
-                  style="push">
-               <visibleWhen
-                     checkEnabled="true">
-                  <reference
-                        definitionId="isSingleRead">
-                  </reference>
-               </visibleWhen>
-            </command>
-         </menuContribution>
       </extension>
       <extension
-            point="org.eclipse.ui.handlers">
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
-            <activeWhen>
-               <with
-                     variable="activePartId">
-                  <equals
-                        value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
-                  </equals>
-               </with>
-            </activeWhen>
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
-               commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
-               commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCopyHandler"
-               commandId="org.eclipse.ui.edit.copy">
-            <activeWhen>
-               <with
-                     variable="activePartId">
-                  <equals
-                        value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
-                  </equals>
-               </with>
-            </activeWhen>
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCutHandler"
-               commandId="org.eclipse.ui.edit.cut">
-            <activeWhen>
-               <with
-                     variable="activePartId">
-                  <equals
-                        value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
-                  </equals>
-               </with>
-            </activeWhen>
-         </handler>
-         <handler
-               class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorPasteHandler"
-               commandId="org.eclipse.ui.edit.paste">
-            <activeWhen>
-               <with
-                     variable="activePartId">
-                  <equals
-                        value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
-                  </equals>
-               </with>
-            </activeWhen>
-         </handler>
+            id="id1"
+            point="org.eclipse.e4.workbench.model">
+         <fragment
+               apply="always"
+               uri="fragment.e4xmi">
+         </fragment>
       </extension>
       <extension
-            point="org.eclipse.ui.bindings">
-         <scheme
-               description="%scheme.description"
-               id="eu.etaxonomy.taxeditor.bindings.scheme.default"
-               name="%scheme.name">
-         </scheme>
-         <key
-               commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
-               schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
-               sequence="M1+O">
-         </key>
+            point="org.eclipse.core.expressions.definitions">
+         <definition
+               id="isAlignmentEditor">
+            <with
+                  variable="activePartId">
+               <equals
+                     value="eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4">
+               </equals>
+            </with>
+         </definition>
+         <definition
+               id="isPherogramView">
+            <with
+                  variable="activePartId">
+               <equals
+                     value="eu.etaxonomy.taxeditor.molecular.editor.e4.PherogramPartE4">
+               </equals>
+            </with>
+         </definition>
       </extension>
       
 </plugin>