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[taxeditor.git] / eu.etaxonomy.taxeditor.molecular / fragment.e4xmi
diff --git a/eu.etaxonomy.taxeditor.molecular/fragment.e4xmi b/eu.etaxonomy.taxeditor.molecular/fragment.e4xmi
index 00286584be4120bb99eb6d9b1c9f15f74b829704..ddb671b5b281649d6e4c72b1e30edb2f38a5f7e9 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/fragment.e4xmi
+++ b/eu.etaxonomy.taxeditor.molecular/fragment.e4xmi
@@ -1,18 +1,69 @@
 <?xml version="1.0" encoding="ASCII"?>
-<fragment:ModelFragments xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:commands="http://www.eclipse.org/ui/2010/UIModel/application/commands" xmlns:fragment="http://www.eclipse.org/ui/2010/UIModel/fragment" xmlns:menu="http://www.eclipse.org/ui/2010/UIModel/application/ui/menu" xmi:id="_OhwnQCTfEeeiN5lBIuqN3g">
+<fragment:ModelFragments xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:basic="http://www.eclipse.org/ui/2010/UIModel/application/descriptor/basic" xmlns:commands="http://www.eclipse.org/ui/2010/UIModel/application/commands" xmlns:fragment="http://www.eclipse.org/ui/2010/UIModel/fragment" xmlns:menu="http://www.eclipse.org/ui/2010/UIModel/application/ui/menu" xmlns:ui="http://www.eclipse.org/ui/2010/UIModel/application/ui" xmi:id="_OhwnQCTfEeeiN5lBIuqN3g">
+  <imports xsi:type="commands:Command" xmi:id="_q2vnsKUDEeejf7ggYkp-TA" elementId="org.eclipse.ui.edit.copy"/>
+  <imports xsi:type="commands:Command" xmi:id="_rlhZQKUDEeejf7ggYkp-TA" elementId="org.eclipse.ui.edit.cut"/>
+  <imports xsi:type="commands:Command" xmi:id="_tLkxEKUDEeejf7ggYkp-TA" elementId="org.eclipse.ui.edit.paste"/>
   <fragments xsi:type="fragment:StringModelFragment" xmi:id="__mwtMDVpEee_b7RlBzTDRw" featurename="commands" parentElementId="xpath:/">
     <elements xsi:type="commands:Command" xmi:id="_JZdQ0H2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.editSequence" commandName="%command.EDIT_SEQUENCE"/>
     <elements xsi:type="commands:Command" xmi:id="_IXQocH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile" commandName="%command.label.EXPORT_SEQUENCE_TO_FILE"/>
     <elements xsi:type="commands:Command" xmi:id="_m9gZAH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.showPherogram" commandName="%command.name.SHOW_PHEROGRAM"/>
+    <elements xsi:type="commands:Command" xmi:id="_YLPrgKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft" commandName="%command.name.CUT_PHEROGRAM_LEFT"/>
+    <elements xsi:type="commands:Command" xmi:id="_akezwKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight" commandName="%command.name.CUT_PHEROGRAM_RIGHT"/>
+    <elements xsi:type="commands:Command" xmi:id="_cnIoAKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows" commandName="%command.name.REVERSE_COMPLEMENT_SELECTED_ROWS"/>
+    <elements xsi:type="commands:Command" xmi:id="_d28DAKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus" commandName="%command.name.CREATE_CONSENUS_SEQUENCE"/>
+    <elements xsi:type="commands:Command" xmi:id="_gnsTYKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus" commandName="%command.name.UPDATE_CONSENSUS_SEQUENCE"/>
+    <elements xsi:type="commands:Command" xmi:id="_h1lC0KT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities" commandName="%command.name.TOGGLE_SHOW_PROBABILITY_VALUES"/>
+    <elements xsi:type="commands:Command" xmi:id="_j-w84KT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines" commandName="%command.name.TOGGLE_SHOW_BASE_CALL_LINES"/>
+    <elements xsi:type="commands:Command" xmi:id="_lyJmEKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput" commandName="%command.name.CHANGE_QUALITY_OUTPUT"/>
+    <elements xsi:type="commands:Command" xmi:id="_ncVP8KT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram" commandName="%command.name.LOAD_PHEROGRAM"/>
+    <elements xsi:type="commands:Command" xmi:id="_pfKDUKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite" commandName="%command.name.TOGGLE_INSERT_OVERWRITE"/>
+    <elements xsi:type="commands:Command" xmi:id="_rz8wcKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion" commandName="%command.name.TOGGLE_LEFT_RIGHT_INSERTION"/>
   </fragments>
   <fragments xsi:type="fragment:StringModelFragment" xmi:id="_RCmzgH2sEeeVL5aZ55YsWA" featurename="handlers" parentElementId="eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView">
-    <elements xsi:type="commands:Handler" xmi:id="_XuBioH2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler" command="_JZdQ0H2sEeeVL5aZ55YsWA"/>
-    <elements xsi:type="commands:Handler" xmi:id="_QwuNwH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler" command="_IXQocH22EeeVL5aZ55YsWA"/>
-    <elements xsi:type="commands:Handler" xmi:id="_reIrkH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler" command="_m9gZAH22EeeVL5aZ55YsWA"/>
+    <elements xsi:type="commands:Handler" xmi:id="_XuBioH2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.EditSequenceHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.EditSequenceHandlerE4" command="_JZdQ0H2sEeeVL5aZ55YsWA"/>
+    <elements xsi:type="commands:Handler" xmi:id="_QwuNwH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ExportSequenceToFileHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ExportSequenceToFileHandlerE4" command="_IXQocH22EeeVL5aZ55YsWA"/>
+    <elements xsi:type="commands:Handler" xmi:id="_reIrkH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ShowPherogramHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ShowPherogramHandlerE4" command="_m9gZAH22EeeVL5aZ55YsWA"/>
   </fragments>
   <fragments xsi:type="fragment:StringModelFragment" xmi:id="_o08AQH2sEeeVL5aZ55YsWA" featurename="children" parentElementId="eu.etaxonomy.taxeditor.editor.popupmenu.specimeneditor" positionInList="before:eu.etaxonomy.taxeditor.editor.menuseparator.beforeDelete">
     <elements xsi:type="menu:HandledMenuItem" xmi:id="_txARoH2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.commandlabeledit_sequence" label="%command.label.EDIT_SEQUENCE" command="_JZdQ0H2sEeeVL5aZ55YsWA"/>
     <elements xsi:type="menu:HandledMenuItem" xmi:id="_VRC-UH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.commandlabelexport_sequence_to_file" label="%command.label.EXPORT_SEQUENCE_TO_FILE" command="_IXQocH22EeeVL5aZ55YsWA"/>
     <elements xsi:type="menu:HandledMenuItem" xmi:id="_xftzgH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.commandnameshow_pherogram" label="%command.name.SHOW_PHEROGRAM" command="_m9gZAH22EeeVL5aZ55YsWA"/>
   </fragments>
+  <fragments xsi:type="fragment:StringModelFragment" xmi:id="_paaYIKT5Eeejf7ggYkp-TA" featurename="descriptors" parentElementId="xpath:/">
+    <elements xsi:type="basic:PartDescriptor" xmi:id="_sAK5cKT5Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4" label="%editor.ALIGNMENT_EDITOR" closeable="true" dirtyable="true" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4">
+      <handlers xmi:id="_8S4OwKUAEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.UpdateConsensusSequenceHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.UpdateConsensusSequenceHandlerE4" command="_gnsTYKT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="__mR5MKUAEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CreateConsensusSequenceHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CreateConsensusSequenceHandlerE4" command="_d28DAKT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="_DD3aYKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ReverseComplementHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ReverseComplementHandlerE4" command="_cnIoAKT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="_FoONgKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CutPherogramRightHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CutPherogramRightHandlerE4" command="_akezwKT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="_I78oEKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CutPherogramLeftHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CutPherogramLeftHandlerE4" command="_YLPrgKT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="_NLSWUKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleLeftRightInsertionHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleLeftRightInsertionHandlerE4" command="_rz8wcKT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="_WV0zQKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleInsertOverwriteHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleInsertOverwriteHandlerE4" command="_pfKDUKT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="_ar1KMKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.LoadPherogramHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.LoadPherogramHandlerE4" command="_ncVP8KT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="_myRFoKUDEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorCutHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorCutHandlerE4" command="_rlhZQKUDEeejf7ggYkp-TA"/>
+      <handlers xmi:id="_vvnbIKUDEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorCopyHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorCopyHandlerE4" command="_q2vnsKUDEeejf7ggYkp-TA"/>
+      <handlers xmi:id="_x70M8KUDEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorPasteHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorPasteHandlerE4" command="_tLkxEKUDEeejf7ggYkp-TA"/>
+    </elements>
+    <elements xsi:type="basic:PartDescriptor" xmi:id="_v8GjgKT5Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.PherogramPartE4" label="%view.PHEROGRAM_VIEW" allowMultiple="true" closeable="true" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.PherogramPartE4">
+      <handlers xmi:id="_6ioEAKT-Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleShowPherogramProbabilitiesHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleShowPherogramProbabilitiesHandlerE4" command="_h1lC0KT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="_-IewYKT-Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleShowPherogramBaseCallLinesHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleShowPherogramBaseCallLinesHandlerE4" command="_j-w84KT7Eeejf7ggYkp-TA"/>
+      <handlers xmi:id="_36J7AKUAEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ChangePherogramQualityOutputTypeE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ChangePherogramQualityOutputTypeE4" command="_lyJmEKT7Eeejf7ggYkp-TA"/>
+    </elements>
+  </fragments>
+  <fragments xsi:type="fragment:StringModelFragment" xmi:id="_1hS_gKT7Eeejf7ggYkp-TA" featurename="children" parentElementId="eu.etaxonomy.taxeditor.workbench.menu">
+    <elements xsi:type="menu:Menu" xmi:id="_nWX8cKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.menu.editoralignment_editor" label="%editor.ALIGNMENT_EDITOR">
+      <visibleWhen xsi:type="ui:CoreExpression" xmi:id="_wWCx4KUXEeejf7ggYkp-TA" coreExpressionId="isAlignmentEditor"/>
+      <children xsi:type="menu:HandledMenuItem" xmi:id="__HWTwKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.loadpherogram" label="%command.name.LOAD_PHEROGRAM" command="_ncVP8KT7Eeejf7ggYkp-TA"/>
+      <children xsi:type="menu:HandledMenuItem" xmi:id="_J3mKQKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.cutleft" label="%command.name.CUT_PHEROGRAM_LEFT" command="_YLPrgKT7Eeejf7ggYkp-TA"/>
+      <children xsi:type="menu:HandledMenuItem" xmi:id="_OCpOYKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.cutright" label="%command.name.CUT_PHEROGRAM_RIGHT" command="_akezwKT7Eeejf7ggYkp-TA"/>
+      <children xsi:type="menu:HandledMenuItem" xmi:id="_PYK24KT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.reversecomplement" label="%command.name.REVERSE_COMPLEMENT_SELECTED_ROWS" command="_cnIoAKT7Eeejf7ggYkp-TA"/>
+      <children xsi:type="menu:HandledMenuItem" xmi:id="_RRcFoKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.createconsensus" label="%command.name.CREATE_CONSENUS_SEQUENCE" command="_d28DAKT7Eeejf7ggYkp-TA"/>
+      <children xsi:type="menu:HandledMenuItem" xmi:id="_TUGg8KT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.updateconsensus" label="%command.name.UPDATE_CONSENSUS_SEQUENCE" command="_gnsTYKT7Eeejf7ggYkp-TA"/>
+    </elements>
+    <elements xsi:type="menu:Menu" xmi:id="_yuMJQKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.menu.viewpherogram_view" label="%view.PHEROGRAM_VIEW">
+      <visibleWhen xsi:type="ui:CoreExpression" xmi:id="_45_BMKjuEeejedk4mZQIGw" coreExpressionId="isPherogramView"/>
+      <children xsi:type="menu:HandledMenuItem" xmi:id="_0r-EkKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.pherogrameditor.changeQuality" label="%command.name.CHANGE_QUALITY_OUTPUT" command="_lyJmEKT7Eeejf7ggYkp-TA"/>
+      <children xsi:type="menu:HandledMenuItem" xmi:id="_7_ShMKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.pherogrameditor.toggleProbabilities" label="%command.name.TOGGLE_SHOW_PROBABILITY_VALUES" command="_h1lC0KT7Eeejf7ggYkp-TA"/>
+      <children xsi:type="menu:HandledMenuItem" xmi:id="_93JasKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.pherogrameditor.toggleBaseCallLines" label="%command.name.TOGGLE_SHOW_BASE_CALL_LINES" command="_j-w84KT7Eeejf7ggYkp-TA"/>
+    </elements>
+  </fragments>
 </fragment:ModelFragments>