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="%extension.name.0" id="eu.etaxonomy.taxeditor.markers.validationerror">
<super type="org.eclipse.core.resources.problemmarker"/>
<attribute name="databaseId"/>
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">
<visibleWhen
checkEnabled="true">
<and>
- <with
- variable="selection">
- <count
- value="+">
- </count>
- </with>
+ <with
+ variable="selection">
+ <count
+ value="+">
+ </count>
+ </with>
<reference
definitionId="isIndividualsAssociation">
</reference>
name="eu.etaxonomy.taxeditor.taxonDescriptionEditor.separator.afterNew"
visible="true">
</separator>
- <command
+ <command
commandId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.delete"
label="%command.label.30"
style="push">
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"
+ icon="icons/pherogram-insert-left-16x16.png"
+ 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">
value="eu.etaxonomy.taxeditor.editor.view.uses">
</equals>
</or>
- </with>
- </activeWhen>
+ </with>
+ </activeWhen>
</handler>
<handler
class="eu.etaxonomy.taxeditor.editor.key.polytomous.handler.DeleteNodeHandler"
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"
commandId="eu.etaxonomy.taxeditor.editor.view.derivate.command.delete">
class="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.ToggleShowOnlyIndividualAssociationsHandler"
commandId="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations">
</handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleInsertOverwriteHandler"
+ commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleLeftRightInsertionHandler"
+ commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion">
+ </handler>
</extension>
<extension
name="%extension.name"
id="eu.etaxonomy.taxeditor.editor.name.swapSynonymAndAccepted"
name="%command.name.6">
</command>
- <command
+ <command
categoryId="eu.etaxonomy.taxeditor.editor.taxon.name.command.category"
defaultHandler="eu.etaxonomy.taxeditor.editor.name.handler.MoveSynonymToAnotherAcceptedTaxonHandler"
id="eu.etaxonomy.taxeditor.editor.name.moveSynonymToAnotherAcceptedTaxon"
id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.adddescription"
name="%command.name.11">
</command>
- <command
- categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
+ <command
+ categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.DeleteHandler"
id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.delete"
name="%command.name.48">
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="%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"
id="eu.etaxonomy.taxeditor.description.commands.moveDescriptionElements"
name="%command.name.12">
</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">