--- /dev/null
+<?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="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="PherogramView"
+ 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="Edit Sequence">
+ </command>
+ <command
+ defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler"
+ id="eu.etaxonomy.taxeditor.molecular.showPherogram"
+ name="Show Pherogram">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
+ name="Cut pherogram left">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
+ name="Cut pherogram right">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
+ name="Reverse complement selected rows">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
+ name="(Re)create consensus sequence">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
+ name="Update consensus sequence">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
+ name="Toggle show probability values">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
+ name="Toggle show base call lines">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
+ name="Change quality output">
+ </command>
+ <command
+ defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.OpenAlignmentEditorHandler"
+ id="eu.etaxonomy.taxeditor.molecular.OpenAlignmentEditor"
+ name="Open Alignment Editor">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
+ name="Load Pherogram">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
+ name="Toggle insert/overwrite">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
+ name="Toggle left/right insertion in base call sequence">
+ </command>
+ </extension>
+ <extension
+ point="org.eclipse.ui.menus">
+ <menuContribution
+ locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
+ <toolbar
+ id="eu.etaxonomy.taxeditor.molecular.alignmentToolbar">
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
+ label="Toggle insert/overwrite"
+ style="push">
+ <visibleWhen
+ checkEnabled="true">
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ </with>
+ </visibleWhen>
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
+ icon="icons/pherogram-insert-left-16x16.png"
+ style="push">
+ <visibleWhen
+ checkEnabled="false">
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ </with>
+ </visibleWhen>
+ </command>
+ </toolbar>
+ </menuContribution>
+ <menuContribution
+ allPopups="false"
+ locationURI="menu:org.eclipse.ui.main.menu">
+ <menu
+ label="View">
+ <menu
+ label="Pherogram">
+ <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">
+ <or>
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.PherogramView">
+ </equals>
+ </or>
+ </with>
+ </visibleWhen>
+ </menu>
+ </menu>
+ <menu
+ label="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>
+ </menuContribution>
+ <menuContribution
+ locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView">
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
+ label="Edit Sequence"
+ style="push">
+ <visibleWhen
+ checkEnabled="true">
+ <reference
+ definitionId="isSequence">
+ </reference>
+ </visibleWhen>
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
+ 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>
+ </extension>
+ <extension
+ point="org.eclipse.core.expressions.definitions">
+ <definition
+ id="isSequence">
+ <with
+ variable="selection">
+ <test
+ property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSequence">
+ </test>
+ </with>
+ </definition>
+ <definition
+ id="isSingleRead">
+ <with
+ variable="selection">
+ <test
+ property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSingleRead">
+ </test>
+ </with>
+ </definition>
+ </extension>
+ <extension
+ point="org.eclipse.core.expressions.propertyTesters">
+ <propertyTester
+ class="eu.etaxonomy.taxeditor.molecular.handler.SpecimenPropertyTester"
+ id="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
+ namespace="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
+ properties="isSequence,isSingleRead"
+ type="org.eclipse.jface.viewers.IStructuredSelection">
+ </propertyTester>
+ </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>
+ </extension>
+
+</plugin>
BGBM BDI Projects / taxeditor.git / blobdiff