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<?xml version="1.0" encoding="UTF-8"?>
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<?eclipse version="3.4"?>
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<plugin>
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<extension
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point="org.eclipse.ui.editors">
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<editor
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class="eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor"
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default="false"
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"
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name="Alignment Editor">
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</editor>
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</extension>
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<extension
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point="org.eclipse.ui.views">
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<view
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allowMultiple="true"
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class="eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart"
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id="eu.etaxonomy.taxeditor.molecular.PherogramView"
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name="PherogramView"
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restorable="true">
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</view>
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</extension>
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<extension
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point="org.eclipse.ui.commands">
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<command
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defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler"
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id="eu.etaxonomy.taxeditor.molecular.editSequence"
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name="Edit Sequence">
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</command>
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<command
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defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler"
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id="eu.etaxonomy.taxeditor.molecular.showPherogram"
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name="Show Pherogram">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
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name="Cut pherogram left">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
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name="Cut pherogram right">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
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name="Reverse complement selected rows">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
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name="(Re)create consensus sequence">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
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name="Update consensus sequence">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
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name="Toggle show probability values">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
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name="Toggle show base call lines">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
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name="Change quality output">
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</command>
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<command
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defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.OpenAlignmentEditorHandler"
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id="eu.etaxonomy.taxeditor.molecular.OpenAlignmentEditor"
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name="Open Alignment Editor">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
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name="Load Pherogram">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
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name="Toggle insert/overwrite">
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</command>
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<command
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
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name="Toggle left/right insertion in base call sequence">
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</command>
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</extension>
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<extension
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point="org.eclipse.ui.menus">
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<menuContribution
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locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
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<toolbar
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id="eu.etaxonomy.taxeditor.molecular.alignmentToolbar">
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
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label="Toggle insert/overwrite"
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style="push">
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<visibleWhen
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checkEnabled="true">
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<with
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variable="activePartId">
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<equals
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
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</equals>
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</with>
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</visibleWhen>
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</command>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
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icon="icons/pherogram-insert-left-16x16.png"
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style="push">
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<visibleWhen
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checkEnabled="false">
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<with
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variable="activePartId">
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<equals
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
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</equals>
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</with>
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</visibleWhen>
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</command>
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</toolbar>
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</menuContribution>
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<menuContribution
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allPopups="false"
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locationURI="menu:org.eclipse.ui.main.menu">
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<menu
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label="View">
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<menu
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label="Pherogram">
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
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style="push">
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</command>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
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style="push">
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</command>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
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style="push">
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</command>
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<visibleWhen
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checkEnabled="true">
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<with
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variable="activePartId">
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<or>
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<equals
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
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</equals>
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<equals
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value="eu.etaxonomy.taxeditor.molecular.PherogramView">
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</equals>
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</or>
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</with>
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</visibleWhen>
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</menu>
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</menu>
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<menu
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label="Alignment Editor">
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
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style="push">
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</command>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
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name="Cut pherogram left">
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</command>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
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style="push">
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</command>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
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mnemonic="r"
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style="push">
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</command>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
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style="push">
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</command>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
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style="push">
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</command>
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<visibleWhen
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checkEnabled="true">
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<with
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variable="activePartId">
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<equals
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
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</equals>
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</with>
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</visibleWhen>
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</menu>
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</menuContribution>
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<menuContribution
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locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView">
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
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label="Edit Sequence"
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style="push">
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<visibleWhen
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checkEnabled="true">
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<reference
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definitionId="isSequence">
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</reference>
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</visibleWhen>
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</command>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
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label="Show Pherogram"
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style="push">
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<visibleWhen
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checkEnabled="true">
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<reference
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definitionId="isSingleRead">
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</reference>
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</visibleWhen>
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</command>
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</menuContribution>
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</extension>
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<extension
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point="org.eclipse.ui.handlers">
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
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<activeWhen>
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<with
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variable="activePartId">
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<equals
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
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</equals>
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</with>
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</activeWhen>
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
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commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
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</handler>
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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
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commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
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</handler>
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</extension>
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<extension
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point="org.eclipse.core.expressions.definitions">
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<definition
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id="isSequence">
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<with
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variable="selection">
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<test
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property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSequence">
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</test>
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</with>
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</definition>
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<definition
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id="isSingleRead">
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<with
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variable="selection">
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<test
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property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSingleRead">
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</test>
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</with>
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</definition>
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</extension>
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<extension
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point="org.eclipse.core.expressions.propertyTesters">
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<propertyTester
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class="eu.etaxonomy.taxeditor.molecular.handler.SpecimenPropertyTester"
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id="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
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namespace="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
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properties="isSequence,isSingleRead"
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type="org.eclipse.jface.viewers.IStructuredSelection">
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</propertyTester>
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</extension>
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<extension
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point="org.eclipse.ui.bindings">
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<scheme
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description="%scheme.description"
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id="eu.etaxonomy.taxeditor.bindings.scheme.default"
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name="%scheme.name">
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</scheme>
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<key
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
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schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
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sequence="M1+O">
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</key>
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</extension>
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</plugin>
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