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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="%editor.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="%view.PHEROGRAM_VIEW"
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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="%command.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="%command.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="%command.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="%command.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="%command.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="%command.name.CREATE_CONSENUS_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="%command.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="%command.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="%command.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="%command.name.CHANGE_QUALITY_OUTPUT">
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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="%command.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="%command.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="%command.name.TOGGLE_LEFT_RIGHT_INSERTION">
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</command>
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<command
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defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler"
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id="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile"
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name="%command.name.EXPORT_SEQUENCE_TO_FILE">
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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="%command.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="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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</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="%menu.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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<menu
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label="%menu.label.PHEROGRAM_VIEW">
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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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<equals
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value="eu.etaxonomy.taxeditor.molecular.PherogramView">
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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?before=eu.etaxonomy.taxeditor.editor.derivative.reuseSingleReadMenuItem">
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<separator
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name="eu.etaxonomy.taxeditor.molecular.separator5"
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visible="true">
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</separator>
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
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label="%command.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.exportSequenceToFile"
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label="%command.label.EXPORT_SEQUENCE_TO_FILE"
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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="%command.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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<handler
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class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCopyHandler"
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commandId="org.eclipse.ui.edit.copy">
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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.AlignmentEditorCutHandler"
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commandId="org.eclipse.ui.edit.cut">
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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.AlignmentEditorPasteHandler"
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commandId="org.eclipse.ui.edit.paste">
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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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</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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