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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%editor.ALIGNMENT_EDITOR">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%view.PHEROGRAM_VIEW"
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.EDIT_SEQUENCE">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.SHOW_PHEROGRAM">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.CUT_PHEROGRAM_LEFT">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.CUT_PHEROGRAM_RIGHT">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.REVERSE_COMPLEMENT_SELECTED_ROWS">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.CREATE_CONSENUS_SEQUENCE">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.UPDATE_CONSENSUS_SEQUENCE">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.TOGGLE_SHOW_PROBABILITY_VALUES">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.TOGGLE_SHOW_BASE_CALL_LINES">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.CHANGE_QUALITY_OUTPUT">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.LOAD_PHEROGRAM">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.TOGGLE_INSERT_OVERWRITE">
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29b09b3a
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Patric Plitzner
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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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5ac8a8c8
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Patrick Plitzner
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name="%command.name.TOGGLE_LEFT_RIGHT_INSERTION">
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29b09b3a
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Patric Plitzner
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</command>
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b4979250
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b.stoever
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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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29b09b3a
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Patric Plitzner
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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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91 |
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
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5ac8a8c8
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Patrick Plitzner
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label="%command.TOGGLE_INSERT_OVERWRITE"
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29b09b3a
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Patric Plitzner
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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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98 |
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variable="activePartId">
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99 |
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<equals
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100 |
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
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</equals>
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102 |
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</with>
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103 |
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</visibleWhen>
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104 |
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</command>
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105 |
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<command
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
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107 |
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icon="icons/pherogram-insert-left-16x16.png"
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108 |
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style="push">
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109 |
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<visibleWhen
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6fa5e6c3
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Patric Plitzner
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checkEnabled="true">
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29b09b3a
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Patric Plitzner
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<with
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112 |
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variable="activePartId">
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<equals
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114 |
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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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119 |
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</toolbar>
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120 |
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</menuContribution>
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121 |
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<menuContribution
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122 |
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allPopups="false"
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123 |
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locationURI="menu:org.eclipse.ui.main.menu">
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124 |
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<menu
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125 |
5ac8a8c8
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Patrick Plitzner
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label="%menu.ALIGNMENT_EDITOR">
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126 |
29b09b3a
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Patric Plitzner
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<command
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127 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
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128 |
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style="push">
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129 |
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</command>
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130 |
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<command
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131 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
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132 |
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
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name="Cut pherogram left">
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134 |
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</command>
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135 |
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<command
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136 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
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137 |
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id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
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138 |
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style="push">
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139 |
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</command>
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140 |
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<command
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141 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
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142 |
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mnemonic="r"
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143 |
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style="push">
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144 |
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</command>
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145 |
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<command
|
146 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
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147 |
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style="push">
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148 |
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</command>
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149 |
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<command
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150 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
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151 |
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style="push">
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152 |
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</command>
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153 |
a5e0f609
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Patric Plitzner
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<visibleWhen
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29b09b3a
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Patric Plitzner
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checkEnabled="true">
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<with
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156 |
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variable="activePartId">
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157 |
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<equals
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158 |
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
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</equals>
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</with>
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a5e0f609
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Patric Plitzner
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</visibleWhen>
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162 |
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</menu>
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163 |
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<menu
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164 |
5ac8a8c8
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Patrick Plitzner
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label="%menu.label.PHEROGRAM_VIEW">
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165 |
a5e0f609
|
Patric Plitzner
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<command
|
166 |
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commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
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167 |
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style="push">
|
168 |
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</command>
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169 |
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<command
|
170 |
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commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
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171 |
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style="push">
|
172 |
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</command>
|
173 |
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<command
|
174 |
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commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
|
175 |
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style="push">
|
176 |
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</command>
|
177 |
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<visibleWhen
|
178 |
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checkEnabled="true">
|
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<with
|
180 |
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variable="activePartId">
|
181 |
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<equals
|
182 |
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value="eu.etaxonomy.taxeditor.molecular.PherogramView">
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183 |
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</equals>
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184 |
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</with>
|
185 |
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</visibleWhen>
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186 |
29b09b3a
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Patric Plitzner
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</menu>
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187 |
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</menuContribution>
|
188 |
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<menuContribution
|
189 |
32746e43
|
Patrick Plitzner
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locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView?before=eu.etaxonomy.taxeditor.editor.derivative.reuseSingleReadMenuItem">
|
190 |
5d5c3c75
|
Patrick Plitzner
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<separator
|
191 |
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name="eu.etaxonomy.taxeditor.molecular.separator5"
|
192 |
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visible="true">
|
193 |
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</separator>
|
194 |
29b09b3a
|
Patric Plitzner
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<command
|
195 |
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commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
|
196 |
5ac8a8c8
|
Patrick Plitzner
|
label="%command.label.EDIT_SEQUENCE"
|
197 |
29b09b3a
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Patric Plitzner
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style="push">
|
198 |
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<visibleWhen
|
199 |
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checkEnabled="true">
|
200 |
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<reference
|
201 |
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definitionId="isSequence">
|
202 |
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</reference>
|
203 |
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</visibleWhen>
|
204 |
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</command>
|
205 |
b4979250
|
b.stoever
|
<command
|
206 |
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commandId="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile"
|
207 |
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label="%command.label.EXPORT_SEQUENCE_TO_FILE"
|
208 |
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style="push">
|
209 |
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<visibleWhen
|
210 |
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checkEnabled="true">
|
211 |
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<reference
|
212 |
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definitionId="isSequence">
|
213 |
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</reference>
|
214 |
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</visibleWhen>
|
215 |
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</command>
|
216 |
29b09b3a
|
Patric Plitzner
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<command
|
217 |
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commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
|
218 |
5ac8a8c8
|
Patrick Plitzner
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label="%command.label.SHOW_PHEROGRAM"
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219 |
29b09b3a
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Patric Plitzner
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style="push">
|
220 |
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<visibleWhen
|
221 |
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checkEnabled="true">
|
222 |
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<reference
|
223 |
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definitionId="isSingleRead">
|
224 |
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</reference>
|
225 |
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</visibleWhen>
|
226 |
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</command>
|
227 |
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</menuContribution>
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228 |
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</extension>
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229 |
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<extension
|
230 |
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point="org.eclipse.ui.handlers">
|
231 |
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<handler
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232 |
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class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
|
233 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
|
234 |
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<activeWhen>
|
235 |
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<with
|
236 |
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variable="activePartId">
|
237 |
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<equals
|
238 |
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
239 |
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</equals>
|
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</with>
|
241 |
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</activeWhen>
|
242 |
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</handler>
|
243 |
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<handler
|
244 |
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class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
|
245 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
|
246 |
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</handler>
|
247 |
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<handler
|
248 |
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class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
|
249 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
|
250 |
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</handler>
|
251 |
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<handler
|
252 |
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class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
|
253 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
|
254 |
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</handler>
|
255 |
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<handler
|
256 |
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class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
|
257 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
|
258 |
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</handler>
|
259 |
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<handler
|
260 |
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class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
|
261 |
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
|
262 |
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</handler>
|
263 |
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<handler
|
264 |
|
|
class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
|
265 |
|
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
|
266 |
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</handler>
|
267 |
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<handler
|
268 |
|
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class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
|
269 |
|
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commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
|
270 |
|
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</handler>
|
271 |
|
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<handler
|
272 |
|
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class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
|
273 |
|
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
|
274 |
|
|
</handler>
|
275 |
|
|
<handler
|
276 |
|
|
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
|
277 |
|
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
|
278 |
|
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</handler>
|
279 |
|
|
<handler
|
280 |
|
|
class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
|
281 |
|
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
|
282 |
|
|
</handler>
|
283 |
7929348c
|
Patrick Plitzner
|
<handler
|
284 |
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class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCopyHandler"
|
285 |
|
|
commandId="org.eclipse.ui.edit.copy">
|
286 |
65fe133d
|
b.stoever
|
<activeWhen>
|
287 |
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<with
|
288 |
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variable="activePartId">
|
289 |
|
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<equals
|
290 |
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
291 |
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</equals>
|
292 |
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</with>
|
293 |
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</activeWhen>
|
294 |
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</handler>
|
295 |
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<handler
|
296 |
|
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class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCutHandler"
|
297 |
|
|
commandId="org.eclipse.ui.edit.cut">
|
298 |
ab9f98b3
|
b.stoever
|
<activeWhen>
|
299 |
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<with
|
300 |
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variable="activePartId">
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301 |
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<equals
|
302 |
|
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value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
303 |
|
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</equals>
|
304 |
|
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</with>
|
305 |
|
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</activeWhen>
|
306 |
|
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</handler>
|
307 |
|
|
<handler
|
308 |
|
|
class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorPasteHandler"
|
309 |
|
|
commandId="org.eclipse.ui.edit.paste">
|
310 |
7929348c
|
Patrick Plitzner
|
<activeWhen>
|
311 |
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|
<with
|
312 |
|
|
variable="activePartId">
|
313 |
|
|
<equals
|
314 |
|
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
315 |
|
|
</equals>
|
316 |
|
|
</with>
|
317 |
|
|
</activeWhen>
|
318 |
|
|
</handler>
|
319 |
29b09b3a
|
Patric Plitzner
|
</extension>
|
320 |
|
|
<extension
|
321 |
|
|
point="org.eclipse.ui.bindings">
|
322 |
|
|
<scheme
|
323 |
|
|
description="%scheme.description"
|
324 |
|
|
id="eu.etaxonomy.taxeditor.bindings.scheme.default"
|
325 |
|
|
name="%scheme.name">
|
326 |
|
|
</scheme>
|
327 |
|
|
<key
|
328 |
|
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
|
329 |
|
|
schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
|
330 |
|
|
sequence="M1+O">
|
331 |
|
|
</key>
|
332 |
|
|
</extension>
|
333 |
|
|
|
334 |
|
|
</plugin>
|