Revision 960d1a20
Added by Patrick Plitzner over 6 years ago
eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF | ||
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19 | 19 |
org.eclipse.core.databinding.property;bundle-version="1.4.0", |
20 | 20 |
org.eclipse.e4.core.di.annotations, |
21 | 21 |
org.eclipse.e4.ui.services, |
22 |
org.eclipse.e4.ui.model.workbench |
|
22 |
org.eclipse.e4.ui.model.workbench, |
|
23 |
org.eclipse.e4.ui.workbench, |
|
24 |
org.eclipse.e4.ui.di |
|
23 | 25 |
Bundle-RequiredExecutionEnvironment: JavaSE-1.8 |
24 | 26 |
Bundle-ActivationPolicy: lazy |
25 | 27 |
Bundle-Vendor: EDIT |
eu.etaxonomy.taxeditor.molecular/fragment.e4xmi | ||
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1 | 1 |
<?xml version="1.0" encoding="ASCII"?> |
2 |
<fragment:ModelFragments xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:commands="http://www.eclipse.org/ui/2010/UIModel/application/commands" xmlns:fragment="http://www.eclipse.org/ui/2010/UIModel/fragment" xmlns:menu="http://www.eclipse.org/ui/2010/UIModel/application/ui/menu" xmi:id="_OhwnQCTfEeeiN5lBIuqN3g"> |
|
2 |
<fragment:ModelFragments xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:basic="http://www.eclipse.org/ui/2010/UIModel/application/descriptor/basic" xmlns:commands="http://www.eclipse.org/ui/2010/UIModel/application/commands" xmlns:fragment="http://www.eclipse.org/ui/2010/UIModel/fragment" xmlns:menu="http://www.eclipse.org/ui/2010/UIModel/application/ui/menu" xmlns:ui="http://www.eclipse.org/ui/2010/UIModel/application/ui" xmi:id="_OhwnQCTfEeeiN5lBIuqN3g"> |
|
3 |
<imports xsi:type="commands:Command" xmi:id="_q2vnsKUDEeejf7ggYkp-TA" elementId="org.eclipse.ui.edit.copy"/> |
|
4 |
<imports xsi:type="commands:Command" xmi:id="_rlhZQKUDEeejf7ggYkp-TA" elementId="org.eclipse.ui.edit.cut"/> |
|
5 |
<imports xsi:type="commands:Command" xmi:id="_tLkxEKUDEeejf7ggYkp-TA" elementId="org.eclipse.ui.edit.paste"/> |
|
3 | 6 |
<fragments xsi:type="fragment:StringModelFragment" xmi:id="__mwtMDVpEee_b7RlBzTDRw" featurename="commands" parentElementId="xpath:/"> |
4 | 7 |
<elements xsi:type="commands:Command" xmi:id="_JZdQ0H2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.editSequence" commandName="%command.EDIT_SEQUENCE"/> |
5 | 8 |
<elements xsi:type="commands:Command" xmi:id="_IXQocH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile" commandName="%command.label.EXPORT_SEQUENCE_TO_FILE"/> |
6 | 9 |
<elements xsi:type="commands:Command" xmi:id="_m9gZAH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.showPherogram" commandName="%command.name.SHOW_PHEROGRAM"/> |
10 |
<elements xsi:type="commands:Command" xmi:id="_YLPrgKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft" commandName="%command.name.CUT_PHEROGRAM_LEFT"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_akezwKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight" commandName="%command.name.CUT_PHEROGRAM_RIGHT"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_cnIoAKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows" commandName="%command.name.REVERSE_COMPLEMENT_SELECTED_ROWS"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_d28DAKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus" commandName="%command.name.CREATE_CONSENUS_SEQUENCE"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_gnsTYKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus" commandName="%command.name.UPDATE_CONSENSUS_SEQUENCE"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_h1lC0KT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities" commandName="%command.name.TOGGLE_SHOW_PROBABILITY_VALUES"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_j-w84KT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines" commandName="%command.name.TOGGLE_SHOW_BASE_CALL_LINES"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_lyJmEKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput" commandName="%command.name.CHANGE_QUALITY_OUTPUT"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_ncVP8KT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram" commandName="%command.name.LOAD_PHEROGRAM"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_pfKDUKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite" commandName="%command.name.TOGGLE_INSERT_OVERWRITE"/> |
|
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<elements xsi:type="commands:Command" xmi:id="_rz8wcKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion" commandName="%command.name.TOGGLE_LEFT_RIGHT_INSERTION"/> |
|
7 | 21 |
</fragments> |
8 | 22 |
<fragments xsi:type="fragment:StringModelFragment" xmi:id="_RCmzgH2sEeeVL5aZ55YsWA" featurename="handlers" parentElementId="eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView"> |
9 |
<elements xsi:type="commands:Handler" xmi:id="_XuBioH2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler" command="_JZdQ0H2sEeeVL5aZ55YsWA"/>
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|
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<elements xsi:type="commands:Handler" xmi:id="_QwuNwH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler" command="_IXQocH22EeeVL5aZ55YsWA"/>
|
|
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<elements xsi:type="commands:Handler" xmi:id="_reIrkH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler" command="_m9gZAH22EeeVL5aZ55YsWA"/>
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|
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<elements xsi:type="commands:Handler" xmi:id="_XuBioH2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.EditSequenceHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.EditSequenceHandlerE4" command="_JZdQ0H2sEeeVL5aZ55YsWA"/>
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|
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<elements xsi:type="commands:Handler" xmi:id="_QwuNwH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ExportSequenceToFileHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ExportSequenceToFileHandlerE4" command="_IXQocH22EeeVL5aZ55YsWA"/>
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|
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<elements xsi:type="commands:Handler" xmi:id="_reIrkH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ShowPherogramHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ShowPherogramHandlerE4" command="_m9gZAH22EeeVL5aZ55YsWA"/>
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|
12 | 26 |
</fragments> |
13 | 27 |
<fragments xsi:type="fragment:StringModelFragment" xmi:id="_o08AQH2sEeeVL5aZ55YsWA" featurename="children" parentElementId="eu.etaxonomy.taxeditor.editor.popupmenu.specimeneditor" positionInList="before:eu.etaxonomy.taxeditor.editor.menuseparator.beforeDelete"> |
14 | 28 |
<elements xsi:type="menu:HandledMenuItem" xmi:id="_txARoH2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.commandlabeledit_sequence" label="%command.label.EDIT_SEQUENCE" command="_JZdQ0H2sEeeVL5aZ55YsWA"/> |
15 | 29 |
<elements xsi:type="menu:HandledMenuItem" xmi:id="_VRC-UH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.commandlabelexport_sequence_to_file" label="%command.label.EXPORT_SEQUENCE_TO_FILE" command="_IXQocH22EeeVL5aZ55YsWA"/> |
16 | 30 |
<elements xsi:type="menu:HandledMenuItem" xmi:id="_xftzgH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.commandnameshow_pherogram" label="%command.name.SHOW_PHEROGRAM" command="_m9gZAH22EeeVL5aZ55YsWA"/> |
17 | 31 |
</fragments> |
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<fragments xsi:type="fragment:StringModelFragment" xmi:id="_paaYIKT5Eeejf7ggYkp-TA" featurename="descriptors" parentElementId="org.eclipse.e4.legacy.ide.application"> |
|
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<elements xsi:type="basic:PartDescriptor" xmi:id="_sAK5cKT5Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4" label="%editor.ALIGNMENT_EDITOR" closeable="true" dirtyable="true" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4"> |
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<handlers xmi:id="_8S4OwKUAEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.UpdateConsensusSequenceHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.UpdateConsensusSequenceHandlerE4" command="_gnsTYKT7Eeejf7ggYkp-TA"/> |
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<handlers xmi:id="__mR5MKUAEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CreateConsensusSequenceHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CreateConsensusSequenceHandlerE4" command="_d28DAKT7Eeejf7ggYkp-TA"/> |
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<handlers xmi:id="_DD3aYKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ReverseComplementHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ReverseComplementHandlerE4" command="_cnIoAKT7Eeejf7ggYkp-TA"/> |
|
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<handlers xmi:id="_FoONgKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CutPherogramRightHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CutPherogramRightHandlerE4" command="_akezwKT7Eeejf7ggYkp-TA"/> |
|
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<handlers xmi:id="_I78oEKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CutPherogramLeftHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.CutPherogramLeftHandlerE4" command="_YLPrgKT7Eeejf7ggYkp-TA"/> |
|
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<handlers xmi:id="_NLSWUKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleLeftRightInsertionHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleLeftRightInsertionHandlerE4" command="_rz8wcKT7Eeejf7ggYkp-TA"/> |
|
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<handlers xmi:id="_WV0zQKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleInsertOverwriteHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleInsertOverwriteHandlerE4" command="_pfKDUKT7Eeejf7ggYkp-TA"/> |
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<handlers xmi:id="_ar1KMKUBEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.LoadPherogramHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.LoadPherogramHandlerE4" command="_ncVP8KT7Eeejf7ggYkp-TA"/> |
|
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<handlers xmi:id="_myRFoKUDEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorCutHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorCutHandlerE4" command="_rlhZQKUDEeejf7ggYkp-TA"/> |
|
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<handlers xmi:id="_vvnbIKUDEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorCopyHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorCopyHandlerE4" command="_q2vnsKUDEeejf7ggYkp-TA"/> |
|
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<handlers xmi:id="_x70M8KUDEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorPasteHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.AlignmentEditorPasteHandlerE4" command="_tLkxEKUDEeejf7ggYkp-TA"/> |
|
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</elements> |
|
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<elements xsi:type="basic:PartDescriptor" xmi:id="_v8GjgKT5Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.PherogramPartE4" label="%view.PHEROGRAM_VIEW" allowMultiple="true" closeable="true" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.PherogramPartE4"> |
|
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<handlers xmi:id="_6ioEAKT-Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleShowPherogramProbabilitiesHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleShowPherogramProbabilitiesHandlerE4" command="_h1lC0KT7Eeejf7ggYkp-TA"/> |
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<handlers xmi:id="_-IewYKT-Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleShowPherogramBaseCallLinesHandlerE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleShowPherogramBaseCallLinesHandlerE4" command="_j-w84KT7Eeejf7ggYkp-TA"/> |
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<handlers xmi:id="_36J7AKUAEeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ChangePherogramQualityOutputTypeE4" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ChangePherogramQualityOutputTypeE4" command="_lyJmEKT7Eeejf7ggYkp-TA"/> |
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</elements> |
|
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</fragments> |
|
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<fragments xsi:type="fragment:StringModelFragment" xmi:id="_1hS_gKT7Eeejf7ggYkp-TA" featurename="children" parentElementId="eu.etaxonomy.taxeditor.workbench.menu"> |
|
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<elements xsi:type="menu:Menu" xmi:id="_nWX8cKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.menu.editoralignment_editor" label="%editor.ALIGNMENT_EDITOR"> |
|
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<visibleWhen xsi:type="ui:CoreExpression" xmi:id="_wWCx4KUXEeejf7ggYkp-TA"/> |
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<children xsi:type="menu:HandledMenuItem" xmi:id="__HWTwKT7Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.loadpherogram" label="%command.name.LOAD_PHEROGRAM" command="_ncVP8KT7Eeejf7ggYkp-TA"/> |
|
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<children xsi:type="menu:HandledMenuItem" xmi:id="_J3mKQKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.cutleft" label="%command.name.CUT_PHEROGRAM_LEFT" command="_YLPrgKT7Eeejf7ggYkp-TA"/> |
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<children xsi:type="menu:HandledMenuItem" xmi:id="_OCpOYKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.cutright" label="%command.name.CUT_PHEROGRAM_RIGHT" command="_akezwKT7Eeejf7ggYkp-TA"/> |
|
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<children xsi:type="menu:HandledMenuItem" xmi:id="_PYK24KT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.reversecomplement" label="%command.name.REVERSE_COMPLEMENT_SELECTED_ROWS" command="_cnIoAKT7Eeejf7ggYkp-TA"/> |
|
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<children xsi:type="menu:HandledMenuItem" xmi:id="_RRcFoKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.createconsensus" label="%command.name.CREATE_CONSENUS_SEQUENCE" command="_d28DAKT7Eeejf7ggYkp-TA"/> |
|
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<children xsi:type="menu:HandledMenuItem" xmi:id="_TUGg8KT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.alignmenteditor.updateconsensus" label="%command.name.UPDATE_CONSENSUS_SEQUENCE" command="_gnsTYKT7Eeejf7ggYkp-TA"/> |
|
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</elements> |
|
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<elements xsi:type="menu:Menu" xmi:id="_yuMJQKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.menu.viewpherogram_view" label="%view.PHEROGRAM_VIEW"> |
|
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<children xsi:type="menu:HandledMenuItem" xmi:id="_0r-EkKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.pherogrameditor.changeQuality" label="%command.name.CHANGE_QUALITY_OUTPUT" command="_lyJmEKT7Eeejf7ggYkp-TA"/> |
|
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<children xsi:type="menu:HandledMenuItem" xmi:id="_7_ShMKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.pherogrameditor.toggleProbabilities" label="%command.name.TOGGLE_SHOW_PROBABILITY_VALUES" command="_h1lC0KT7Eeejf7ggYkp-TA"/> |
|
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<children xsi:type="menu:HandledMenuItem" xmi:id="_93JasKT8Eeejf7ggYkp-TA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.mainmenu.pherogrameditor.toggleBaseCallLines" label="%command.name.TOGGLE_SHOW_BASE_CALL_LINES" command="_j-w84KT7Eeejf7ggYkp-TA"/> |
|
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</elements> |
|
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</fragments> |
|
18 | 68 |
</fragment:ModelFragments> |
eu.etaxonomy.taxeditor.molecular/plugin.xml | ||
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1 | 1 |
<?xml version="1.0" encoding="UTF-8"?> |
2 | 2 |
<?eclipse version="3.4"?> |
3 | 3 |
<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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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> |
|
69 |
</extension> |
|
70 | 4 |
<extension |
71 | 5 |
point="org.eclipse.ui.menus"> |
72 | 6 |
<menuContribution |
... | ... | |
103 | 37 |
</command> |
104 | 38 |
</toolbar> |
105 | 39 |
</menuContribution> |
106 |
<menuContribution |
|
107 |
allPopups="false" |
|
108 |
locationURI="menu:org.eclipse.ui.main.menu"> |
|
109 |
<menu |
|
110 |
label="%menu.ALIGNMENT_EDITOR"> |
|
111 |
<command |
|
112 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram" |
|
113 |
style="push"> |
|
114 |
</command> |
|
115 |
<command |
|
116 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft" |
|
117 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft" |
|
118 |
name="Cut pherogram left"> |
|
119 |
</command> |
|
120 |
<command |
|
121 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight" |
|
122 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight" |
|
123 |
style="push"> |
|
124 |
</command> |
|
125 |
<command |
|
126 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows" |
|
127 |
mnemonic="r" |
|
128 |
style="push"> |
|
129 |
</command> |
|
130 |
<command |
|
131 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus" |
|
132 |
style="push"> |
|
133 |
</command> |
|
134 |
<command |
|
135 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus" |
|
136 |
style="push"> |
|
137 |
</command> |
|
138 |
<visibleWhen |
|
139 |
checkEnabled="true"> |
|
140 |
<with |
|
141 |
variable="activePartId"> |
|
142 |
<equals |
|
143 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
144 |
</equals> |
|
145 |
</with> |
|
146 |
</visibleWhen> |
|
147 |
</menu> |
|
148 |
<menu |
|
149 |
label="%menu.label.PHEROGRAM_VIEW"> |
|
150 |
<command |
|
151 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput" |
|
152 |
style="push"> |
|
153 |
</command> |
|
154 |
<command |
|
155 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities" |
|
156 |
style="push"> |
|
157 |
</command> |
|
158 |
<command |
|
159 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines" |
|
160 |
style="push"> |
|
161 |
</command> |
|
162 |
<visibleWhen |
|
163 |
checkEnabled="true"> |
|
164 |
<with |
|
165 |
variable="activePartId"> |
|
166 |
<equals |
|
167 |
value="eu.etaxonomy.taxeditor.molecular.PherogramView"> |
|
168 |
</equals> |
|
169 |
</with> |
|
170 |
</visibleWhen> |
|
171 |
</menu> |
|
172 |
</menuContribution> |
|
173 |
</extension> |
|
174 |
<extension |
|
175 |
point="org.eclipse.ui.handlers"> |
|
176 |
<handler |
|
177 |
class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler" |
|
178 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"> |
|
179 |
<activeWhen> |
|
180 |
<with |
|
181 |
variable="activePartId"> |
|
182 |
<equals |
|
183 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
184 |
</equals> |
|
185 |
</with> |
|
186 |
</activeWhen> |
|
187 |
</handler> |
|
188 |
<handler |
|
189 |
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler" |
|
190 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"> |
|
191 |
</handler> |
|
192 |
<handler |
|
193 |
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler" |
|
194 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"> |
|
195 |
</handler> |
|
196 |
<handler |
|
197 |
class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler" |
|
198 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"> |
|
199 |
</handler> |
|
200 |
<handler |
|
201 |
class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler" |
|
202 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"> |
|
203 |
</handler> |
|
204 |
<handler |
|
205 |
class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler" |
|
206 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"> |
|
207 |
</handler> |
|
208 |
<handler |
|
209 |
class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler" |
|
210 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"> |
|
211 |
</handler> |
|
212 |
<handler |
|
213 |
class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler" |
|
214 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"> |
|
215 |
</handler> |
|
216 |
<handler |
|
217 |
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler" |
|
218 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"> |
|
219 |
</handler> |
|
220 |
<handler |
|
221 |
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler" |
|
222 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"> |
|
223 |
</handler> |
|
224 |
<handler |
|
225 |
class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType" |
|
226 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"> |
|
227 |
</handler> |
|
228 |
<handler |
|
229 |
class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCopyHandler" |
|
230 |
commandId="org.eclipse.ui.edit.copy"> |
|
231 |
<activeWhen> |
|
232 |
<with |
|
233 |
variable="activePartId"> |
|
234 |
<equals |
|
235 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
236 |
</equals> |
|
237 |
</with> |
|
238 |
</activeWhen> |
|
239 |
</handler> |
|
240 |
<handler |
|
241 |
class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCutHandler" |
|
242 |
commandId="org.eclipse.ui.edit.cut"> |
|
243 |
<activeWhen> |
|
244 |
<with |
|
245 |
variable="activePartId"> |
|
246 |
<equals |
|
247 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
248 |
</equals> |
|
249 |
</with> |
|
250 |
</activeWhen> |
|
251 |
</handler> |
|
252 |
<handler |
|
253 |
class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorPasteHandler" |
|
254 |
commandId="org.eclipse.ui.edit.paste"> |
|
255 |
<activeWhen> |
|
256 |
<with |
|
257 |
variable="activePartId"> |
|
258 |
<equals |
|
259 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
260 |
</equals> |
|
261 |
</with> |
|
262 |
</activeWhen> |
|
263 |
</handler> |
|
264 | 40 |
</extension> |
265 | 41 |
<extension |
266 | 42 |
point="org.eclipse.ui.bindings"> |
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/e4/AlignmentEditorE4.java | ||
---|---|---|
1 |
/** |
|
2 |
* Copyright (C) 2014 EDIT |
|
3 |
* European Distributed Institute of Taxonomy |
|
4 |
* http://www.e-taxonomy.eu |
|
5 |
* |
|
6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
8 |
*/ |
|
9 |
package eu.etaxonomy.taxeditor.molecular.editor.e4; |
|
10 |
|
|
11 |
|
|
12 |
import java.io.File; |
|
13 |
import java.io.IOException; |
|
14 |
import java.io.InputStream; |
|
15 |
import java.net.URI; |
|
16 |
import java.util.ArrayList; |
|
17 |
import java.util.Collection; |
|
18 |
import java.util.Collections; |
|
19 |
import java.util.Iterator; |
|
20 |
import java.util.List; |
|
21 |
import java.util.Map; |
|
22 |
import java.util.TreeMap; |
|
23 |
|
|
24 |
import javax.annotation.PostConstruct; |
|
25 |
import javax.annotation.PreDestroy; |
|
26 |
import javax.inject.Inject; |
|
27 |
|
|
28 |
import org.biojava.bio.chromatogram.ChromatogramFactory; |
|
29 |
import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException; |
|
30 |
import org.eclipse.core.runtime.IProgressMonitor; |
|
31 |
import org.eclipse.e4.ui.di.Focus; |
|
32 |
import org.eclipse.e4.ui.di.Persist; |
|
33 |
import org.eclipse.e4.ui.model.application.ui.MDirtyable; |
|
34 |
import org.eclipse.swt.SWT; |
|
35 |
import org.eclipse.swt.dnd.Clipboard; |
|
36 |
import org.eclipse.swt.widgets.Composite; |
|
37 |
import org.eclipse.swt.widgets.Display; |
|
38 |
import org.eclipse.ui.PartInitException; |
|
39 |
import org.eclipse.ui.PlatformUI; |
|
40 |
import org.eclipse.ui.commands.ICommandService; |
|
41 |
|
|
42 |
import eu.etaxonomy.cdm.api.conversation.ConversationHolder; |
|
43 |
import eu.etaxonomy.cdm.api.service.molecular.ISequenceService; |
|
44 |
import eu.etaxonomy.cdm.model.media.MediaUtils; |
|
45 |
import eu.etaxonomy.cdm.model.molecular.Sequence; |
|
46 |
import eu.etaxonomy.cdm.model.molecular.SequenceString; |
|
47 |
import eu.etaxonomy.cdm.model.molecular.SingleRead; |
|
48 |
import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment; |
|
49 |
import eu.etaxonomy.taxeditor.model.MessagingUtils; |
|
50 |
import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin; |
|
51 |
import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditorActionUpdater; |
|
52 |
import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditorInput; |
|
53 |
import eu.etaxonomy.taxeditor.molecular.editor.PherogramMouseListener; |
|
54 |
import eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler; |
|
55 |
import eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler; |
|
56 |
import eu.etaxonomy.taxeditor.molecular.l10n.Messages; |
|
57 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
|
58 |
import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateLabelProvider; |
|
59 |
import info.bioinfweb.commons.swt.SWTUtils; |
|
60 |
import info.bioinfweb.libralign.alignmentarea.AlignmentArea; |
|
61 |
import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel; |
|
62 |
import info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter; |
|
63 |
import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea; |
|
64 |
import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea; |
|
65 |
import info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea; |
|
66 |
import info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent; |
|
67 |
import info.bioinfweb.libralign.editsettings.EditSettingsListener; |
|
68 |
import info.bioinfweb.libralign.model.AlignmentModel; |
|
69 |
import info.bioinfweb.libralign.model.AlignmentModelChangeListener; |
|
70 |
import info.bioinfweb.libralign.model.adapters.StringAdapter; |
|
71 |
import info.bioinfweb.libralign.model.events.SequenceChangeEvent; |
|
72 |
import info.bioinfweb.libralign.model.events.SequenceRenamedEvent; |
|
73 |
import info.bioinfweb.libralign.model.events.TokenChangeEvent; |
|
74 |
import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel; |
|
75 |
import info.bioinfweb.libralign.model.tokenset.CharacterTokenSet; |
|
76 |
import info.bioinfweb.libralign.model.tokenset.TokenSet; |
|
77 |
import info.bioinfweb.libralign.model.utils.AlignmentModelUtils; |
|
78 |
import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList; |
|
79 |
import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer; |
|
80 |
import info.bioinfweb.libralign.pherogram.model.PherogramAlignmentRelation; |
|
81 |
import info.bioinfweb.libralign.pherogram.model.PherogramAreaModel; |
|
82 |
import info.bioinfweb.libralign.pherogram.model.ShiftChange; |
|
83 |
import info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider; |
|
84 |
import info.bioinfweb.libralign.pherogram.provider.PherogramProvider; |
|
85 |
import info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider; |
|
86 |
import info.bioinfweb.tic.SWTComponentFactory; |
|
87 |
|
|
88 |
|
|
89 |
|
|
90 |
/** |
|
91 |
* Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to |
|
92 |
* a consensus sequence. |
|
93 |
* <p> |
|
94 |
* The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>. |
|
95 |
* |
|
96 |
* @author Ben Stöver |
|
97 |
* @author pplitzner |
|
98 |
* @date 04.08.2014 |
|
99 |
*/ |
|
100 |
public class AlignmentEditorE4 { |
|
101 |
public static final String ID = "eu.etaxonomy.taxeditor.molecular.AlignmentEditor"; //$NON-NLS-1$ |
|
102 |
|
|
103 |
public static final int READS_AREA_INDEX = 1; |
|
104 |
public static final int EDITABLE_CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1; |
|
105 |
public static final int CONSENSUS_HINT_AREA_INDEX = EDITABLE_CONSENSUS_AREA_INDEX + 1; |
|
106 |
public static final int PHEROGRAM_AREA_INDEX = 0; |
|
107 |
public static final int CONSENSUS_DATA_AREA_INDEX = 0; |
|
108 |
public static final String DEFAULT_READ_NAME_PREFIX = "Read "; //$NON-NLS-1$ |
|
109 |
public static final String CONSENSUS_NAME = "Consensus"; //$NON-NLS-1$ |
|
110 |
|
|
111 |
|
|
112 |
private ConversationHolder conversationHolder; |
|
113 |
private final AlignmentModelChangeListener DIRTY_LISTENER = new AlignmentModelChangeListener() { |
|
114 |
@Override |
|
115 |
public <T> void afterTokenChange(TokenChangeEvent<T> e) { |
|
116 |
setDirty(); |
|
117 |
} |
|
118 |
|
|
119 |
@Override |
|
120 |
public <T> void afterSequenceRenamed(SequenceRenamedEvent<T> e) { |
|
121 |
setDirty(); |
|
122 |
} |
|
123 |
|
|
124 |
@Override |
|
125 |
public <T> void afterSequenceChange(SequenceChangeEvent<T> e) { |
|
126 |
setDirty(); |
|
127 |
} |
|
128 |
|
|
129 |
@Override |
|
130 |
public <T, U> void afterProviderChanged(AlignmentModel<T> oldProvider, |
|
131 |
AlignmentModel<U> newProvider) { // Not expected. |
|
132 |
|
|
133 |
setDirty(); |
|
134 |
} |
|
135 |
}; |
|
136 |
private final AlignmentEditorActionUpdater ACTION_UPDATER = new AlignmentEditorActionUpdater(); |
|
137 |
public final Clipboard CLIPBOARD = new Clipboard(Display.getCurrent()); //TODO Move to global EDITor class. |
|
138 |
|
|
139 |
|
|
140 |
private MultipleAlignmentsContainer alignmentsContainer = null; |
|
141 |
private final Map<String, SingleReadAlignment> cdmMap = new TreeMap<String, SingleReadAlignment>(); //TODO Move this to ContigSequenceDataProvider |
|
142 |
|
|
143 |
|
|
144 |
@Inject |
|
145 |
private MDirtyable dirty; |
|
146 |
|
|
147 |
private AlignmentEditorInput input; |
|
148 |
|
|
149 |
@Inject |
|
150 |
public AlignmentEditorE4() { |
|
151 |
} |
|
152 |
|
|
153 |
|
|
154 |
private void refreshToolbarElement(String id) { |
|
155 |
ICommandService commandService = |
|
156 |
PlatformUI.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService.class); |
|
157 |
if (commandService != null) { |
|
158 |
commandService.refreshElements(id, Collections.EMPTY_MAP); |
|
159 |
} |
|
160 |
} |
|
161 |
|
|
162 |
|
|
163 |
private void registerEditSettingListener(MultipleAlignmentsContainer container) { |
|
164 |
container.getEditSettings().addListener(new EditSettingsListener() { |
|
165 |
@Override |
|
166 |
public void workingModeChanged(EditSettingsChangeEvent e) {} // Currently nothing to do |
|
167 |
|
|
168 |
@Override |
|
169 |
public void insertLeftInDataAreaChanged(EditSettingsChangeEvent e) { |
|
170 |
updateStatusBar(); |
|
171 |
refreshToolbarElement(ToggleLeftRightInsertionHandler.COMMAND_ID); |
|
172 |
} |
|
173 |
|
|
174 |
@Override |
|
175 |
public void insertChanged(EditSettingsChangeEvent e) { |
|
176 |
updateStatusBar(); |
|
177 |
refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID); |
|
178 |
} |
|
179 |
}); |
|
180 |
} |
|
181 |
|
|
182 |
|
|
183 |
private AlignmentArea createIndexArea(MultipleAlignmentsContainer container, AlignmentArea labeledArea) { |
|
184 |
AlignmentArea result = new AlignmentArea(container); |
|
185 |
result.setAllowVerticalScrolling(false); |
|
186 |
result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea(), labeledArea)); |
|
187 |
return result; |
|
188 |
} |
|
189 |
|
|
190 |
|
|
191 |
private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) { |
|
192 |
AlignmentArea result = new AlignmentArea(container); |
|
193 |
result.setAllowVerticalScrolling(allowVerticalScrolling); |
|
194 |
|
|
195 |
CharacterTokenSet tokenSet = CharacterTokenSet.newDNAInstance(); //TODO Should NUCLEOTIDE be used instead? |
|
196 |
AlignmentModel<Character> model = new PackedAlignmentModel<Character>(tokenSet); |
|
197 |
result.setAlignmentModel(model, false); |
|
198 |
model.getChangeListeners().add(DIRTY_LISTENER); |
|
199 |
result.getPaintSettings().getTokenPainterList().set(0, new NucleotideTokenPainter()); |
|
200 |
|
|
201 |
return result; |
|
202 |
} |
|
203 |
|
|
204 |
|
|
205 |
private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container, |
|
206 |
AlignmentArea labeledArea) { |
|
207 |
|
|
208 |
AlignmentArea result = new AlignmentArea(container); |
|
209 |
result.setAllowVerticalScrolling(false); |
|
210 |
result.getDataAreas().getBottomAreas().add( |
|
211 |
new ConsensusSequenceArea(result.getContentArea(), labeledArea)); |
|
212 |
return result; |
|
213 |
} |
|
214 |
|
|
215 |
|
|
216 |
private MultipleAlignmentsContainer getAlignmentsContainer() { |
|
217 |
if (alignmentsContainer == null) { |
|
218 |
alignmentsContainer = new MultipleAlignmentsContainer(); |
|
219 |
|
|
220 |
AlignmentAreaList list = alignmentsContainer.getAlignmentAreas(); |
|
221 |
AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true); |
|
222 |
readsArea.getSelection().addSelectionListener(ACTION_UPDATER); |
|
223 |
list.add(createIndexArea(alignmentsContainer, readsArea)); |
|
224 |
list.add(readsArea); // Make sure READS_AREA_INDEX is correct. |
|
225 |
AlignmentArea editableConsensusArea = createEditableAlignmentArea(alignmentsContainer, false); |
|
226 |
editableConsensusArea.getSelection().addSelectionListener(ACTION_UPDATER); |
|
227 |
list.add(editableConsensusArea); // Make sure COMSENSUS_AREA_INDEX is correct. |
|
228 |
list.add(createConsensusHintArea(alignmentsContainer, readsArea)); |
|
229 |
|
|
230 |
registerEditSettingListener(alignmentsContainer); |
|
231 |
} |
|
232 |
return alignmentsContainer; |
|
233 |
} |
|
234 |
|
|
235 |
|
|
236 |
public AlignmentArea getReadsArea() { |
|
237 |
return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX); |
|
238 |
} |
|
239 |
|
|
240 |
|
|
241 |
public AlignmentArea getEditableConsensusArea() { |
|
242 |
return getAlignmentsContainer().getAlignmentAreas().get(EDITABLE_CONSENSUS_AREA_INDEX); |
|
243 |
} |
|
244 |
|
|
245 |
|
|
246 |
/** |
|
247 |
* Checks whether {@link #getReadsArea()} or {@link #getEditableConsensusArea()} currently |
|
248 |
* have the user focus and returns the according component. |
|
249 |
* |
|
250 |
* @return either the reads or the consensus alignment area or {@code null} if none of these |
|
251 |
* components is currently focused |
|
252 |
*/ |
|
253 |
public AlignmentArea getFocusedArea() { |
|
254 |
AlignmentArea result = getReadsArea(); |
|
255 |
if (hasFocus(result)) { |
|
256 |
return result; |
|
257 |
} |
|
258 |
else { |
|
259 |
result = getEditableConsensusArea(); |
|
260 |
if (hasFocus(result)) { |
|
261 |
return result; |
|
262 |
} |
|
263 |
else { |
|
264 |
return null; |
|
265 |
} |
|
266 |
} |
|
267 |
} |
|
268 |
|
|
269 |
|
|
270 |
/** |
|
271 |
* Checks whether the specified alignment area or one of its subcomponents currently has the |
|
272 |
* focus. |
|
273 |
* |
|
274 |
* @param area the alignment area to be checked (Can only be {@link #getReadsArea()} or |
|
275 |
* {@link #getEditableConsensusArea()}.) |
|
276 |
* @return {@code true} if the specified component is focused and is either equal to |
|
277 |
* {@link #getReadsArea()} or {@link #getEditableConsensusArea()}or {@code false} otherwise |
|
278 |
*/ |
|
279 |
private boolean hasFocus(AlignmentArea area) { |
|
280 |
return SWTUtils.childHasFocus((Composite)area.getToolkitComponent()); |
|
281 |
} |
|
282 |
|
|
283 |
|
|
284 |
public boolean hasPherogram(String sequenceID) { |
|
285 |
return getReadsArea().getDataAreas().getSequenceAreas(sequenceID).size() > PHEROGRAM_AREA_INDEX; |
|
286 |
} |
|
287 |
|
|
288 |
|
|
289 |
public PherogramArea getPherogramArea(String sequenceID) { |
|
290 |
if (hasPherogram(sequenceID)) { |
|
291 |
return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(PHEROGRAM_AREA_INDEX); |
|
292 |
} |
|
293 |
else { |
|
294 |
return null; |
|
295 |
} |
|
296 |
} |
|
297 |
|
|
298 |
|
|
299 |
private ConsensusSequenceArea getConsensusHintDataArea() { |
|
300 |
return (ConsensusSequenceArea)getAlignmentsContainer().getAlignmentAreas(). |
|
301 |
get(CONSENSUS_HINT_AREA_INDEX).getDataAreas().getBottomAreas(). |
|
302 |
get(CONSENSUS_DATA_AREA_INDEX); |
|
303 |
} |
|
304 |
|
|
305 |
|
|
306 |
@Deprecated //TODO Remove as soon as testing period is over |
|
307 |
private void createTestContents() { |
|
308 |
// Just for testing: |
|
309 |
try { |
|
310 |
addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1").toURI(), false); //$NON-NLS-1$ |
|
311 |
//addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1").toURI(), false); |
|
312 |
addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/Test_qualityScore.scf").toURI(), false); //$NON-NLS-1$ |
|
313 |
|
|
314 |
// Add test consensus sequence: |
|
315 |
AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel(); |
|
316 |
String id = consensusModel.addSequence(CONSENSUS_NAME); |
|
317 |
Collection<Object> tokens = new ArrayList<Object>(); // First save tokens in a collection to avoid GUI updated for each token. |
|
318 |
tokens.add(consensusModel.getTokenSet().tokenByRepresentation("A")); //$NON-NLS-1$ |
|
319 |
tokens.add(consensusModel.getTokenSet().tokenByRepresentation("C")); //$NON-NLS-1$ |
|
320 |
tokens.add(consensusModel.getTokenSet().tokenByRepresentation("G")); //$NON-NLS-1$ |
|
321 |
tokens.add(consensusModel.getTokenSet().tokenByRepresentation("T")); //$NON-NLS-1$ |
|
322 |
consensusModel.insertTokensAt(id, 0, tokens); |
|
323 |
} |
|
324 |
catch (Exception e) { |
|
325 |
throw new RuntimeException(e); |
|
326 |
} |
|
327 |
} |
|
328 |
|
|
329 |
|
|
330 |
private void readCDMData(Sequence sequenceNode) { |
|
331 |
//TODO If called from somewhere else than createPartControl() the editorInput needs to be checked and previous contents need to be cleared (or updated). |
|
332 |
|
|
333 |
// Add reads: |
|
334 |
for (SingleReadAlignment singleReadAlignment : sequenceNode.getSingleReadAlignments()) { |
|
335 |
try { |
|
336 |
SingleRead pherogramInfo = singleReadAlignment.getSingleRead(); |
|
337 |
String id = addRead(DerivateLabelProvider.getDerivateText(pherogramInfo, conversationHolder), |
|
338 |
getPherogramURI(pherogramInfo), |
|
339 |
singleReadAlignment.isReverseComplement(), |
|
340 |
singleReadAlignment.getEditedSequence(), |
|
341 |
singleReadAlignment.getFirstSeqPosition(), |
|
342 |
singleReadAlignment.getLeftCutPosition(), |
|
343 |
singleReadAlignment.getRightCutPosition(), |
|
344 |
singleReadAlignment.getShifts()); |
|
345 |
cdmMap.put(id, singleReadAlignment); |
|
346 |
} |
|
347 |
catch (Exception e) { // Usually due to an error while trying to read the pherogram (e.g. due to an unsupported format or an invalid URI). |
|
348 |
MessagingUtils.errorDialog(Messages.AlignmentEditor_ERROR_SINGLE_READ, null, Messages.AlignmentEditor_ERROR_SINGLE_READ_MESSAGE + |
|
349 |
e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID, e, false); |
|
350 |
} |
|
351 |
} |
|
352 |
|
|
353 |
// Set consensus sequence: |
|
354 |
AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel(); |
|
355 |
String id = consensusModel.addSequence(CONSENSUS_NAME); |
|
356 |
consensusModel.insertTokensAt(id, 0, AlignmentModelUtils.charSequenceToTokenList( |
|
357 |
sequenceNode.getConsensusSequence().getString(), consensusModel.getTokenSet())); |
|
358 |
//TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB? |
|
359 |
} |
|
360 |
|
|
361 |
|
|
362 |
@PostConstruct |
|
363 |
public void createPartControl(Composite parent) { |
|
364 |
if (CdmStore.isActive()){ |
|
365 |
if(conversationHolder == null){ |
|
366 |
conversationHolder = CdmStore.createConversation(); |
|
367 |
} |
|
368 |
} |
|
369 |
else{ |
|
370 |
return; |
|
371 |
} |
|
372 |
SWTComponentFactory.getInstance().getSWTComponent(getAlignmentsContainer(), parent, SWT.NONE); |
|
373 |
Display.getCurrent().addFilter(SWT.FocusIn, ACTION_UPDATER); |
|
374 |
Display.getCurrent().addFilter(SWT.FocusOut, ACTION_UPDATER); |
|
375 |
} |
|
376 |
|
|
377 |
|
|
378 |
@PreDestroy |
|
379 |
public void dispose() { |
|
380 |
Display.getCurrent().removeFilter(SWT.FocusIn, ACTION_UPDATER); |
|
381 |
Display.getCurrent().removeFilter(SWT.FocusOut, ACTION_UPDATER); |
|
382 |
CLIPBOARD.dispose(); |
|
383 |
input.dispose(); |
|
384 |
} |
|
385 |
|
|
386 |
|
|
387 |
private void updateStatusBar() { |
|
388 |
//FIXME E4 migrate |
|
389 |
// IActionBars bars = getEditorSite().getActionBars(); |
|
390 |
// bars.getStatusLineManager().setMessage( |
|
391 |
// Messages.AlignmentEditor_EDIT_MODE + (getReadsArea().getEditSettings().isInsert() ? Messages.AlignmentEditor_INSERT : Messages.AlignmentEditor_OVERWRITE) + " " + //$NON-NLS-1$ |
|
392 |
// Messages.AlignmentEditor_INSERTION_PHEROGRAM + |
|
393 |
// (getReadsArea().getEditSettings().isInsertLeftInDataArea() ? Messages.AlignmentEditor_LEFT : Messages.AlignmentEditor_RIGHT)); //TODO multi language |
|
394 |
} |
|
395 |
|
|
396 |
|
|
397 |
private SingleReadAlignment.Shift[] convertToCDMShifts(PherogramAreaModel model) { |
|
398 |
Iterator<ShiftChange> iterator = model.shiftChangeIterator(); |
|
399 |
List<SingleReadAlignment.Shift> shifts = new ArrayList<SingleReadAlignment.Shift>(); |
|
400 |
while (iterator.hasNext()) { |
|
401 |
ShiftChange shiftChange = iterator.next(); |
|
402 |
shifts.add(new SingleReadAlignment.Shift(shiftChange.getBaseCallIndex(), shiftChange.getShiftChange())); |
|
403 |
} |
|
404 |
return shifts.toArray(new SingleReadAlignment.Shift[shifts.size()]); |
|
405 |
} |
|
406 |
|
|
407 |
|
|
408 |
@Persist |
|
409 |
public void doSave(IProgressMonitor monitor) { |
|
410 |
String taskName = Messages.AlignmentEditor_SAVING_ALIGNMENT; //TODO multi language |
|
411 |
monitor.beginTask(taskName, 3); |
|
412 |
|
|
413 |
//re-loading sequence to avoid session conflicts |
|
414 |
Sequence sequenceNode = CdmStore.getService(ISequenceService.class).load(input.getSequenceNodeUuid()); |
|
415 |
input.setSequenceNode(sequenceNode); |
|
416 |
StringAdapter stringProvider = new StringAdapter(getEditableConsensusArea().getAlignmentModel(), false); // Throws an exception if a token has more than one character. |
|
417 |
|
|
418 |
// Write consensus sequence: |
|
419 |
SequenceString consensusSequenceObj = sequenceNode.getConsensusSequence(); |
|
420 |
String newConsensusSequence = stringProvider.getSequence( |
|
421 |
getEditableConsensusArea().getAlignmentModel().sequenceIDByName(CONSENSUS_NAME)); |
|
422 |
if (consensusSequenceObj == null) { |
|
423 |
sequenceNode.setConsensusSequence(SequenceString.NewInstance(newConsensusSequence)); |
|
424 |
} |
|
425 |
else { |
|
426 |
consensusSequenceObj.setString(newConsensusSequence); |
|
427 |
} |
|
428 |
|
|
429 |
// Write single reads: |
|
430 |
stringProvider.setUnderlyingModel(getReadsArea().getAlignmentModel()); |
|
431 |
sequenceNode.getSingleReadAlignments().retainAll(cdmMap.values()); // Remove all reads that are not in the alignment anymore. |
|
432 |
Iterator<String> iterator = getReadsArea().getAlignmentModel().sequenceIDIterator(); |
|
433 |
while (iterator.hasNext()) { |
|
434 |
String id = iterator.next(); |
|
435 |
SingleReadAlignment singleRead = cdmMap.get(id); |
|
436 |
if (singleRead == null) { |
|
437 |
throw new InternalError(Messages.AlignmentEditor_NEW_READ_FAILURE); //TODO multi language |
|
438 |
//TODO Create new read object. => Shall it be allowed to add reads in the alignment editor which are not represented in the CDM tree before the alignment editor is saved? |
|
439 |
//singleRead = SingleReadAlignment.NewInstance(consensusSequence, singleRead, shifts, editedSequence); |
|
440 |
} |
|
441 |
|
|
442 |
singleRead.setEditedSequence(stringProvider.getSequence(id)); |
|
443 |
|
|
444 |
PherogramArea pherogramArea = getPherogramArea(id); |
|
445 |
if (pherogramArea != null) { |
|
446 |
PherogramAreaModel model = pherogramArea.getModel(); |
|
447 |
singleRead.setReverseComplement(model.getPherogramProvider() instanceof ReverseComplementPherogramProvider); // Works only if ReverseComplementPherogramProvider instances are not nested. |
|
448 |
singleRead.setShifts(convertToCDMShifts(getPherogramArea(id).getModel())); |
|
449 |
singleRead.setFirstSeqPosition(model.getFirstSeqPos()); |
|
450 |
singleRead.setLeftCutPosition(model.getLeftCutPosition()); |
|
451 |
singleRead.setRightCutPosition(model.getRightCutPosition()); |
|
452 |
} |
|
453 |
} |
|
454 |
|
|
455 |
if (!conversationHolder.isBound()) { |
|
456 |
conversationHolder.bind(); |
|
457 |
} |
|
458 |
monitor.worked(1); |
|
459 |
|
|
460 |
input.merge(); |
|
461 |
// Commit the conversation and start a new transaction immediately: |
|
462 |
conversationHolder.commit(true); |
|
463 |
monitor.worked(1); |
|
464 |
|
|
465 |
dirty.setDirty(false); |
|
466 |
monitor.worked(1); |
|
467 |
monitor.done(); |
|
468 |
} |
|
469 |
|
|
470 |
|
|
471 |
public void init(AlignmentEditorInput input) throws PartInitException { |
|
472 |
this.input = input; |
|
473 |
|
|
474 |
updateStatusBar(); |
|
475 |
|
|
476 |
if (input.getSequenceNodeUuid() != null) { |
|
477 |
Sequence sequenceNode = CdmStore.getService(ISequenceService.class).load(input.getSequenceNodeUuid()); |
|
478 |
//re-load into the current session if it is already persisted in the DB |
|
479 |
if(sequenceNode!=null && sequenceNode.getId()!=0){ |
|
480 |
sequenceNode = CdmStore.getService(ISequenceService.class).load(sequenceNode.getUuid()); |
|
481 |
} |
|
482 |
readCDMData(sequenceNode); |
|
483 |
} |
|
484 |
else { |
|
485 |
createTestContents(); // This case will removed after the test phase and an exception should probably be thrown. |
|
486 |
} |
|
487 |
} |
|
488 |
|
|
489 |
|
|
490 |
public boolean isDirty() { |
|
491 |
return dirty.isDirty(); |
|
492 |
} |
|
493 |
|
|
494 |
|
|
495 |
private void setDirty() { |
|
496 |
dirty.setDirty(true); |
|
497 |
} |
|
498 |
|
|
499 |
|
|
500 |
@Focus |
|
501 |
public void setFocus() { |
|
502 |
if(conversationHolder != null){ |
|
503 |
conversationHolder.bind(); |
|
504 |
} |
|
505 |
if(input!=null){ |
|
506 |
input.bind(); |
|
507 |
} |
|
508 |
} |
|
509 |
|
|
510 |
public boolean isInsertMode() { |
|
511 |
return getAlignmentsContainer().getEditSettings().isInsert(); |
|
512 |
} |
|
513 |
|
|
514 |
|
|
515 |
public boolean isInsertLeftInPherogram() { |
|
516 |
return getAlignmentsContainer().getEditSettings().isInsertLeftInDataArea(); |
|
517 |
} |
|
518 |
|
|
519 |
|
|
520 |
public void toggleLeftRightInsertionInPherogram() { |
|
521 |
getAlignmentsContainer().getEditSettings().toggleInsertLeftInDataArea(); |
|
522 |
} |
|
523 |
|
|
524 |
|
|
525 |
public void toggleInsertOverwrite() { |
|
526 |
getAlignmentsContainer().getEditSettings().toggleInsert(); |
|
527 |
} |
|
528 |
|
|
529 |
|
|
530 |
private String cutPherogram(boolean left) { |
|
531 |
SelectionModel selection = getReadsArea().getSelection(); |
|
532 |
if (selection.getCursorHeight() != 1) { |
|
533 |
return Messages.AlignmentEditor_CUTTING_FAILURE; //TODO multi language |
|
534 |
} |
|
535 |
else { |
|
536 |
PherogramArea pherogramArea = |
|
537 |
getPherogramArea(getReadsArea().getSequenceOrder().idByIndex(selection.getCursorRow())); |
|
538 |
if (pherogramArea == null) { |
|
539 |
return Messages.AlignmentEditor_NO_ATTACHED_PHEROGRAM; //TODO multi language |
|
540 |
} |
|
541 |
else { |
|
542 |
if (left) { |
|
543 |
if (pherogramArea.setLeftCutPositionBySelection()) { |
|
544 |
return null; |
|
545 |
} |
|
546 |
else { |
|
547 |
return Messages.AlignmentEditor_LEFT_END_OUTSIDE; //TODO multi language |
|
548 |
} |
|
549 |
} |
|
550 |
else { |
|
551 |
if (pherogramArea.setRightCutPositionBySelection()) { |
|
552 |
return null; |
|
553 |
} |
|
554 |
else { |
|
555 |
return Messages.AlignmentEditor_RIGHT_END_OUTSIDE; //TODO multi language |
|
556 |
} |
|
557 |
} |
|
558 |
} |
|
559 |
} |
|
560 |
} |
|
561 |
|
|
562 |
|
|
563 |
public String cutPherogramLeft() { |
|
564 |
return cutPherogram(true); |
|
565 |
} |
|
566 |
|
|
567 |
|
|
568 |
public String cutPherogramRight() { |
|
569 |
return cutPherogram(false); |
|
570 |
} |
|
571 |
|
|
572 |
|
|
573 |
public void reverseComplementSelectedSequences() { |
|
574 |
SelectionModel selection = getReadsArea().getSelection(); |
|
575 |
AlignmentModel<?> model = getReadsArea().getAlignmentModel(); |
|
576 |
for (int row = selection.getFirstRow(); row < selection.getFirstRow() + selection.getCursorHeight(); row++) { |
|
577 |
String sequenceID = getReadsArea().getSequenceOrder().idByIndex(row); |
|
578 |
PherogramArea area = getPherogramArea(sequenceID); |
|
579 |
PherogramAreaModel pherogramAlignmentModel = area.getModel(); |
|
580 |
|
|
581 |
PherogramAlignmentRelation rightRelation = pherogramAlignmentModel.editableIndexByBaseCallIndex( |
|
582 |
pherogramAlignmentModel.getRightCutPosition()); |
|
583 |
int rightBorder; |
|
584 |
if (rightRelation.getCorresponding() == PherogramAlignmentRelation.OUT_OF_RANGE) { |
|
585 |
rightBorder = rightRelation.getBeforeValidIndex() + 1; |
|
586 |
} |
|
587 |
else { |
|
588 |
rightBorder = rightRelation.getAfterValidIndex(); |
|
589 |
} |
|
590 |
|
|
591 |
AlignmentModelUtils.reverseComplement(model, sequenceID, |
|
592 |
pherogramAlignmentModel.editableIndexByBaseCallIndex( |
|
593 |
pherogramAlignmentModel.getLeftCutPosition()).getBeforeValidIndex(), |
|
594 |
rightBorder); |
|
595 |
pherogramAlignmentModel.reverseComplement(); |
|
596 |
} |
|
597 |
} |
|
598 |
|
|
599 |
|
|
600 |
/** |
|
601 |
* Recreates the whole consensus sequence from all single read sequences. The previous consensus |
|
602 |
* sequence is overwritten. |
|
603 |
*/ |
|
604 |
@SuppressWarnings("unchecked") |
|
605 |
public <T> void createConsensusSequence() { |
|
606 |
ConsensusSequenceArea area = getConsensusHintDataArea(); |
|
607 |
AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel(); |
|
608 |
String sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained. |
|
609 |
int length = getReadsArea().getAlignmentModel().getMaxSequenceLength(); |
|
610 |
|
|
611 |
Collection<T> tokens = new ArrayList<T>(length); |
|
612 |
for (int column = 0; column < length; column++) { |
|
613 |
tokens.add(model.getTokenSet().tokenByRepresentation(area.getConsensusToken(column))); |
|
614 |
} |
|
615 |
|
|
616 |
model.removeTokensAt(sequenceID, 0, model.getSequenceLength(sequenceID)); |
|
617 |
model.insertTokensAt(sequenceID, 0, tokens); |
|
618 |
} |
|
619 |
|
|
620 |
|
|
621 |
/** |
|
622 |
* Updates the current consensus sequence by replacing gaps by the according consensus tokens |
|
623 |
* calculated from the single read sequences and extends the consensus sequence if necessary. |
|
624 |
*/ |
|
625 |
@SuppressWarnings("unchecked") |
|
626 |
public <T> void updateConsensusSequence() { |
|
627 |
ConsensusSequenceArea area = getConsensusHintDataArea(); |
|
628 |
AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel(); |
|
629 |
TokenSet<T> tokenSet = model.getTokenSet(); |
|
630 |
String sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained. |
|
631 |
int currentConsensusLength = model.getSequenceLength(sequenceID); |
|
632 |
int overallLength = getReadsArea().getAlignmentModel().getMaxSequenceLength(); |
|
633 |
|
|
634 |
// Replace gaps by new information: |
|
635 |
for (int column = 0; column < currentConsensusLength; column++) { |
|
636 |
if (tokenSet.isGapToken(model.getTokenAt(sequenceID, column))) { |
|
637 |
T newToken = tokenSet.tokenByRepresentation(area.getConsensusToken(column)); |
|
638 |
if (!tokenSet.isGapToken(newToken)) { |
|
639 |
model.setTokenAt(sequenceID, column, newToken); |
|
640 |
} |
|
641 |
} |
|
642 |
} |
|
643 |
|
|
644 |
// Append additional tokens: |
|
645 |
if (overallLength > currentConsensusLength) { |
|
646 |
Collection<T> tokens = new ArrayList<T>(overallLength); |
|
647 |
for (int column = currentConsensusLength; column < overallLength; column++) { |
|
648 |
tokens.add(tokenSet.tokenByRepresentation(area.getConsensusToken(column))); |
|
649 |
} |
|
650 |
model.appendTokens(sequenceID, tokens); |
|
651 |
} |
|
652 |
} |
|
653 |
|
|
654 |
|
|
655 |
public static PherogramProvider readPherogram(URI uri) throws IOException, UnsupportedChromatogramFormatException { |
|
656 |
PherogramProvider result; |
|
657 |
InputStream stream = uri.toURL().openStream(); |
|
658 |
try { |
|
659 |
result = new BioJavaPherogramProvider(ChromatogramFactory.create(stream)); |
|
660 |
} |
|
661 |
finally { |
|
662 |
stream.close(); |
|
663 |
} |
|
664 |
return result; |
|
665 |
} |
|
666 |
|
|
667 |
|
|
668 |
private String newReadName() { |
|
669 |
int index = 1; |
|
670 |
while (getReadsArea().getAlignmentModel().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index) != null) { |
|
671 |
index++; |
|
672 |
} |
|
673 |
return DEFAULT_READ_NAME_PREFIX + index; |
|
674 |
} |
|
675 |
|
|
676 |
|
|
677 |
public void addRead(URI pherogramURI, boolean reverseComplemented) throws IOException, UnsupportedChromatogramFormatException { |
|
678 |
addRead(newReadName(), pherogramURI, reverseComplemented, null, null, null, null, null); |
|
679 |
} |
|
680 |
|
|
681 |
|
|
682 |
/** |
|
683 |
* Adds a new sequence with attached phergram data area to the reads alignment. |
|
684 |
* <p> |
|
685 |
* If {@code null} is specified as {@code editedSequence} the base call sequence from the pherogram will |
|
686 |
* be set as the edited sequence. If {@code null} is specified as {@code shifts} no shifts between the edited |
|
687 |
* and the base calls sequence are assumed. |
|
688 |
* |
|
689 |
* @param name the name of the new sequence |
|
690 |
* @param pherogramURI the URI where the associated pherogram file is located |
|
691 |
* @param reverseComplemented Specify {@code true} here, if the reverse complement of the pherogram data should |
|
692 |
* be added, {@code false} otherwise. |
|
693 |
* @param editedSequence the edited version of the base call sequence (May be {@code null}.) |
|
694 |
* @param shifts the alignment information that links the edited and the base call sequence (May be {@code null}.) |
|
695 |
* @return the sequence ID of the added read |
|
696 |
* @throws IOException if an error occurred when trying to read the pherogram file |
|
697 |
* @throws UnsupportedChromatogramFormatException if the format of the pherogram file is not supported |
|
698 |
*/ |
|
699 |
public String addRead(String name, URI pherogramURI, boolean reverseComplemented, String editedSequence, |
|
700 |
Integer firstSeqPos, Integer leftCutPos, Integer rightCutPos, SingleReadAlignment.Shift[] shifts) |
|
701 |
throws IOException, UnsupportedChromatogramFormatException { |
|
702 |
|
|
703 |
AlignmentModel model = getReadsArea().getAlignmentModel(); |
|
704 |
PherogramProvider pherogramProvider = null; |
|
705 |
if (pherogramURI != null) { |
|
706 |
pherogramProvider = readPherogram(pherogramURI); // Must happen before a sequence is added, because it might throw an exception. |
|
707 |
if (reverseComplemented) { |
|
708 |
pherogramProvider = new ReverseComplementPherogramProvider(pherogramProvider); |
|
709 |
} |
|
710 |
} |
|
711 |
|
|
712 |
// Create sequence: |
|
713 |
model.addSequence(name); |
|
714 |
String id = model.sequenceIDByName(name); |
|
715 |
|
|
716 |
// Set edited sequence: |
|
717 |
Collection<Object> tokens = null; // First save tokens in a collection to avoid GUI updated for each token. |
|
718 |
if (editedSequence != null) { |
|
719 |
tokens = AlignmentModelUtils.charSequenceToTokenList(editedSequence, model.getTokenSet()); |
|
720 |
} |
|
721 |
else if (pherogramProvider != null) { // Copy base call sequence into alignment: |
|
722 |
tokens = new ArrayList<Object>(); |
|
723 |
for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) { |
|
724 |
tokens.add(model.getTokenSet().tokenByRepresentation( |
|
725 |
Character.toString(pherogramProvider.getBaseCall(i)))); |
|
726 |
} |
|
727 |
setDirty(); |
|
728 |
} |
|
729 |
|
|
730 |
if (tokens != null) { // If either an edited sequence or a pherogram URI was provided. |
|
731 |
model.insertTokensAt(id, 0, tokens); |
|
732 |
|
|
733 |
if (pherogramProvider != null) { |
|
734 |
// Create pherogram area: |
|
735 |
PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(), |
|
736 |
new PherogramAreaModel(pherogramProvider)); |
|
737 |
|
|
738 |
// Set position properties and shifts: |
|
739 |
PherogramAreaModel phergramModel = pherogramArea.getModel(); |
|
740 |
if ((firstSeqPos != null) && (leftCutPos != null)) { |
|
741 |
phergramModel.setFirstSeqLeftCutPos(firstSeqPos, leftCutPos); |
|
742 |
} |
|
743 |
if (rightCutPos != null) { |
|
744 |
phergramModel.setRightCutPosition(rightCutPos); |
|
745 |
} |
|
746 |
if ((shifts != null) && (shifts.length > 0)) { |
|
747 |
for (int i = 0; i < shifts.length; i++) { |
|
748 |
phergramModel.addShiftChange(shifts[i].position, shifts[i].shift); |
|
749 |
} |
|
750 |
setDirty(); |
|
751 |
} |
|
752 |
|
|
753 |
// Add pherogram area to GUI: |
|
754 |
pherogramArea.addMouseListener(new PherogramMouseListener(pherogramArea)); |
|
755 |
getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea); |
|
756 |
} |
|
757 |
} |
|
758 |
return id; |
|
759 |
} |
|
760 |
|
|
761 |
|
|
762 |
public static URI getPherogramURI(SingleRead pherogramInfo) { |
|
763 |
if (pherogramInfo.getPherogram() != null) { |
|
764 |
return MediaUtils.getFirstMediaRepresentationPart(pherogramInfo.getPherogram()).getUri(); |
|
765 |
} |
|
766 |
else { |
|
767 |
return null; |
|
768 |
} |
|
769 |
} |
|
770 |
} |
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/e4/PherogramPartE4.java | ||
---|---|---|
1 |
/** |
|
2 |
* Copyright (C) 2007 EDIT |
|
3 |
* European Distributed Institute of Taxonomy |
|
4 |
* http://www.e-taxonomy.eu |
|
5 |
* |
|
6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
8 |
*/ |
|
9 |
package eu.etaxonomy.taxeditor.molecular.editor.e4; |
|
10 |
|
|
11 |
|
|
12 |
import javax.annotation.PostConstruct; |
|
13 |
|
|
14 |
import org.eclipse.swt.SWT; |
|
15 |
import org.eclipse.swt.widgets.Composite; |
|
16 |
|
|
17 |
import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor; |
|
18 |
import info.bioinfweb.libralign.pherogram.PherogramFormats.QualityOutputType; |
|
19 |
import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel; |
|
20 |
import info.bioinfweb.libralign.pherogram.view.PherogramView; |
|
21 |
import info.bioinfweb.tic.SWTComponentFactory; |
|
22 |
|
|
23 |
|
|
24 |
|
|
25 |
/** |
|
26 |
* Component that allows to view a pherogram without the distortion due to aligning it to a sequence as in |
|
27 |
* {@link AlignmentEditor}. |
|
28 |
* |
|
29 |
* @author Ben Stöver |
|
30 |
* @date Nov 20, 2014 |
|
31 |
*/ |
|
32 |
public class PherogramPartE4 { |
|
33 |
public static final String ID = "eu.etaxonomy.taxeditor.molecular.PherogramView"; //$NON-NLS-1$ |
|
34 |
|
|
35 |
private PherogramView pherogramView = null; |
|
36 |
|
|
37 |
public PherogramView getPherogramView() { |
|
38 |
if (pherogramView == null) { |
|
39 |
pherogramView = new PherogramView(); |
|
40 |
pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(true); |
|
41 |
pherogramView.getTraceCurveView().setHorizontalScale(1); |
|
42 |
pherogramView.getTraceCurveView().setVerticalScale(100); |
|
43 |
pherogramView.getTraceCurveView().getFormats().setQualityOutputType(QualityOutputType.NONE); //TODO Make this user defined |
|
44 |
pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(false); |
|
45 |
} |
|
46 |
return pherogramView; |
|
47 |
} |
|
48 |
|
|
49 |
|
|
50 |
@PostConstruct |
|
51 |
public void createPartControl(Composite parent) { |
|
52 |
SWTComponentFactory.getInstance().getSWTComponent(getPherogramView(), parent, SWT.NONE); |
|
53 |
getPherogramView().assignSize(); |
|
54 |
} |
|
55 |
|
|
56 |
public void init(PherogramComponentModel model){ |
|
57 |
getPherogramView().getTraceCurveView().setModel(model); |
|
58 |
getPherogramView().assignSize(); |
|
59 |
} |
|
60 |
|
|
61 |
} |
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/e4/handler/AlignmentEditorCopyHandlerE4.java | ||
---|---|---|
1 |
package eu.etaxonomy.taxeditor.molecular.editor.e4.handler; |
|
2 |
|
|
3 |
|
|
4 |
import javax.inject.Named; |
|
5 |
|
|
6 |
import org.eclipse.e4.core.di.annotations.CanExecute; |
|
7 |
import org.eclipse.e4.core.di.annotations.Execute; |
|
8 |
import org.eclipse.e4.ui.model.application.ui.basic.MPart; |
|
9 |
import org.eclipse.e4.ui.services.IServiceConstants; |
|
10 |
import org.eclipse.swt.dnd.TextTransfer; |
|
11 |
import org.eclipse.swt.dnd.Transfer; |
|
12 |
|
|
13 |
import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4; |
|
14 |
import info.bioinfweb.libralign.alignmentarea.AlignmentArea; |
|
15 |
import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel; |
|
16 |
import info.bioinfweb.libralign.model.utils.AlignmentModelUtils; |
|
17 |
|
|
18 |
|
|
19 |
|
|
20 |
/** |
|
21 |
* Handler that copies the currently selected nucleotides from an alignment editor to the clipboard. |
|
22 |
* <p> |
|
23 |
* The copied contents either come from the single reads or the consensus sequence alignment area, |
|
24 |
* depending on which component currently has the focus. If none of these components has the focus, |
|
25 |
* nothing will be copied, even if nucleotides are currently selected. |
|
26 |
* <p> |
|
27 |
* If the selection contains parts of multiple sequence, these are separated by the line separator |
|
28 |
* of the current operating system. |
|
29 |
* |
|
30 |
* @author Ben Stöver |
|
31 |
* @date 25.08.2015 |
|
32 |
*/ |
|
33 |
public class AlignmentEditorCopyHandlerE4 { |
|
34 |
|
|
35 |
@Execute |
|
36 |
protected void doExecute2(@Named(IServiceConstants.ACTIVE_PART)MPart activePart) { |
|
37 |
AlignmentEditorE4 editor = (AlignmentEditorE4) activePart.getObject(); |
|
38 |
AlignmentArea focusedArea = editor.getFocusedArea(); |
|
39 |
SelectionModel selection = focusedArea.getSelection(); |
|
40 |
if (!selection.isEmpty()) { |
|
41 |
editor.CLIPBOARD.setContents(new Object[]{AlignmentModelUtils.selectionAsString(focusedArea, false)}, |
|
42 |
new Transfer[]{TextTransfer.getInstance()}); |
|
43 |
} |
|
44 |
} |
|
45 |
|
|
46 |
|
|
47 |
@CanExecute |
|
48 |
public boolean isEnabled(@Named(IServiceConstants.ACTIVE_PART)MPart activePart) { |
|
49 |
AlignmentEditorE4 editor = (AlignmentEditorE4) activePart.getObject(); |
|
50 |
if (editor != null) { |
|
51 |
AlignmentArea focusedArea = editor.getFocusedArea(); |
|
52 |
if (focusedArea != null) { |
|
53 |
return !focusedArea.getSelection().isEmpty(); |
|
54 |
} |
|
55 |
} |
|
56 |
return false; |
|
57 |
} |
|
58 |
|
|
59 |
} |
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/e4/handler/AlignmentEditorCutHandlerE4.java | ||
---|---|---|
1 |
package eu.etaxonomy.taxeditor.molecular.editor.e4.handler; |
|
2 |
|
|
3 |
|
|
4 |
import javax.inject.Named; |
|
5 |
|
|
6 |
import org.eclipse.e4.core.di.annotations.CanExecute; |
|
7 |
import org.eclipse.e4.core.di.annotations.Execute; |
|
8 |
import org.eclipse.e4.ui.model.application.ui.basic.MPart; |
|
9 |
import org.eclipse.e4.ui.services.IServiceConstants; |
|
10 |
|
|
11 |
import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4; |
|
12 |
import info.bioinfweb.libralign.alignmentarea.AlignmentArea; |
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
/** |
|
17 |
* Handler that cuts the currently selected nucleotides from an alignment editor to the clipboard. |
|
18 |
* <p> |
|
19 |
* The cut contents either come from the single reads or the consensus sequence alignment area, |
|
20 |
* depending on which component currently has the focus. If none of these components has the focus, |
|
21 |
* nothing will be cut, even if nucleotides are currently selected. |
|
22 |
* <p> |
|
23 |
* If the selection contains parts of multiple sequence, these are separated by the line separator |
|
24 |
* of the current operating system. |
|
25 |
* |
|
26 |
* @author Ben Stöver |
|
27 |
* @date 25.08.2015 |
|
28 |
*/ |
|
29 |
public class AlignmentEditorCutHandlerE4 extends AlignmentEditorCopyHandlerE4 { |
|
30 |
|
|
31 |
@Override |
|
32 |
@Execute |
|
33 |
protected void doExecute2(@Named(IServiceConstants.ACTIVE_PART)MPart activePart) { |
|
34 |
super.doExecute2(activePart); // Copy selected contents. |
|
35 |
AlignmentEditorE4 editor = (AlignmentEditorE4) activePart.getObject(); |
|
36 |
AlignmentArea focusedArea = editor.getFocusedArea(); |
|
37 |
focusedArea.getActionProvider().deleteSelection(); |
|
38 |
} |
|
39 |
|
|
40 |
|
|
41 |
@Override |
|
42 |
@CanExecute |
|
43 |
public boolean isEnabled(@Named(IServiceConstants.ACTIVE_PART)MPart activePart) { |
|
44 |
AlignmentEditorE4 editor = (AlignmentEditorE4) activePart.getObject(); |
|
45 |
if (editor != null) { |
|
46 |
AlignmentArea focusedArea = editor.getFocusedArea(); |
|
47 |
if (focusedArea != null) { |
|
48 |
return !focusedArea.getSelection().isEmpty(); |
|
49 |
} |
|
50 |
} |
|
51 |
return false; |
|
52 |
} |
|
53 |
|
|
54 |
} |
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/e4/handler/AlignmentEditorPasteHandlerE4.java | ||
---|---|---|
1 |
package eu.etaxonomy.taxeditor.molecular.editor.e4.handler; |
|
2 |
|
|
3 |
|
|
4 |
import java.util.ArrayList; |
|
5 |
import java.util.List; |
|
6 |
import java.util.Scanner; |
|
7 |
|
|
8 |
import javax.inject.Named; |
|
9 |
|
|
10 |
import org.eclipse.e4.core.di.annotations.CanExecute; |
|
11 |
import org.eclipse.e4.core.di.annotations.Execute; |
|
12 |
import org.eclipse.e4.ui.model.application.ui.basic.MPart; |
|
13 |
import org.eclipse.e4.ui.services.IServiceConstants; |
|
14 |
import org.eclipse.jface.dialogs.MessageDialog; |
|
15 |
import org.eclipse.swt.dnd.TextTransfer; |
|
16 |
import org.eclipse.swt.widgets.Shell; |
|
17 |
|
|
18 |
import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor; |
|
19 |
import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4; |
|
20 |
import eu.etaxonomy.taxeditor.molecular.l10n.Messages; |
|
21 |
import info.bioinfweb.libralign.alignmentarea.AlignmentArea; |
|
22 |
import info.bioinfweb.libralign.alignmentarea.order.SequenceOrder; |
|
23 |
import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel; |
|
24 |
import info.bioinfweb.libralign.model.AlignmentModel; |
|
25 |
import info.bioinfweb.libralign.model.utils.AlignmentModelUtils; |
|
26 |
|
|
27 |
|
|
28 |
|
|
29 |
/** |
|
30 |
* Handler that pastes the current contents of the clipboard into an active instance of {@link AlignmentEditor}. |
|
31 |
* |
|
32 |
* @author Ben Stöver |
|
33 |
* @date 26.08.2015 |
|
34 |
*/ |
|
35 |
public class AlignmentEditorPasteHandlerE4 { |
|
36 |
|
|
37 |
private void pasteString(AlignmentArea area, String sequenceID, String content) { |
|
38 |
area.getActionProvider().deleteSelection(); // Overwrite selected tokens. |
|
39 |
area.getActionProvider().elongateSequence(sequenceID, area.getSelection().getCursorColumn()); |
|
40 |
|
|
41 |
@SuppressWarnings("unchecked") |
|
42 |
AlignmentModel<Object> alignmentModel = (AlignmentModel<Object>)area.getAlignmentModel(); |
|
43 |
alignmentModel.insertTokensAt(sequenceID, area.getSelection().getCursorColumn(), |
|
44 |
AlignmentModelUtils.charSequenceToTokenList(content, alignmentModel.getTokenSet(), |
|
45 |
true, alignmentModel.getTokenSet().getGapToken())); |
|
46 |
} |
|
47 |
|
|
48 |
|
|
49 |
@Execute |
|
50 |
protected void execute(@Named(IServiceConstants.ACTIVE_PART)MPart activePart, |
|
51 |
@Named(IServiceConstants.ACTIVE_SHELL)Shell shell) { |
|
52 |
AlignmentEditorE4 editor = (AlignmentEditorE4) activePart.getObject(); |
|
53 |
AlignmentArea focusedArea = editor.getFocusedArea(); |
|
54 |
|
|
55 |
SelectionModel selection = focusedArea.getSelection(); |
|
56 |
String clipboardText = (String)editor.CLIPBOARD.getContents(TextTransfer.getInstance()); |
|
57 |
if (clipboardText != null) { |
|
58 |
List<String> lines = new ArrayList<String>(); |
|
59 |
Scanner scanner = new Scanner(clipboardText); |
|
60 |
try { |
|
61 |
while (scanner.hasNext()) { |
|
62 |
lines.add(scanner.nextLine()); |
|
63 |
} |
|
64 |
if (lines.get(lines.size() - 1).equals("")) { //$NON-NLS-1$ |
|
65 |
lines.remove(lines.size() - 1); |
|
66 |
} |
|
67 |
} |
|
68 |
finally { |
|
69 |
scanner.close(); |
|
70 |
} |
|
71 |
|
|
72 |
if (!lines.isEmpty()) { //TODO Can lines be empty? (Can an empty string "" be copied to the clipboard?) |
|
73 |
if (selection.getCursorHeight() == 1) { // If the consensus sequence is focused, this is the only possible case. |
|
74 |
String sequenceID = focusedArea.getSequenceOrder().idByIndex(selection.getCursorRow()); |
|
75 |
if (lines.size() == 1) { |
|
76 |
pasteString(focusedArea, sequenceID, lines.get(0)); |
|
77 |
} |
|
78 |
else { |
|
79 |
MessageDialog dialog = new MessageDialog(shell, |
|
80 |
Messages.AlignmentEditorPasteHandler_PASTING_LINES, null, |
|
81 |
String.format(Messages.AlignmentEditorPasteHandler_PASTING_LINES_QUESTION, lines.size()), |
|
82 |
MessageDialog.QUESTION, |
|
83 |
new String[]{Messages.AlignmentEditorPasteHandler_PASTING_LINES_IGNORE, |
|
84 |
Messages.AlignmentEditorPasteHandler_PASTING_LINES_FIRST_LINE, Messages.AlignmentEditorPasteHandler_CANCEL}, |
|
85 |
0); |
|
86 |
//TODO Does the dialog have to be disposed in some way? |
|
87 |
|
|
88 |
switch (dialog.open()) { |
|
89 |
case 0: // Paste all lines in one sequence. |
|
90 |
pasteString(focusedArea, sequenceID, clipboardText); |
|
91 |
break; |
|
92 |
case 1: // Paste only first line. |
|
93 |
pasteString(focusedArea, sequenceID, lines.get(0)); |
|
94 |
break; |
|
95 |
} |
|
96 |
} |
|
97 |
} |
|
98 |
else { |
|
99 |
if (selection.getCursorHeight() == lines.size()) { |
|
100 |
SequenceOrder order = focusedArea.getSequenceOrder(); |
|
101 |
for (int i = 0; i < selection.getCursorHeight(); i++) { |
|
102 |
pasteString(focusedArea, order.idByIndex(selection.getCursorRow() + i), lines.get(i)); // Multiple calls of deleteSelection() in here are unnecessary, but should have no effect. |
|
103 |
} |
|
104 |
} |
|
105 |
else { |
|
106 |
MessageDialog.openError(shell, |
|
107 |
Messages.AlignmentEditorPasteHandler_PASTE_FAILURE, |
|
108 |
String.format(Messages.AlignmentEditorPasteHandler_PASTE_FAILURE_MESSAGE, selection.getCursorHeight(), lines.size(), System.getProperty("line.separator"))); //$NON-NLS-1$ |
|
109 |
} |
|
110 |
} |
|
111 |
} |
|
112 |
} |
|
113 |
} |
|
114 |
|
|
115 |
|
|
116 |
@CanExecute |
|
117 |
public boolean isEnabled(@Named(IServiceConstants.ACTIVE_PART)MPart activePart) { |
|
118 |
AlignmentEditorE4 editor = (AlignmentEditorE4) activePart.getObject(); |
|
119 |
AlignmentArea focusedArea = editor.getFocusedArea(); |
|
120 |
focusedArea = editor.getFocusedArea(); |
|
121 |
return (focusedArea != null); |
|
122 |
} |
|
123 |
|
|
124 |
} |
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/e4/handler/ChangePherogramQualityOutputTypeE4.java | ||
---|---|---|
1 |
/** |
|
2 |
* Copyright (C) 2015 EDIT |
|
3 |
* European Distributed Institute of Taxonomy |
|
4 |
* http://www.e-taxonomy.eu |
|
5 |
* |
|
6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
8 |
*/ |
|
9 |
package eu.etaxonomy.taxeditor.molecular.editor.e4.handler; |
|
10 |
|
|
11 |
|
|
12 |
import javax.inject.Named; |
|
13 |
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import org.eclipse.e4.core.di.annotations.Execute; |
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import org.eclipse.e4.ui.model.application.ui.basic.MPart; |
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import org.eclipse.e4.ui.services.IServiceConstants; |
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import eu.etaxonomy.taxeditor.molecular.editor.e4.PherogramPartE4; |
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/** |
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* Switches between the quality output types available for components displaying pherograms. |
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* |
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* @author Ben Stöver |
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* @date 19.06.2015 |
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*/ |
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public class ChangePherogramQualityOutputTypeE4 { |
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@Execute |
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public void doExecute(@Named(IServiceConstants.ACTIVE_PART)MPart activePart) { |
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PherogramPartE4 pherogramPart = (PherogramPartE4) activePart.getObject(); |
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pherogramPart.getPherogramView().getTraceCurveView().getFormats().changeQualityOutputType(); |
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} |
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} |
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/e4/handler/CreateConsensusSequenceHandlerE4.java | ||
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/** |
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* Copyright (C) 2007 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.taxeditor.molecular.editor.e4.handler; |
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import javax.inject.Named; |
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import org.eclipse.e4.core.di.annotations.Execute; |
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import org.eclipse.e4.ui.model.application.ui.basic.MPart; |
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import org.eclipse.e4.ui.services.IServiceConstants; |
Also available in: Unified diff
ref #6902 migrate alignment editor and pherogram view