import org.eclipse.e4.ui.services.IServiceConstants;
import org.eclipse.e4.ui.workbench.modeling.EModelService;
import org.eclipse.e4.ui.workbench.modeling.EPartService;
+import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.jface.viewers.TreeNode;
import org.eclipse.ui.PartInitException;
@Execute
- public void execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)TreeNode treeNodeOfSelection,
+ public void execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)IStructuredSelection selection,
EPartService partService, EModelService modelService, MApplication application) {
- if(treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence){
- AlignmentEditorInput input = new AlignmentEditorInput(((Sequence)treeNodeOfSelection.getValue()).getUuid()); //TODO Should there always be a new instance created here? What if the specified CDM node is already opened in an AlignmentEditor? => Possible create Singleton that keeps instances by sequence objects in a map.
- try {
- String partId = AppModelId.PARTDESCRIPTOR_EU_ETAXONOMY_TAXEDITOR_MOLECULAR_EDITOR_E4_ALIGNMENTEDITORE4;
- MPart part = EditorUtil.showPart(partId, modelService, partService, application);
- AlignmentEditorE4 alignmentEditor = (AlignmentEditorE4) part.getObject();
- alignmentEditor.init(input);
- }
- catch (PartInitException e) {
- logger.error(Messages.EditSequenceHandler_COULD_NOT_OPEN, e);
- }
+ Sequence sequence = (Sequence) ((TreeNode) selection.getFirstElement()).getValue();
+ AlignmentEditorInput input = new AlignmentEditorInput(sequence.getUuid()); //TODO Should there always be a new instance created here? What if the specified CDM node is already opened in an AlignmentEditor? => Possible create Singleton that keeps instances by sequence objects in a map.
+ try {
+ String partId = AppModelId.PARTDESCRIPTOR_EU_ETAXONOMY_TAXEDITOR_MOLECULAR_EDITOR_E4_ALIGNMENTEDITORE4;
+ MPart part = EditorUtil.showPart(partId, modelService, partService, application);
+ AlignmentEditorE4 alignmentEditor = (AlignmentEditorE4) part.getObject();
+ alignmentEditor.init(input);
+ }
+ catch (PartInitException e) {
+ logger.error(Messages.EditSequenceHandler_COULD_NOT_OPEN, e);
}
}
@CanExecute
- public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) TreeNode selectedTreeNode, MHandledMenuItem menuItem) {
+ public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) IStructuredSelection selection, MHandledMenuItem menuItem) {
boolean canExecute = false;
- if(selectedTreeNode!=null){
- Object value = selectedTreeNode.getValue();
- canExecute = value instanceof Sequence;
- }
+ canExecute = selection.size()==1
+ && selection.getFirstElement() instanceof TreeNode
+ && ((TreeNode) selection.getFirstElement()).getValue() instanceof Sequence;
menuItem.setVisible(canExecute);
return canExecute;
}
import org.eclipse.e4.core.di.annotations.Optional;
import org.eclipse.e4.ui.model.application.ui.menu.MHandledMenuItem;
import org.eclipse.e4.ui.services.IServiceConstants;
+import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.jface.viewers.TreeNode;
import org.eclipse.jface.wizard.WizardDialog;
import org.eclipse.swt.widgets.Shell;
@Execute
- public Object execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)TreeNode treeNodeOfSelection,
+ public void execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)IStructuredSelection selection,
@Named(IServiceConstants.ACTIVE_SHELL)Shell shell) {
- if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence) {
- Sequence sequence = (Sequence)treeNodeOfSelection.getValue();
-
- final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard();
- final WizardDialog dialog = new WizardDialog(shell, wizard);
- if (dialog.open() == IStatus.OK) {
- // Prepare writer parameters:
- ReadWriteParameterMap parameters = new ReadWriteParameterMap();
- parameters.put(ReadWriteParameterNames.KEY_APPLICATION_NAME, ApplicationUtil.getTitle());
- //parameters.put(ReadWriteParameterNames.KEY_APPLICATION_VERSION, ApplicationUtil.getVersion()); // Setting the version unnecessary, since its already contained in the title.
- parameters.put(ReadWriteParameterNames.KEY_APPLICATION_URL, "http://cybertaxonomy.eu/taxeditor/"); //TODO Specify URL obtained from a central class? //$NON-NLS-1$
- parameters.put(ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN, wizard.getModel().getElongationToken());
-
- // Create and register object translator for writing pherogram alignment shifts:
- ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory();
- translatorFactory.addXSDTranslators(true);
- translatorFactory.addTranslator(new CDMPherogramAlignmentObjectTranslator(), true, SingleReadAlignmentRDFXMLConstants.DATA_TYPE_PHERORAGM_ALIGNMENT);
- parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory);
-
- // Create writer and document adapters:
- JPhyloIOEventWriter writer = factory.getWriter(wizard.getModel().getFormatInfo().getFormatID());
- ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();
- document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel(),
- wizard.getModel().isExportConsensusSequence(), wizard.getModel().isExportSingleReads()));
-
- // Write document:
- File file = new File(wizard.getModel().getFileName());
- if (!file.exists() || MessagingUtils.confirmDialog(Messages.exportSequenceToFileHandlerOverwriteTitle, String.format(
- Messages.exportSequenceToFileHandlerOverwriteText, file.getAbsolutePath()))) {
-
- try {
- writer.writeDocument(document, file, parameters);
- }
- catch (IOException e) {
- e.printStackTrace();
- MessagingUtils.errorDialog(Messages.exportSequenceToFileHandlerIOErrorTitle, this,
- String.format(Messages.exportSequenceToFileHandlerIOErrorMessage,
- file.getAbsolutePath()), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);
- }
+ Sequence sequence = (Sequence) ((TreeNode) selection.getFirstElement()).getValue();
+
+ final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard();
+ final WizardDialog dialog = new WizardDialog(shell, wizard);
+ if (dialog.open() == IStatus.OK) {
+ // Prepare writer parameters:
+ ReadWriteParameterMap parameters = new ReadWriteParameterMap();
+ parameters.put(ReadWriteParameterNames.KEY_APPLICATION_NAME, ApplicationUtil.getTitle());
+ //parameters.put(ReadWriteParameterNames.KEY_APPLICATION_VERSION, ApplicationUtil.getVersion()); // Setting the version unnecessary, since its already contained in the title.
+ parameters.put(ReadWriteParameterNames.KEY_APPLICATION_URL, "http://cybertaxonomy.eu/taxeditor/"); //TODO Specify URL obtained from a central class? //$NON-NLS-1$
+ parameters.put(ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN, wizard.getModel().getElongationToken());
+
+ // Create and register object translator for writing pherogram alignment shifts:
+ ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory();
+ translatorFactory.addXSDTranslators(true);
+ translatorFactory.addTranslator(new CDMPherogramAlignmentObjectTranslator(), true, SingleReadAlignmentRDFXMLConstants.DATA_TYPE_PHERORAGM_ALIGNMENT);
+ parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory);
+
+ // Create writer and document adapters:
+ JPhyloIOEventWriter writer = factory.getWriter(wizard.getModel().getFormatInfo().getFormatID());
+ ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();
+ document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel(),
+ wizard.getModel().isExportConsensusSequence(), wizard.getModel().isExportSingleReads()));
+
+ // Write document:
+ File file = new File(wizard.getModel().getFileName());
+ if (!file.exists() || MessagingUtils.confirmDialog(Messages.exportSequenceToFileHandlerOverwriteTitle, String.format(
+ Messages.exportSequenceToFileHandlerOverwriteText, file.getAbsolutePath()))) {
+
+ try {
+ writer.writeDocument(document, file, parameters);
+ }
+ catch (IOException e) {
+ e.printStackTrace();
+ MessagingUtils.errorDialog(Messages.exportSequenceToFileHandlerIOErrorTitle, this,
+ String.format(Messages.exportSequenceToFileHandlerIOErrorMessage,
+ file.getAbsolutePath()), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);
}
-
}
+
}
- return null;
}
@CanExecute
- public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) TreeNode selectedTreeNode, MHandledMenuItem menuItem) {
+ public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) IStructuredSelection selection, MHandledMenuItem menuItem) {
boolean canExecute = false;
- if(selectedTreeNode!=null){
- Object value = selectedTreeNode.getValue();
- canExecute = value instanceof Sequence;
- }
+ canExecute = selection.size()==1
+ && selection.getFirstElement() instanceof TreeNode
+ && ((TreeNode) selection.getFirstElement()).getValue() instanceof Sequence;
menuItem.setVisible(canExecute);
return canExecute;
}
import org.eclipse.e4.ui.services.IServiceConstants;
import org.eclipse.e4.ui.workbench.modeling.EPartService;
import org.eclipse.e4.ui.workbench.modeling.EPartService.PartState;
+import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.jface.viewers.TreeNode;
import eu.etaxonomy.cdm.model.media.MediaUtils;
*/
public class ShowPherogramHandlerE4 {
- @Execute
- public Object execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)TreeNode treeNodeOfSelection,
- EPartService partService) {
- if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof SingleRead) {
- //TODO Can the parent node (containing the cut positions) be extracted from SingleRead?
- try {
- SingleRead singleRead = (SingleRead)treeNodeOfSelection.getValue();
- URI uri = null;
- if (singleRead.getPherogram() != null) { // Pherogram objects without URI are possible.
- uri = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri();
- }
+ @Execute
+ public void execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)IStructuredSelection selection,
+ EPartService partService) {
+ //TODO Can the parent node (containing the cut positions) be extracted from SingleRead?
+ try {
+ SingleRead singleRead = (SingleRead) ((TreeNode) selection.getFirstElement()).getValue();
+ URI uri = null;
+ if (singleRead.getPherogram() != null) { // Pherogram objects without URI are possible.
+ uri = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri();
+ }
- if (uri == null) {
- MessagingUtils.messageDialog(Messages.ShowPherogramHandler_NO_PHEROGRAM, this,
- Messages.ShowPherogramHandler_NO_PHEROGRAM_MESSAGE);
- }
- else {
- MPart part = partService.createPart(eu.etaxonomy.taxeditor.molecular.AppModelId.PARTDESCRIPTOR_EU_ETAXONOMY_TAXEDITOR_MOLECULAR_EDITOR_E4_PHEROGRAMPARTE4);
- part = partService.showPart(part, PartState.ACTIVATE);
- PherogramPartE4 pherogramPart = (PherogramPartE4) part.getObject();
- pherogramPart.init(new PherogramComponentModel(AlignmentEditorE4.readPherogram(uri)));
- }
- }
- catch (Exception e) {
- MessagingUtils.errorDialog(Messages.ShowPherogramHandler_ERROR, null, e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID,
- e, false);
- }
+ if (uri == null) {
+ MessagingUtils.messageDialog(Messages.ShowPherogramHandler_NO_PHEROGRAM, this,
+ Messages.ShowPherogramHandler_NO_PHEROGRAM_MESSAGE);
+ }
+ else {
+ MPart part = partService.createPart(eu.etaxonomy.taxeditor.molecular.AppModelId.PARTDESCRIPTOR_EU_ETAXONOMY_TAXEDITOR_MOLECULAR_EDITOR_E4_PHEROGRAMPARTE4);
+ part = partService.showPart(part, PartState.ACTIVATE);
+ PherogramPartE4 pherogramPart = (PherogramPartE4) part.getObject();
+ pherogramPart.init(new PherogramComponentModel(AlignmentEditorE4.readPherogram(uri)));
+ }
+ }
+ catch (Exception e) {
+ MessagingUtils.errorDialog(Messages.ShowPherogramHandler_ERROR, null, e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID,
+ e, false);
}
- return null;
}
@CanExecute
- public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) TreeNode selectedTreeNode, MHandledMenuItem menuItem) {
+ public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) IStructuredSelection selection, MHandledMenuItem menuItem) {
boolean canExecute = false;
- if(selectedTreeNode!=null){
- Object value = selectedTreeNode.getValue();
- canExecute = value instanceof SingleRead;
- }
+ canExecute = selection.size()==1
+ && selection.getFirstElement() instanceof TreeNode
+ && ((TreeNode) selection.getFirstElement()).getValue() instanceof SingleRead;
menuItem.setVisible(canExecute);
return canExecute;
}
BGBM BDI Projects / taxeditor.git / commitdiff