Example usage for org.eclipse.jface.viewers IStructuredSelection toList

List of usage examples for org.eclipse.jface.viewers IStructuredSelection toList

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Introduction

In this page you can find the example usage for org.eclipse.jface.viewers IStructuredSelection toList.

Prototype

public List toList();

Source Link

Document

Returns the elements in this selection as a List.

Usage

From source file:mx.itesm.imb.handlers.Util.java

License:Open Source License

/**
 * Get the current selected elements when a plugin operation is executed.
 * //from   w w w.  j  a va2s. c om
 * @param event
 * @return
 */
public static List<?> getSelectedItems(final ExecutionEvent event) {
    List<?> returnValue;
    IStructuredSelection currentSelection;

    currentSelection = (IStructuredSelection) HandlerUtil.getCurrentSelection(event);
    returnValue = currentSelection.toList();

    return returnValue;
}

From source file:name.martingeisse.esdk.eclipse.EsdkNatureDelegate.java

License:Open Source License

@Override
public void run(final IAction action) {
    if (selection instanceof IStructuredSelection) {
        final IStructuredSelection structuredSelection = (IStructuredSelection) selection;
        for (final Object element : structuredSelection.toList()) {
            if (element instanceof IProject) {
                final IProject project = (IProject) element;
                if (action.getId()
                        .equals("name.martingeisse.esdk.ProjectPopupMenuContribution.AddEsdkNature")) {
                    addNature(project);/*from  ww  w  .j  a va 2s .  c o m*/
                } else if (action.getId()
                        .equals("name.martingeisse.esdk.ProjectPopupMenuContribution.RemoveEsdkNature")) {
                    deleteNature(project);
                } else {
                    Activator.getDefault()
                            .logWarning("EsdkNatureDelegate invoked for unknown action id: " + action.getId());
                }
            } else {
                Activator.getDefault()
                        .logWarning("EsdkNatureDelegate invoked for unknown target object: " + element);
            }
        }
    }
}

From source file:name.schedenig.eclipse.grepconsole.view.styles.StylesPanel.java

License:Open Source License

/**
 * Returns the selected styles./* w  ww .  j  a v a  2  s.  c  om*/
 * 
 * @return Styles. May be empty.
 */
public Collection<GrepStyle> getSelectedStyles() {
    List<GrepStyle> styles = new LinkedList<GrepStyle>();
    IStructuredSelection selection = (IStructuredSelection) viewer.getSelection();

    if (selection != null) {
        for (Object o : selection.toList()) {
            if (o instanceof GrepStyle) {
                styles.add((GrepStyle) o);
            }
        }
    }

    return styles;
}

From source file:net.bhl.cdt.paxelerate.ui.handlers.MoveObjectHandler.java

License:Open Source License

@Override
public final Object execute(final ExecutionEvent event) throws ExecutionException {
    ISelection sel = HandlerUtil.getActiveMenuSelection(event);
    IStructuredSelection selection = (IStructuredSelection) sel;

    for (Object object : selection.toList()) {
        if (object instanceof Row) {
            rowlist.add((Row) object);//  w w  w  .  ja va 2s .  c o  m
        } else if (object instanceof Seat) {
            seatlist.add((Seat) object);
        } else if (object instanceof Galley) {
            galleylist.add((Galley) object);
        } else if (object instanceof Lavatory) {
            lavatorylist.add((Lavatory) object);
        } else if (object instanceof Curtain) {
            curtainlist.add((Curtain) object);
        } else {
            /* ignore other objects */
        }
    }
    if (!rowlist.isEmpty()) {
        cabin = ModelHelper.getParent(Cabin.class, rowlist.get(0));
    } else if (!seatlist.isEmpty()) {
        cabin = ModelHelper.getParent(Cabin.class, seatlist.get(0));
    } else if (!galleylist.isEmpty()) {
        cabin = ModelHelper.getParent(Cabin.class, galleylist.get(0));
    } else if (!lavatorylist.isEmpty()) {
        cabin = ModelHelper.getParent(Cabin.class, lavatorylist.get(0));
    } else if (!curtainlist.isEmpty()) {
        cabin = ModelHelper.getParent(Cabin.class, curtainlist.get(0));
    } else {
        cabin = null;
    }

    new MoveObjectCommand(cabin, rowlist, seatlist, galleylist, lavatorylist, curtainlist).execute();

    /*
     * clear all lists in order to prevent the unintentioal movement of
     * several items edited before
     */
    rowlist.clear();
    seatlist.clear();
    galleylist.clear();
    lavatorylist.clear();
    curtainlist.clear();

    return null;
}

From source file:net.bioclipse.align.kalign.ws.handlers.KalignPopupHandler.java

License:Open Source License

public Object execute(ExecutionEvent event) throws ExecutionException {

    ISelection sel = HandlerUtil.getCurrentSelection(event);
    if (!(sel instanceof IStructuredSelection))
        return null;

    IStructuredSelection ssel = (IStructuredSelection) sel;

    final Shell shell = HandlerUtil.getActiveShell(event);

    final IBiojavaManager biojava = net.bioclipse.biojava.business.Activator.getDefault()
            .getJavaBiojavaManager();//from   ww w .jav a2  s .  c o  m

    final List<IProtein> proteins = new ArrayList<IProtein>();
    final List<String> names = new ArrayList<String>();
    IProject firstProject = null;
    for (Object obj : ssel.toList()) {
        if (obj instanceof IFile) {
            IFile file = (IFile) obj;
            if (firstProject == null)
                firstProject = file.getProject();
            try {

                List<IProtein> readProts = biojava.proteinsFromFile(file);

                proteins.addAll(readProts);
                String fname = file.getName();
                if (fname.lastIndexOf(".") > 0)
                    fname = fname.substring(0, fname.lastIndexOf("."));
                names.add(fname);
            } catch (FileNotFoundException e) {
                logger.error("Could not find file: " + file.getLocation());
            } catch (Exception e) {
                MessageDialog.openError(shell, "Kalign",
                        "Error parsing proteins. Make sure you have valid files!");
                return null;
            }
        }
    }

    if (firstProject == null) {
        MessageDialog.openError(shell, "Kalign", "No output project could be located.");
        return null;
    }

    if (proteins.size() <= 0) {
        MessageDialog.openError(shell, "Kalign", "No proteins could be parsed");
        return null;
    }
    if (proteins.size() == 0) {
        MessageDialog.openError(shell, "Kalign",
                "Only one protein could be parsed, " + "need a minimum of two proteins to align.");
        return null;
    }

    final IProject project = firstProject;

    Job job = new Job("Kalign") {

        @Override
        protected IStatus run(IProgressMonitor monitor) {

            IKalignManager kalign = Activator.getDefault().getKalignManager();
            List<IProtein> alignedProteins;
            try {
                alignedProteins = kalign.alignProteins(proteins, monitor);
            } catch (BioclipseException e) {
                LogUtils.handleException(e, logger, "net.bioclipse.align.kalign.ws");
                return Status.CANCEL_STATUS;
            }
            List<ISequence> alignedSequences = new ArrayList<ISequence>();
            for (ISequence seq : alignedProteins)
                alignedSequences.add(IProtein.class.cast(seq));

            //Generate a new filename
            String newFileName = "";
            for (String name : names) {
                newFileName = newFileName.concat(name + "_");
            }
            newFileName = newFileName.substring(0, newFileName.length() - 1);
            newFileName = newFileName.concat("_aligned.fasta");

            logger.debug("New alignment file to save: " + newFileName);

            //Serialize to temp file and open in SeqEditor
            IFile newfile = project.getFile(newFileName);
            if (newfile.exists()) {
                final Boolean[] ret = new Boolean[1];
                final String name = newFileName;
                final Boolean[] valueSet = new Boolean[] { false };

                Display.getDefault().asyncExec(new Runnable() {
                    public void run() {
                        synchronized (ret) {
                            ret[0] = MessageDialog.openConfirm(shell, "Overwrite?",
                                    "Resulting alignment file " + name + " exists. Overwrite?");
                        }
                        synchronized (valueSet) {
                            valueSet[0] = true;
                            valueSet.notifyAll();
                        }
                    }
                });

                while (!valueSet[0]) {
                    synchronized (valueSet) {
                        try {
                            valueSet.wait();
                        } catch (InterruptedException e) {
                            throw new RuntimeException("Interruped", e);
                        }
                    }
                }
                if (ret[0] == false)
                    return Status.CANCEL_STATUS;
            }

            //Save aligned proteins to file
            biojava.proteinsToFASTAfile(alignedProteins, newfile);

            try {
                project.refreshLocal(1, new NullProgressMonitor());
            } catch (CoreException e) {
                //Not much we can do if refresh fails. Should not happen.
            }

            //Open saved file
            IUIManager ui = net.bioclipse.ui.business.Activator.getDefault().getUIManager();
            ui.open(newfile);

            return Status.OK_STATUS;
        }
    };
    job.setUser(true);
    job.schedule();

    return null;
}

From source file:net.bioclipse.balloon.handlers.BalloonConformerHandler.java

License:Open Source License

public Object execute(ExecutionEvent event) throws ExecutionException {

    ISelection sel = HandlerUtil.getCurrentSelection(event);
    if (sel == null)
        return null;
    if (!(sel instanceof StructuredSelection))
        return null;
    IStructuredSelection ssel = (IStructuredSelection) sel;

    //We operate on files and IMolecules
    List<String> filenames = new ArrayList<String>();
    List<IResource> foldersToRefresh = new ArrayList<IResource>();
    //Collect files
    for (Object obj : ssel.toList()) {
        if (obj instanceof IFile) {
            IFile file = (IFile) obj;//from   w ww . j a  v  a 2s .  com
            //                filenames.add( file.getRawLocation().toOSString() );
            filenames.add(file.getFullPath().toOSString());
            foldersToRefresh.add(file.getParent());
        }
    }

    logger.debug("Balloon selection contained: " + filenames.size() + " files.");

    if (filenames.size() <= 0)
        return null;

    BalloonDialog dlg = new BalloonDialog(HandlerUtil.getActiveShell(event));
    int ret = dlg.open();
    if (ret == Window.CANCEL)
        return null;

    final int numconf = dlg.getNumConformers();

    logger.debug("User selected: " + numconf + " confomers.");

    final List<String> final_fnames = filenames;
    final List<IResource> final_foldersToRefresh = foldersToRefresh;

    //Set up a job
    Job job = new Job("Ballon 3D conformer generation") {
        protected IStatus run(IProgressMonitor monitor) {

            monitor.beginTask("Running Balloon 3D conformer generation: " + numconf + " conformers for "
                    + final_fnames + " files", 2);
            monitor.worked(1);

            //Run balloon on the files
            IBalloonManager balloon = Activator.getDefault().getJavaBalloonManager();
            List<String> ret = null;
            try {
                ret = balloon.generate3Dconformations(final_fnames, numconf);
            } catch (BioclipseException e) {
                logger.error("Balloon failed: " + e.getMessage());
                return new Status(IStatus.ERROR, Activator.PLUGIN_ID, "Balloon failed: " + e.getMessage());
            }

            if (ret == null) {
                logger.error("Balloon failed: " + ret);
                return new Status(IStatus.ERROR, Activator.PLUGIN_ID, "Balloon failed.");
            }
            for (String r : ret) {
                logger.debug("Balloon wrote output file: " + r);
            }

            //Refresh folders in UI thread
            Display.getDefault().syncExec(new Runnable() {
                public void run() {
                    for (IResource res : final_foldersToRefresh) {
                        try {
                            res.refreshLocal(IResource.DEPTH_ONE, new NullProgressMonitor());
                        } catch (CoreException e) {
                            logger.error("Could not refresh resource: " + res + " - " + e.getMessage());
                        }
                    }

                }
            });

            monitor.done();

            return Status.OK_STATUS;
        }
    };
    job.setPriority(Job.LONG);
    job.setUser(true);
    job.schedule(); // start as soon as possible

    return null;
}

From source file:net.bioclipse.balloon.handlers.BalloonGen3DHandler.java

License:Open Source License

/**
 * the command has been executed, so extract extract the needed information
 * from the application context.//from   w ww.j a v a  2s. c o  m
 */
public Object execute(ExecutionEvent event) throws ExecutionException {

    ISelection sel = HandlerUtil.getCurrentSelection(event);
    if (sel == null)
        return null;
    if (!(sel instanceof StructuredSelection))
        return null;
    IStructuredSelection ssel = (IStructuredSelection) sel;

    //We operate on files and IMolecules
    List<IFile> inputFiles = new ArrayList<IFile>();
    List<IResource> foldersToRefresh = new ArrayList<IResource>();
    //Collect files
    for (Object obj : ssel.toList()) {
        if (obj instanceof IFile) {
            IFile file = (IFile) obj;
            //                filenames.add( file.getRawLocation().toOSString() );
            inputFiles.add(file);
            foldersToRefresh.add(file.getParent());
        }
    }

    logger.debug("Balloon selection contained: " + inputFiles.size() + " files.");

    if (inputFiles.size() <= 0)
        return null;

    final List<String> final_fnames = null;
    final List<IResource> final_foldersToRefresh = foldersToRefresh;

    IContentType cmlType = Platform.getContentTypeManager()
            .getContentType("net.bioclipse.contenttypes.cml.singleMolecule2d");

    IBalloonManager balloon = Activator.getDefault().getJavaBalloonManager();
    for (IFile input : inputFiles) {
        try {
            IContentDescription contentDescirpton = input.getContentDescription();
            if (contentDescirpton != null && contentDescirpton.getContentType().isKindOf(cmlType)) {
                String output = balloon.generate3Dcoordinates(input.getRawLocation().toOSString());
                Display.getDefault().syncExec(new Runnable() {
                    public void run() {
                        for (IResource res : final_foldersToRefresh) {
                            try {
                                res.refreshLocal(IResource.DEPTH_ONE, new NullProgressMonitor());
                            } catch (CoreException e) {
                                logger.error("Could not refresh resource: " + res + " - " + e.getMessage());
                            }
                        }

                    }
                });
                ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
                List<ICDKMolecule> molecules = cdk.loadMolecules(output);
                cdk.saveMolecule(molecules.get(0), output, true);

                return null;
            }
        } catch (Exception e) {
            LogUtils.handleException(e, logger, "net.bioclipse.balloon.business");
            return null;
        }

        balloon.generate3Dcoordinates(input, new BioclipseUIJob<IFile>() {

            @Override
            public void runInUI() {

                try {
                    IFile result = this.getReturnValue();
                    result.getParent().refreshLocal(IResource.DEPTH_ONE, new NullProgressMonitor());
                } catch (CoreException e) {
                    LogUtils.handleException(e, logger, "net.bioclipse.balloon.business");
                }
            }
        });
    }
    //Set up a job
    Job job = new Job("Ballon 3D conformer generation") {
        protected IStatus run(IProgressMonitor monitor) {

            monitor.beginTask("Running Balloon 3D conformer generation", 2);
            monitor.worked(1);

            //Run balloon on the files
            IBalloonManager balloon = Activator.getDefault().getJavaBalloonManager();
            List<String> ret = null;
            try {
                ret = balloon.generate3Dcoordinates(final_fnames);
            } catch (BioclipseException e) {
                logger.error("Balloon failed: " + e.getMessage());
                return new Status(IStatus.ERROR, Activator.PLUGIN_ID, "Balloon failed: " + e.getMessage());
            }

            if (ret == null) {
                logger.error("Balloon failed: " + ret);
                return new Status(IStatus.ERROR, Activator.PLUGIN_ID, "Balloon failed.");
            }
            for (String r : ret) {
                logger.debug("Balloon wrote output file: " + r);
            }

            //Refresh folders in UI thread
            Display.getDefault().syncExec(new Runnable() {
                public void run() {
                    for (IResource res : final_foldersToRefresh) {
                        try {
                            res.refreshLocal(IResource.DEPTH_ONE, new NullProgressMonitor());
                        } catch (CoreException e) {
                            logger.error("Could not refresh resource: " + res + " - " + e.getMessage());
                        }
                    }

                }
            });

            monitor.done();

            return Status.OK_STATUS;
        }
    };
    // job.setPriority(Job.LONG);
    // job.setUser( true );
    // job.schedule(); // start as soon as possible

    //Bring forth the ProgressView

    /*
    //Collect and serialize smiles to temp file, 
    String smilesfile="";
    String linesep=System.getProperty("line.separator");
    if (linesep==null) linesep="\n";
            
    for (Object obj : ssel.toList()){
    if ( obj instanceof IMolecule ) {
        IMolecule mol = (IMolecule) obj;
        String smilestext;
        try {
            smilestext = mol.getSMILES();
            smilesfile=smilesfile+smilestext+ linesep;
        } catch ( BioclipseException e ) {
            logger.debug("Could not get smiles from Imol: " + mol 
                         + ". Skipped in balloon: " + e.getMessage());
        }
    }
    }
            
            
            
    try {
    File tfile = File.createTempFile( "balloontemp", "smi" );
    FileWriter writer= new FileWriter(tfile);
    writer.write( smilesfile );
    writer.close();
            
    //Run balloon on this file
            
    } catch ( IOException e ) {
    e.printStackTrace();
    }
     */

    return null;

}

From source file:net.bioclipse.cdk.smartsmatching.views.SmartsMatchingView.java

License:Open Source License

private void makeActions() {

    collapseAllAction = new Action() {
        public void run() {
            viewer.collapseAll();// w  w  w  .j  a  v  a 2s.c o m
        }
    };
    collapseAllAction.setText("Collapse all");
    collapseAllAction.setToolTipText("Collapse all SMARTS");
    collapseAllAction.setImageDescriptor(Activator.getImageDecriptor("icons/collapseall.gif"));

    expandAllAction = new Action() {
        public void run() {
            viewer.expandAll();
        }
    };
    expandAllAction.setText("Expand all");
    expandAllAction.setToolTipText("Expand all SMARTS to reveal hits");
    expandAllAction.setImageDescriptor(Activator.getImageDecriptor("icons/expandall.gif"));

    runAction = new Action() {
        public void run() {
            runSmartsMatching();
        }
    };
    runAction.setText("Run matching");
    runAction.setToolTipText("Run SMARTS matching for the active aditor");
    runAction.setImageDescriptor(Activator.getImageDecriptor("icons/smallRun.gif"));

    clearAction = new Action() {
        public void run() {
            //Re-read from prefs, creates new objects
            smartsInView = SmartsMatchingPrefsHelper.getPreferences();
            viewer.setInput(smartsInView);
        }
    };
    clearAction.setText("Clear matches");
    clearAction.setToolTipText("Clear all SMARTS matches");
    clearAction.setImageDescriptor(Activator.getImageDecriptor("icons/clear_co.gif"));

    addSmartsAction = new Action() {
        public void run() {

            AddEditSmartsDialog dlg = new AddEditSmartsDialog(getSite().getShell());
            int ret = dlg.open();
            if (ret == Window.CANCEL)
                return;

            SmartsWrapper wrapper = dlg.getSmartsWrapper();

            //Add to current list
            smartsInView.add(wrapper);

            savePrefsAndUpdate();

        }
    };
    addSmartsAction.setText("Add SMARTS");
    addSmartsAction.setToolTipText("Add a SMARTS entry");
    addSmartsAction.setImageDescriptor(Activator.getImageDecriptor("icons/add_obj.gif"));

    removeSmartsAction = new Action() {
        public void run() {

            if (!(viewer.getSelection() instanceof IStructuredSelection)) {
                showError("Please select one or more SMARTS to remove");
                return;
            }
            IStructuredSelection ssel = (IStructuredSelection) viewer.getSelection();

            boolean prefsChanged = false;
            for (Object obj : ssel.toList()) {
                if (obj instanceof SmartsWrapper) {
                    prefsChanged = true;
                    SmartsWrapper swToRemove = (SmartsWrapper) obj;
                    //For all lists, remove this smart
                    for (Iterator<IWorkbenchPart> it = editorSmartsMap.keySet().iterator(); it.hasNext();) {
                        IWorkbenchPart part = it.next();
                        editorSmartsMap.get(part).remove(swToRemove);
                    }
                    smartsInView.remove(swToRemove);
                }
            }

            if (prefsChanged) {
                //Write list to preferences
                SmartsMatchingPrefsHelper.setPreferences(smartsInView);
                viewer.refresh();
            }

        }
    };
    removeSmartsAction.setText("Remove SMARTS");
    removeSmartsAction.setToolTipText("Remove the selected SMARTS");
    removeSmartsAction.setImageDescriptor(Activator.getImageDecriptor("icons/delete_obj.gif"));

    showPropertiesViewAction = new Action() {
        public void run() {
            IWorkbenchPage page = getSite().getWorkbenchWindow().getActivePage();
            try {
                page.showView(IPageLayout.ID_PROP_SHEET);
            } catch (PartInitException e) {
                showError("Could not show Properties View: " + e.getMessage());
            }
        }
    };
    showPropertiesViewAction.setText("Show Properties");
    showPropertiesViewAction.setToolTipText("Show the Properties View");
    showPropertiesViewAction.setImageDescriptor(Activator.getImageDecriptor("icons/table_row_props.gif"));

}

From source file:net.bioclipse.cdk.ui.handlers.CalculateRMSDMatrixHandler.java

License:Open Source License

public Object execute(ExecutionEvent event) throws ExecutionException {
    ISelection sel = PlatformUI.getWorkbench().getActiveWorkbenchWindow().getSelectionService().getSelection();
    if (!sel.isEmpty() && sel instanceof IStructuredSelection) {
        IStructuredSelection ssel = (IStructuredSelection) sel;
        ICDKManager cdk = Activator.getDefault().getJavaCDKManager();
        IUIManager ui = net.bioclipse.ui.business.Activator.getDefault().getUIManager();
        List<IMolecule> molecules = new ArrayList<IMolecule>(ssel.size());
        for (Object file : ssel.toList())
            molecules.add(cdk.loadMolecule((IFile) file));
        String path = "/Virtual/rmsd.csv";
        while (ui.fileExists(path))
            path = "/Virtual/rmsd" + UUID.randomUUID() + ".csv";
        try {//from w  w w .j ava2s .c om
            String matrix = cdk.calculateRMSD(molecules, path);
            ui.open(matrix);
        } catch (BioclipseException cause) {
            throw new ExecutionException("Error while calculating RMSD matrix...", cause);
        }
    }
    return null;
}

From source file:net.bioclipse.cdk.ui.handlers.CalculateTanimotoMatrixHandler.java

License:Open Source License

public Object execute(ExecutionEvent event) throws ExecutionException {
    ISelection sel = PlatformUI.getWorkbench().getActiveWorkbenchWindow().getSelectionService().getSelection();
    if (!sel.isEmpty() && sel instanceof IStructuredSelection) {
        IStructuredSelection ssel = (IStructuredSelection) sel;
        ICDKManager cdk = Activator.getDefault().getJavaCDKManager();
        IUIManager ui = net.bioclipse.ui.business.Activator.getDefault().getUIManager();
        List<IMolecule> molecules = new ArrayList<IMolecule>(ssel.size());
        for (Object file : ssel.toList())
            molecules.add(cdk.loadMolecule((IFile) file));
        String path = "/Virtual/matrix.csv";
        while (ui.fileExists(path))
            path = "/Virtual/matrix" + UUID.randomUUID() + ".csv";
        try {//  w  w w . j  a v a  2  s . c om
            String matrix = cdk.calculateTanimoto(molecules, path);
            ui.open(matrix, "net.bioclipse.editors.MatrixGridEditor");
        } catch (BioclipseException cause) {
            throw new ExecutionException("Error while calculating Tanimoto matrix...", cause);
        }
    }
    return null;
}