net.bioclipse.balloon.handlers.BalloonConformerHandler.java Source code

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Here is the source code for net.bioclipse.balloon.handlers.BalloonConformerHandler.java

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/* *****************************************************************************
 * Copyright (c) 2009 Ola Spjuth.
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 * 
 * Contributors:
 *     Ola Spjuth - initial API and implementation
 ******************************************************************************/
package net.bioclipse.balloon.handlers;

import java.util.ArrayList;
import java.util.List;

import net.bioclipse.balloon.business.Activator;
import net.bioclipse.balloon.business.IBalloonManager;
import net.bioclipse.balloon.ui.BalloonDialog;
import net.bioclipse.core.business.BioclipseException;

import org.apache.log4j.Logger;
import org.eclipse.core.commands.AbstractHandler;
import org.eclipse.core.commands.ExecutionEvent;
import org.eclipse.core.commands.ExecutionException;
import org.eclipse.core.resources.IFile;
import org.eclipse.core.resources.IResource;
import org.eclipse.core.runtime.CoreException;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.IStatus;
import org.eclipse.core.runtime.NullProgressMonitor;
import org.eclipse.core.runtime.Status;
import org.eclipse.core.runtime.jobs.Job;
import org.eclipse.jface.viewers.ISelection;
import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.jface.viewers.StructuredSelection;
import org.eclipse.jface.window.Window;
import org.eclipse.swt.widgets.Display;
import org.eclipse.ui.handlers.HandlerUtil;

public class BalloonConformerHandler extends AbstractHandler {

    private static final Logger logger = Logger.getLogger(BalloonConformerHandler.class);

    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;
                //                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;
    }
}