net.bioclipse.cdk.ui.wizards.NewSdfWizard.java Source code

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Here is the source code for net.bioclipse.cdk.ui.wizards.NewSdfWizard.java

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/*
 * Copyright (C) 2005 Bioclipse Project
 *
 * 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:
 *     Stefan Kuhn - Implementation of new sdf wizard
 */
package net.bioclipse.cdk.ui.wizards;

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

import net.bioclipse.cdk.business.Activator;
import net.bioclipse.chemoinformatics.wizards.WizardHelper;
import net.bioclipse.core.domain.IMolecule;
import net.bioclipse.core.util.LogUtils;

import org.apache.log4j.Logger;
import org.eclipse.core.resources.IContainer;
import org.eclipse.core.resources.IFile;
import org.eclipse.core.runtime.CoreException;
import org.eclipse.jface.dialogs.MessageDialog;
import org.eclipse.jface.viewers.ISelection;
import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.jface.viewers.StructuredSelection;
import org.eclipse.ui.IWorkbench;
import org.eclipse.ui.PlatformUI;
import org.eclipse.ui.dialogs.WizardNewFileCreationPage;
import org.eclipse.ui.wizards.newresource.BasicNewResourceWizard;

/**
 * A wizard to create a new sd file from existing structure files.
 *
 */
public class NewSdfWizard extends BasicNewResourceWizard {
    private SelectFilesWizardPage specPage;
    private WizardNewFileCreationPage newsdPage;
    private static final Logger logger = Logger.getLogger(NewSdfWizard.class);

    public NewSdfWizard() {
        super();
        setWindowTitle("Create a New SD File");
    }

    /**
     * Adding the pages to the wizard.
     */
    public void addPages() {
        ISelection sel = PlatformUI.getWorkbench().getActiveWorkbenchWindow().getSelectionService().getSelection();
        if (sel instanceof IStructuredSelection) {
            newsdPage = new WizardNewFileCreationPage("newFilePage1", (IStructuredSelection) sel);
            newsdPage.setFileName(WizardHelper.findUnusedFileName((IStructuredSelection) sel, "unnamed", ".sdf"));
        } else {
            newsdPage = new WizardNewFileCreationPage("newFilePage1", StructuredSelection.EMPTY);
        }
        newsdPage.setTitle("Choose name and location for new file");
        newsdPage.setDescription("Extension will be .sdf if none is given");
        addPage(newsdPage);
        specPage = new SelectFilesWizardPage(true, sel);
        addPage(specPage);

    }

    @Override
    public boolean performFinish() {
        try {
            if (newsdPage.getFileExtension() == null || newsdPage.getFileExtension().equals(""))
                newsdPage.setFileExtension("sdf");
            IFile newFile = newsdPage.createNewFile();
            newFile.delete(true, null);
            Iterator<?> it = specPage.getSelectedRes().iterator();
            List<IMolecule> entries = new ArrayList<IMolecule>();
            List<IFile> failures = new ArrayList<IFile>();
            while (it.hasNext()) {
                Object selection = it.next();
                if (selection instanceof IFile) {
                    try {
                        entries.add(
                                Activator.getDefault().getJavaCDKManager().loadMolecules((IFile) selection).get(0));
                    } catch (Exception e) {
                        failures.add((IFile) selection);
                    }
                }
                if (selection instanceof IContainer && specPage.doRecursive()) {
                    try {
                        doRecursion((IContainer) selection, entries, failures);
                    } catch (CoreException e) {
                        LogUtils.handleException(e, logger);
                    }
                }
            }
            if (failures.size() > 0) {
                StringBuffer sb = new StringBuffer();
                for (int i = 0; i < failures.size(); i++) {
                    sb.append(failures.get(i).getName() + "; ");
                }
                MessageDialog.openError(this.getShell(), "Problems parsings files",
                        "Some of the files you selected could not be read ("
                                + sb.toString().substring(0, sb.toString().length() - 2)
                                + "). We will still use the rest!");
            }
            if (entries.size() == 0) {
                MessageDialog.openError(this.getShell(), "No valid entries found",
                        "Your selection does not contain any valid molecule files. No file can be created!");
            } else {
                Activator.getDefault().getJavaCDKManager().saveSDFile(newFile, entries);
                selectAndReveal(newFile);
            }
        } catch (Exception e) {
            LogUtils.handleException(e, logger);
        }
        return true;
    }

    private void doRecursion(IContainer selection, List<IMolecule> entries, List<IFile> failures)
            throws CoreException {
        for (int i = 0; i < selection.members().length; i++) {
            if (selection.members()[i] instanceof IContainer)
                doRecursion((IContainer) selection.members()[i], entries, failures);
            if (selection.members()[i] instanceof IFile) {
                try {
                    entries.add(Activator.getDefault().getJavaCDKManager()
                            .loadMolecules((IFile) selection.members()[i]).get(0));
                } catch (Exception e) {
                    failures.add((IFile) selection.members()[i]);
                }
            }
        }
    }

    public void init(IWorkbench workbench, IStructuredSelection selection) {
        super.init(workbench, selection);
    }
}