net.bioclipse.chembl.ui.wizard.ChemblWizard.java Source code

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Here is the source code for net.bioclipse.chembl.ui.wizard.ChemblWizard.java

Source

/* Copyright (c) 2010  Egon Willighagen <egonw@users.sf.net>
 *               2010  Annsofie Andersson <annzi.andersson@gmail.com>
 *
 * 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
 *
 * Contact: http://www.bioclipse.net/
 */
package net.bioclipse.chembl.ui.wizard;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.ObjectOutput;
import java.io.ObjectOutputStream;
import java.util.ArrayList;

import net.bioclipse.chembl.Activator;
import net.bioclipse.chembl.business.IChEMBLManager;
import net.bioclipse.chembl.business.WizardHelper;
import net.bioclipse.core.ResourcePathTransformer;
import net.bioclipse.core.business.BioclipseException;

import org.apache.log4j.Logger;
import org.eclipse.core.resources.IFile;
import org.eclipse.core.runtime.CoreException;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.NullProgressMonitor;
import org.eclipse.jface.viewers.ISelection;
import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.jface.viewers.StructuredSelection;
import org.eclipse.jface.wizard.Wizard;
import org.eclipse.swt.SWT;
import org.eclipse.swt.widgets.Table;
import org.eclipse.swt.widgets.TableItem;
import org.eclipse.ui.INewWizard;
import org.eclipse.ui.IWorkbench;
import org.eclipse.ui.PlatformUI;
import org.eclipse.ui.dialogs.WizardNewFileCreationPage;

public class ChemblWizard extends Wizard implements INewWizard {

    private static final Logger logger = Logger.getLogger(ChemblWizard.class);
    private ChemblWizardPage firstpage;
    //   private ChemblWizardPage2 secondpage;
    private WizardNewFileCreationPage filePage;
    private IChEMBLManager chembl;
    ChemblData data = new ChemblData();

    public ChemblWizard() {
        super();
        setWindowTitle("ChEMBL wizard");
        chembl = Activator.getDefault().getJavaChEMBLManager();
    }

    public void addPages() {
        firstpage = new ChemblWizardPage("ChEMBL page");
        addPage(firstpage);
        //        secondpage = new ChemblWizardPage2("ChEMBL page");
        //        addPage(secondpage);

        ISelection sel = PlatformUI.getWorkbench().getActiveWorkbenchWindow().getSelectionService().getSelection();
        if (sel instanceof IStructuredSelection) {
            filePage = new WizardNewFileCreationPage("newFilePage", (IStructuredSelection) sel);

            filePage.setFileName(WizardHelper.findUnusedFileName((IStructuredSelection) sel, "chembl", ".txt"));
        } else {
            filePage = new WizardNewFileCreationPage("newFilePage", StructuredSelection.EMPTY);
        }
        filePage.setTitle("Choose location and add a file name to create a new file");
        filePage.setDescription("Extension will be .txt if none is given");
        addPage(filePage);
    }

    @Override
    public boolean isHelpAvailable() {
        return true;
    }

    //Writes compounds to a MoSS supported file
    @Override
    public boolean performFinish() {
        try {
            if (filePage.getFileExtension() == null || filePage.getFileExtension().equals(""))
                filePage.setFileExtension("txt");
            IFile newFile = filePage.createNewFile();
            newFile.delete(true, null);
            chembl.saveCSVT(newFile, data.tab, null);
            //old version         chembl.saveCSVT(data.file,data.tab, null);
        } catch (BioclipseException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (CoreException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return true;
    }

    @Override
    public void init(IWorkbench workbench, IStructuredSelection selection) {
        // TODO Auto-generated method stub

    }
}