net.bioclipse.chembl.moss.ui.wizard.ChemblMossWizard.java Source code

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Here is the source code for net.bioclipse.chembl.moss.ui.wizard.ChemblMossWizard.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.moss.ui.wizard;

import java.io.IOException;
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.jface.dialogs.MessageDialog;
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.ui.INewWizard;
import org.eclipse.ui.IWorkbench;
import org.eclipse.ui.PlatformUI;
import org.eclipse.ui.dialogs.WizardNewFileCreationPage;

public class ChemblMossWizard extends Wizard implements INewWizard {

    private static final Logger logger = Logger.getLogger(ChemblMossWizard.class);
    private ChemblMossWizardPage1 firstpage;
    private ChemblMossWizardPage2 secondpage;
    private ChemblMossWizardPage3 thirdpage;
    private WizardNewFileCreationPage filePage, queryfile;
    private IChEMBLManager chembl;
    ChemblMossData data = new ChemblMossData();

    public ChemblMossWizard() {
        super();
        setWindowTitle("ChEMBL-MoSS");
        chembl = Activator.getDefault().getJavaChEMBLManager();
    }

    public void addPages() {
        firstpage = new ChemblMossWizardPage1("ChEMBL MoSS page");
        addPage(firstpage);

        secondpage = new ChemblMossWizardPage2("ChEMBL MoSS page 2");
        addPage(secondpage);

        //      thirdpage = new ChemblMossWizardPage3("ChEMBL MoSS page 3");
        //      addPage(thirdpage);

        ISelection sel = PlatformUI.getWorkbench().getActiveWorkbenchWindow().getSelectionService().getSelection();
        if (sel instanceof IStructuredSelection) {
            filePage = new WizardNewFileCreationPage("newFilePage", (IStructuredSelection) sel);
            filePage.setFileName(WizardHelper.findUnusedFileName((IStructuredSelection) sel, "chemblMoss", ".txt"));
            //         queryfile = new WizardNewFileCreationPage("newFilePage", (IStructuredSelection) sel);
            //         queryfile.setFileName(WizardHelper.findUnusedFileName((IStructuredSelection)sel, "chemblMoss", ".sparql") );
        } 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;
    }

    public boolean performCancel() {
        boolean answer = MessageDialog.openConfirm(getShell(), "Confirmation", "Are you sure you want to cancel?");
        if (answer)
            return true;
        else
            return false;
    }

    /*Writes compounds to a MoSS supported file.
     * Uses ChemblMossData to collect stored information.*/
    @Override
    public boolean performFinish() {
        try {

            if (filePage.getFileExtension() == null || filePage.getFileExtension().equals(""))
                filePage.setFileExtension("txt");
            IFile newFile = filePage.createNewFile();
            newFile.delete(true, null);
            int help = newFile.getFullPath().toString().length();
            IFile sparqlFile = ResourcePathTransformer.getInstance()
                    .transform(newFile.getFullPath().toString().substring(0, help - 4) + "Sparql.sparql");
            IFile infoFile = ResourcePathTransformer.getInstance()
                    .transform(newFile.getFullPath().toString().substring(0, help - 4) + "CompleteInfo.txt");

            //         chembl.saveMossFormatFile(data.mm, data.matrix);
            //         if(data.matrix != null && data.matrix2 == null)
            //            chembl.saveToMossFormat(data.m, data.matrix);
            //         else if(data.matrix != null && data.matrix2 != null){
            //            chembl.saveToMossFormat(data.m, data.matrix, data.matrix2);}
            //         else if(data.matrix == null && data.matrix2 != null)
            //            chembl.saveToMossFormat(data.m, data.matrix2);

            if (data.matrix != null && data.matrix2 == null)
                chembl.saveToMossFormat(newFile, data.matrix);
            else if (data.matrix != null && data.matrix2 != null)
                chembl.saveToMossFormat(newFile, data.matrix, data.matrix2);
            else if (data.matrix == null && data.matrix2 != null)
                chembl.saveToMossFormat(newFile, data.matrix2);

            //         chembl.saveFile(data.queryFile, data.query);
            chembl.saveFile(sparqlFile, data.query);
            chembl.saveCSV(infoFile, data.matrix3);
        } 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

    }

}