/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package jalview.io;

import jalview.datamodel.*;

import jalview.gui.*;

import org.apache.axis.client.*;

import java.util.*;

import javax.swing.*;

import javax.xml.namespace.QName;
import jalview.analysis.AlignSeq;

import uk.ac.ebi.www.*;

/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class WSWUBlastClient
{
    AlignmentPanel ap;
    AlignmentI al;
    CutAndPasteTransfer output = new CutAndPasteTransfer();
    int jobsRunning = 0;

    Vector suggestedIds = new Vector();
    /**
     * Creates a new WSWUBlastClient object.
     *
     * @param al DOCUMENT ME!
     * @param ids DOCUMENT ME!
     */
    public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
    {
        this.ap = ap;
        this.al = al;
        output.setText(
            "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
            +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
            +"\n\nRunning WSWUBlast at EBI."
            +"\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
            +"\nSOAP-based services provided by the European Bioinformatics Institute."
            +"\nNucleic Acids Res. 33(1):W25-W28 (2005));");

        Desktop.addInternalFrame(output,
            "BLASTing for unidentified sequences ", 800, 300);

        for (int i = 0; i < ids.size(); i++)
        {
            Sequence sequence = (Sequence)ids.get(i);
            System.out.println(sequence.getName());

            BlastThread thread = new BlastThread(sequence);
            thread.start();
            jobsRunning++;
        }

        ImageTwirler thread = new ImageTwirler();
        thread.start();
    }


    /**
     * DOCUMENT ME!
     *
     * @param id1 DOCUMENT ME!
     * @param res DOCUMENT ME!
     */
    void parseResult(Sequence seq, String res)
    {
        StringTokenizer st = new StringTokenizer(res, "\n");
        String data;
        String id2;
        int maxFound = 90;
        StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");

        while (st.hasMoreTokens())
        {
            data = st.nextToken();

            if (data.indexOf(">UNIPROT") > -1)
            {
                int index = data.indexOf(">UNIPROT") + 9;
                id2 = data.substring(index, data.indexOf(" ", index));

                boolean identitiesFound = false;
                while (!identitiesFound)
                {
                    data = st.nextToken();

                    if (data.indexOf("Identities") > -1)
                    {
                       identitiesFound = true;

                       int value = Integer.parseInt(data.substring(data.indexOf(
                           "(") + 1,
                                                                   data.indexOf("%")));

                        if (value >= maxFound)
                        {
                            maxFound = value;
                            buffer.append(" " + id2 + " " + value + "%; ");
                            suggestedIds.addElement( new Object[]{seq, id2});
                        }
                    }
                }
            }
        }

        output.appendText(buffer.toString());
    }

    void updateIds()
    {
        // This must be outside the run() body as java 1.5
     // will not return any value from the OptionPane to the expired thread.
      int reply = JOptionPane.showConfirmDialog(
          Desktop.desktop, "Automatically update suggested ids?",
          "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);

      if (reply == JOptionPane.YES_OPTION)
      {
        Enumeration keys = suggestedIds.elements();
        while(keys.hasMoreElements())
        {
          Object [] object = (Object[])keys.nextElement();

          Sequence oldseq = (Sequence)object[0];

          oldseq.setName( object[1].toString() );

          // Oldseq is actually in the dataset, we must find the
          // Visible seq and change its name also.
          for (int i = 0; i < al.getHeight(); i++)
          {
            if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
            {
              al.getSequenceAt(i).setName(oldseq.getName());
              break;
            }
          }

          Vector entries = oldseq.getDBRef();
          if (entries != null)
          {
            DBRefEntry entry = (DBRefEntry) entries.elementAt(0);
            oldseq.addDBRef(new jalview.datamodel.
                                                 DBRefEntry("UNIPROT",
                "0",
                entry.getAccessionId()));
          }
        }
      }
      ap.repaint();

    }

    class ImageTwirler extends Thread
    {
        ImageIcon[] imageIcon;
        int imageIndex = 0;

        public ImageTwirler()
        {
            imageIcon = new ImageIcon[9];

            for (int i = 0; i < 9; i++)
            {
                java.net.URL url = getClass().getResource("/images/dna" +
                        (i + 1) + ".gif");

                if (url != null)
                {
                    imageIcon[i] = new ImageIcon(url);
                }
            }
        }

        public void run()
        {
            while (jobsRunning > 0)
            {
                try
                {
                    Thread.sleep(100);
                    imageIndex++;
                    imageIndex %= 9;
                    output.setFrameIcon(imageIcon[imageIndex]);
                    output.setTitle("BLASTing for unidentified sequences - " +
                        jobsRunning + " jobs running.");
                }
                catch (Exception ex)
                {
                }
            }

            if (jobsRunning == 0)
            {
              updateIds();
            }
        }
    }

    class BlastThread extends Thread
    {
        Sequence sequence;
        String jobid;
        boolean jobComplete = false;

        BlastThread(Sequence sequence)
        {
          System.out.println("blasting for: "+sequence.getName());
          this.sequence = sequence;
        }

        public void run()
        {
            StartJob();

            while (!jobComplete)
            {
                try
                {
                  WSWUBlastService service =  new WSWUBlastServiceLocator();
                  WSWUBlast wublast = service.getWSWUBlast();
                  WSFile[] results = wublast.getResults(jobid);

                  if(results!=null)
                  {
                      String result = new String(wublast.poll(jobid, "tooloutput"));
                      parseResult(sequence, result);
                      jobComplete = true;
                      jobsRunning--;
                  }
                  else
                  {
                    Thread.sleep(10000);
                    System.out.println("WSWuBlastClient: I'm alive " +
                                       sequence.getName() + " " + jobid); // log.debug
                  }
                }
                catch (Exception ex)
                {
                }
            }
        }

        void StartJob()
        {
          InputParams params = new InputParams();

          params.setProgram("blastp");
          params.setDatabase("uniprot");
          params.setMatrix("pam10");

          params.setNumal(5);
          params.setSensitivity("low");
          params.setSort("totalscore");
          params.setOutformat("txt");
          params.setAsync(true);

            try
            {
              Data inputs[] = new Data[1];
              Data input= new Data();
              input.setType("sequence");
              input.setContent(AlignSeq.extractGaps("-. ",sequence.getSequence()));
              inputs[0]=input;

              WSWUBlastService service = new WSWUBlastServiceLocator();
              WSWUBlast wublast = service.getWSWUBlast();
              jobid = wublast.runWUBlast(params, inputs);
            }
            catch (Exception exp)
            {
              jobComplete = true;
              jobsRunning--;
              System.err.println("WSWUBlastClient error:\n" + exp.toString());
              exp.printStackTrace();
            }
        }
    }
}