/*
* 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 org.apache.axis.client.*;
import javax.xml.namespace.QName;
import java.util.*;
import jalview.datamodel.*;
import jalview.gui.*;
import javax.swing.*;
import java.util.*;
import java.awt.*;

public class WSWUBlastClient
{
  CutAndPasteTransfer output = new CutAndPasteTransfer();
  int jobsRunning = 0;

  public WSWUBlastClient(AlignmentI al, ArrayList ids)
  {
    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.");
    Desktop.addInternalFrame(output, "BLASTing for unidentified sequences ", 800,300);

    for(int i=0; i<ids.size(); i++)
    {
     SequenceI sequence =  al.findName( ids.get(i).toString() );
     StringBuffer nonGapped = new StringBuffer();
      for (int n = 0; n < sequence.getSequence().length(); n++)
      {
        if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))
          nonGapped.append(sequence.getCharAt(n));
      }

     BlastThread thread = new BlastThread(ids.get(i).toString(),  nonGapped.toString());
     thread.start();
     jobsRunning ++;
     }
     ImageTwirler thread = new ImageTwirler();
     thread.start();
  }

  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){}

      }
    }
  }




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

    BlastThread(String id, String sequence)
    {
      this.sequence = sequence;
      seqid = id;
    }

    public void run()
    {
      StartJob();

      while (!jobComplete)
      {
        try
        {
          Call call = (Call)new Service().createCall();
          call.setTargetEndpointAddress(new java.net.URL(
              "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
          call.setOperationName(new QName("WSWUBlast", "polljob"));
          String result = (String) call.invoke(new Object[]
                                               {jobid, "xml"});
          if(result.indexOf("JOB PENDING")==-1 && result.indexOf("JOB RUNNING")==-1)
          {
                parseResult(seqid, result);
                jobComplete = true;
                jobsRunning --;
          }
          Thread.sleep(5000);
          // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug
        }
        catch (Exception ex)
        {}
      }
    }

    void StartJob()
    {
      HashMap params = new HashMap();
      params.put("database", "uniprot");
      params.put("sensitivity", "low");
      params.put("sort", "totalscore");
      params.put("matrix", "pam10");
      params.put("program", "blastp");
      params.put("alignments", "5");
      params.put("outformat", "xml");
      params.put("searchtype", "1");
      byte[] seqbytes = sequence.getBytes();

      try
      {
        Call call = (Call)new Service().createCall();
        call.setTargetEndpointAddress(new java.net.URL(
            "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
        call.setOperationName(new QName("WSWUBlast", "doWUBlast"));
        String result = (String) call.invoke(new Object[]
                                             {params, seqbytes});
        jobid = result;
        System.out.println("http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '"+jobid+"'");

      }
      catch (Exception exp)
      {
        System.err.println("WSWUBlastClient error:\n" + exp.toString());
        exp.printStackTrace();
      }
    }
  }

    void parseResult(String id1, String res)
    {
      StringTokenizer st = new StringTokenizer(res, "\n");
      String data;
      String id2;
      int maxFound = 90;
      StringBuffer buffer = new StringBuffer("\n\n"+id1+" :");

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

        if(data.indexOf("database=\"uniprot\" id=")>-1)
        {
          int index =  data.indexOf("database=\"uniprot\" id=")+ 23;
          id2 = data.substring( index, data.indexOf("\"", index) );
          while( data.indexOf("</alignment>")==-1)
          {
            data = st.nextToken();
            if(data.indexOf("<identity>")>-1)
            {
              int value = Integer.parseInt( data.substring(data.indexOf("<identity>")+10, data.indexOf("</identity>")));
              if(value>=maxFound)
              {
                maxFound = value;
                buffer.append(" "+ id2 + " " + value+"%; ");
              }
            }
          }

        }


      }

      output.setText(output.getText()+buffer.toString());
    }

}