/*
* 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 java.io.*;

import java.util.*;

import org.exolab.castor.mapping.Mapping;

import org.exolab.castor.xml.*;
import jalview.analysis.AlignSeq;



/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class SequenceFeatureFetcher implements Runnable
{

  AlignmentI align;
  AlignmentPanel ap;
  ArrayList unknownSequences;
  CutAndPasteTransfer output = new CutAndPasteTransfer();
  StringBuffer sbuffer = new StringBuffer();

  Vector localCache = new Vector();

  Vector getUniprotEntries(File file)
  {

    UniprotFile uni = new UniprotFile();
    try
    {
      // 1. Load the mapping information from the file
      Mapping map = new Mapping(uni.getClass().getClassLoader());
      java.net.URL url = uni.getClass().getResource("/uniprot_mapping.xml");
      map.loadMapping(url);

      // 2. Unmarshal the data
      Unmarshaller unmar = new Unmarshaller();
      unmar.setIgnoreExtraElements(true);
      unmar.setMapping(map);
      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
      localCache.addAll( uni.getUniprotEntries() );

      // 3. marshal the data with the total price back and print the XML in the console
    //    Marshaller marshaller = new Marshaller(
      //      new FileWriter(jalview.bin.Cache.getProperty("UNIPROT_CACHE"))
     //       );
       //  marshaller.setMapping(map);
       //  marshaller.marshal(uni);

    }
    catch (Exception e)
    {
      System.out.println("Error getUniprotEntries() "+e);
     // e.printStackTrace();
     // if(!updateLocalCache)
      //  file.delete();

    }
    return uni.getUniprotEntries();
  }

  /**
   * Creates a new SequenceFeatureFetcher object.
   *
   * @param align DOCUMENT ME!
   * @param ap DOCUMENT ME!
   */
  public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)
  {
    unknownSequences = new ArrayList();
    this.align = align;
    this.ap = ap;

    Thread thread = new Thread(this);
    thread.start();
  }

  /**
   * DOCUMENT ME!
   */
  public void run()
  {
    try
    {
      int seqIndex = 0;
      Vector sequences = align.getSequences();

      while (seqIndex < sequences.size())
      {
        Vector ids = new Vector();

        for (int i = 0; (seqIndex < sequences.size()) && (i < 50);
             seqIndex++, i++)
        {
          SequenceI sequence = (SequenceI) sequences.get(seqIndex);
          ids.add(sequence.getName());
          unknownSequences.add(sequence.getName());
        }

        ///////////////////////////////////
        ///READ FROM EBI
        if (ids.size() > 0)
        {
          StringBuffer remainingIds = new StringBuffer("uniprot:");
          for (int i = 0; i < ids.size(); i++)
           {
             remainingIds.append(ids.get(i) + ";");
           }
          EBIFetchClient ebi = new EBIFetchClient();
          File file = ebi.fetchDataAsFile(remainingIds.toString(),
                                          "xml", null);


          if (file != null)
          {
            ReadUniprotFile(file, align, ids);
          }
        }
      }
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }

    if (sbuffer.length() > 0)
    {
      output.setText(
          "Your sequences have been matched to Uniprot. Some of the ids have been\n" +
          "altered, most likely the start/end residue will have been updated.\n" +
          "Save your alignment to maintain the updated id.\n\n" +
          sbuffer.toString());
      Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
    }

    if (unknownSequences.size() > 0)
    {
       new WSWUBlastClient(ap, align, unknownSequences);
    }
    else
       ((Alignment)align).featuresAdded = true;


    ap.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param result DOCUMENT ME!
   * @param out DOCUMENT ME!
   * @param align DOCUMENT ME!
   */
  void ReadUniprotFile(File file, AlignmentI align, Vector ids)
  {
    if(!file.exists())
      return;

    SequenceI sequence = null;
    //       String pdb = null;

    Vector entries = getUniprotEntries(file);

    int i, iSize = entries==null?0:entries.size();
    UniprotEntry entry;
    for (i = 0; i < iSize; i++)
    {
      entry = (UniprotEntry) entries.elementAt(i);
      String idmatch = entry.getAccession();
      sequence = align.findName(idmatch);

      if (sequence == null)
      {
        //Sequence maybe Name, not Accession
        idmatch = entry.getName();
        sequence = align.findName(idmatch);
      }

      if (sequence == null)
      {
        continue;
      }

      ids.remove(sequence.getName());
      unknownSequences.remove(sequence.getName());

      String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());

      int absStart = entry.getUniprotSequence().getContent().indexOf(
          nonGapped.toString());

      if (absStart == -1)
      {
        unknownSequences.add(sequence.getName());
        sbuffer.append(sequence.getName() +
                       " SEQUENCE NOT %100 MATCH \n");

        continue;
      }

      int absEnd = absStart + nonGapped.toString().length();
      absStart += 1;

      if ( (absStart != sequence.getStart()) ||
          (absEnd != sequence.getEnd()))
      {
        sbuffer.append("Updated: " + sequence.getName() + " " +
                       sequence.getStart() + "/" + sequence.getEnd() +
                       "  to  " + absStart + "/" + absEnd + "\n");
      }

      sequence.setSequenceFeatures(entry.getFeatures());
      sequence.setStart(absStart);
      sequence.setEnd(absEnd);
    }
  }
}