/*
* 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;
  AlignmentI dataset;
  AlignmentPanel ap;
  ArrayList unknownSequences;
  CutAndPasteTransfer output = new CutAndPasteTransfer();
  StringBuffer sbuffer = new StringBuffer();

  public SequenceFeatureFetcher()
  {}

  public 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 = 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));

    }
    catch (Exception e)
    {
      System.out.println("Error getUniprotEntries() "+e);
    }
    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.dataset = align.getDataset();
    this.ap = ap;

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

  /**
   * DOCUMENT ME!
   */
  public void run()
  {
    try
    {
      int seqIndex = 0;
      Vector sequences = dataset.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);
          if(sequence.getSequenceFeatures()==null)
          {
            if (!ids.contains(sequence.getName()))
            {
              ids.add(sequence.getName());
              unknownSequences.add(sequence);
            }
          }
        }

        ///////////////////////////////////
        ///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", "raw");



          if (file != null)
          {
            ReadUniprotFile(file, 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);
      // The above is the dataset, we must now find out the index
      // of the viewed sequence

    }

    promptBeforeBlast();

  }


  void promptBeforeBlast()
   {
     // This must be outside the run() body as java 1.5
     // will not return any value from the OptionPane to the expired thread.
      if (unknownSequences.size() > 0)
      {
        int reply = javax.swing.JOptionPane.showConfirmDialog(
            Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences."
                +"\nPerform blast for unknown sequences?",
                    "Blast for Unidentified Sequences",
                     javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);

        if(reply == javax.swing.JOptionPane.YES_OPTION)
         new WSWUBlastClient(ap, align, unknownSequences);
      }


    ap.repaint();
  }

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

    SequenceI sequence = 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().elementAt(0).toString();
      sequence = dataset.findName(idmatch);

      if (sequence == null)
      {
        //Sequence maybe Name, not Accession
        idmatch = entry.getName().elementAt(0).toString();
        sequence = dataset.findName(idmatch);
      }

      if (sequence == null)
      {
        System.out.println(idmatch+" not found");
        continue;
      }

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

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

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

      if (absStart == -1)
      {
        // Is UniprotSequence contained in dataset sequence?
        absStart = nonGapped.toString().indexOf(entry.getUniprotSequence().getContent());
        if(absStart == -1)
        {
          unknownSequences.add(sequence.getName());
          sbuffer.append(sequence.getName() +
                         " SEQUENCE NOT %100 MATCH \n");

          continue;
        }
        else
        {
          if(entry.getFeature()!=null)
          {
            Enumeration e = entry.getFeature().elements();
            while (e.hasMoreElements())
            {
              SequenceFeature sf = (SequenceFeature) e.nextElement();
              sf.setBegin(sf.getBegin() + absStart + 1);
              sf.setEnd(sf.getEnd() + absStart + 1);
            }
          }

          sbuffer.append(sequence.getName() +
                         " HAS "+absStart+" PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"
                        +" HAVE BEEN ADJUSTED ACCORDINGLY \n");
          absStart = 0;
        }

      }

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

      Enumeration e = entry.getDbReference().elements();
      Vector onlyPdbEntries = new Vector();
      while(e.hasMoreElements())
      {
        PDBEntry pdb = (PDBEntry)e.nextElement();
        if(!pdb.getType().equals("PDB"))
          continue;

        onlyPdbEntries.addElement(pdb);
      }

      sequence.setPDBId(onlyPdbEntries);
      sequence.setSequenceFeatures(entry.getFeature());
      sequence.setStart(absStart);
      sequence.setEnd(absEnd);


      int n = 0;
      SequenceI seq2;
      while (n < align.getHeight())
      {
        //This loop enables multiple sequences with the same
        //id to have features added and seq limits updated
        seq2 = align.getSequenceAt(n);
        if (seq2.getName().equals(idmatch))
        {

          nonGapped = AlignSeq.extractGaps("-. ", seq2.getSequence());

          absStart = sequence.getSequence().indexOf(nonGapped);
          absEnd = absStart + nonGapped.toString().length() - 1;

          // This is the Viewd alignment sequences
          // No need to tell the user of the dataset updates
          if ( (seq2.getStart() != absStart+sequence.getStart())
             || (seq2.getEnd() != absEnd+sequence.getStart()))
          {
            sbuffer.append("Updated: " + seq2.getName() + " " +
                           seq2.getStart() + "/" + seq2.getEnd() +
                           "  to  " + (absStart + sequence.getStart()) + "/" +
                           (absEnd + sequence.getStart()) + "\n");

            seq2.setStart(absStart + sequence.getStart());
            seq2.setEnd(absEnd + sequence.getStart());
          }
        }

        n++;
      }
    }
  }
}