/*
* 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.util.*;

import java.net.URL;

import org.biojava.dasobert.das.FeatureThread;
import org.biojava.dasobert.dasregistry.Das1Source;
import org.biojava.dasobert.eventmodel.FeatureEvent;
import org.biojava.dasobert.eventmodel.FeatureListener;
import org.biojava.services.das.registry.DasRegistryAxisClient;
import org.biojava.services.das.registry.DasSource;


import jalview.bin.Cache;



/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class DasSequenceFeatureFetcher implements Runnable
{
  final AlignmentI dataset;
  final AlignmentPanel ap;
  StringBuffer sbuffer = new StringBuffer();



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

    Thread thread = new Thread(this);
    thread.start();
  }
  /**
   * creates a jalview sequence feature from a das feature document
   * @param dasfeature
   * @return sequence feature object created using dasfeature information
   */
  SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
  {
	  try {
		/**
	   * Different qNames for a DAS Feature - are string keys to the HashMaps in features
	   * "METHOD") ||
	   qName.equals("TYPE") ||
	   qName.equals("START") ||
	   qName.equals("END") ||
	   qName.equals("NOTE") ||
	   qName.equals("LINK") ||
	   qName.equals("SCORE")
	   */
		  String desc = new String();
		  if (dasfeature.containsKey("NOTE"))
				desc+=(String) dasfeature.get("NOTE");


                  int start = 0, end = 0;
                  float score = 0f;

                  try{ start = Integer.parseInt( dasfeature.get("START").toString()); }
                  catch( Exception ex){}
                  try{ end = Integer.parseInt( dasfeature.get("END").toString()); }
                  catch (Exception ex){}
                  try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }
                  catch (Exception ex){}


		  SequenceFeature f = new SequenceFeature(
				  (String) dasfeature.get("TYPE"),
				  desc,
				  start,
				  end,
                                  score,
				  nickname);

                  if (dasfeature.containsKey("LINK"))
                 {
                      f.addLink(f.getType()+" "+f.begin+"_"+f.end
                                +"|"+ dasfeature.get("LINK"));
		  }
                  // (String) dasfeature.get("ID"),
                  ////  (String) dasfeature.get("METHOD"),
				//  (String) dasfeature.get("SCORE"),
				//  null
		  	// );

                     // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);
	  return f;
	  }
	  catch (Exception e) {
            e.printStackTrace();
		  Cache.log.debug("Failed to parse "+dasfeature.toString(), e);
		  return null;
	  }
  }
  /**
   * fetch and add das features to a sequence using the given source URL and Id to create a feature request
   * @param seq
   * @param SourceUrl
   * @param id
   */
  protected void createFeatureFetcher(final Sequence seq,
                                      final String sourceUrl,
                                      String id,
                                      String nickname)  {
	  //////////////
	  /// fetch DAS features
          final Das1Source source = new Das1Source();
          source.setUrl(sourceUrl);
          source.setNickname(nickname);


          Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
                          sourceUrl);
          if (id != null && id.length() > 0)
          {
            FeatureThread fetcher = new FeatureThread(id + ":" + seq.getStart() + "," +seq.getEnd()
                , source);

            fetcher.addFeatureListener(new FeatureListener()
            {
              public void comeBackLater(FeatureEvent e)
              {
                Cache.log.debug("das source " + e.getDasSource().getNickname() +
                                " asked us to come back in " + e.getComeBackLater() +
                                " secs.");
              }

              public void newFeatures(FeatureEvent e)
              {
                Das1Source ds = e.getDasSource();

                Map[] features = e.getFeatures();
                // add features to sequence
                Cache.log.debug("das source " + ds.getUrl() + " returned " +
                                features.length + " features");


                if (features.length > 0)
                {
                  for (int i = 0; i < features.length; i++)
                  {

                    SequenceFeature f = newSequenceFeature(features[i],
                        source.getNickname());

                    if (seq.sequenceFeatures != null)
                    {
                      for (int j = 0; (f != null) && j < seq.sequenceFeatures.length;
                           j++)
                      {
                        if (seq.sequenceFeatures[j].equals(f))
                        {
                          f = null;
                        }
                      }
                    }
                    if (f != null)
                    {
                      seq.addSequenceFeature(f);
                    }
                  }
                }
              }

            }

            );

            //NOTE alignPanel listener will be called after the previous
            //anonymous listener!!!
            fetcher.addFeatureListener(ap);

            fetcher.start();
	  }
  }
  /**
   * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
   */
  public void run()
  {
    DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();

    String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
    StringTokenizer st = new StringTokenizer(active, "\t");
    Vector selectedSources = new Vector();
    String token;
    while (st.hasMoreTokens())
    {
      token = st.nextToken();
      for(int i=0; i<sources.length; i++)
      {
        if(sources[i].getNickname().equals(token))
        {
          selectedSources.addElement(sources[i]);
          break;
        }
      }
    }
 // DasSource test = new DasSource();
 // test.setUrl("http://localhost:8080/das/gffdb/");
  //test.setNickname("Trixkid");
 // selectedSources.addElement(test);


    if(selectedSources == null || selectedSources.size()==0)
    {
      System.out.println("No DAS Sources active");
      return;
    }

    try
    {
      int seqIndex = 0;
      Vector sequences = dataset.getSequences();
      while (seqIndex < sequences.size())
      {
          Sequence sequence = (Sequence) sequences.get(seqIndex);
          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[]  {"DBREF"});

          for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)
          {
            DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);

            if (uprefs != null)
            {
              // we know the id for this entry, so don't note its ID in the unknownSequences list
              for (int j = 0, k = uprefs.size(); j < k; j++)
              {

                createFeatureFetcher(sequence,
                                     dasSource.getUrl(),
                                     ( (DBRefEntry) uprefs.get(j)).getAccessionId(),
                                     dasSource.getNickname());
              }
            }
            else
            {
              String id = null;
              // try and use the name as the sequence id
              if (sequence.getName().indexOf("|") > -1)
              {
                id = sequence.getName().substring(
                    sequence.getName().lastIndexOf("|") + 1);
              }
              else
              {
                id = sequence.getName();
              }
              if (id != null)
              {
                // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
                createFeatureFetcher(sequence,
                                     dasSource.getUrl(),
                                     id,
                                     dasSource.getNickname());
              }
            }
          }

          seqIndex++;
    }
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }


 public static DasSource[] getDASSources()
  {
    try
    {
      String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
          "http://servlet.sanger.ac.uk/dasregistry/services/das_registry");


      URL url = new URL(registryURL);

      DasRegistryAxisClient client = new DasRegistryAxisClient(url);

      DasSource[] services = client.listServices();

      return services;
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }
    return null;

  }

}