/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 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.eventmodel.FeatureEvent;
import org.biojava.dasobert.eventmodel.FeatureListener;
import org.biojava.dasobert.dasregistry.DasSource;

import org.biojava.dasobert.das2.io.DasSourceReaderImpl;
import org.biojava.dasobert.dasregistry.Das1Source;
import org.biojava.dasobert.dasregistry.DasSource;
import org.biojava.dasobert.das2.Das2Source;
import org.biojava.dasobert.das2.DasSourceConverter;


import jalview.bin.Cache;
import org.biojava.dasobert.dasregistry.DasCoordinateSystem;

import javax.swing.*;

/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class DasSequenceFeatureFetcher implements Runnable
{
  SequenceI [] sequences;
  AlignFrame af;
  StringBuffer sbuffer = new StringBuffer();
  Vector selectedSources;

  long startTime;
  int threadsRunning = 0;


  /**
   * Creates a new SequenceFeatureFetcher object.
   * Uses default
   *
   * @param align DOCUMENT ME!
   * @param ap DOCUMENT ME!
   */
  public DasSequenceFeatureFetcher(SequenceI [] sequences,
                                   final AlignFrame af,
                                   Vector selectedSources)
  {
    this.selectedSources = selectedSources;
    this.sequences = sequences;
    this.af = af;

    int uniprotCount = 0;
    for (int i = 0; i < selectedSources.size(); i++)
    {
      DasSource source = (DasSource) selectedSources.elementAt(i);
      DasCoordinateSystem[] coords = source.getCoordinateSystem();
      for (int c = 0; c < coords.length; c++)
      {
        if (coords[c].getName().indexOf("UniProt")>-1)
        {
          uniprotCount++;
          break;
        }
      }
    }

    int refCount = 0;
    for(int i=0; i<sequences.length; i++)
    {
      DBRefEntry [] dbref = sequences[i].getDBRef();
      if(dbref!=null)
      {
        for(int j=0; j<dbref.length; j++)
        {
          if(dbref[j].getSource()
             .equals(jalview.datamodel.DBRefSource.UNIPROT))
          {
            refCount++;
            break;
          }
        }
      }
    }

    if(refCount<sequences.length && uniprotCount>0)
    {

     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
          "Do you want Jalview to find\n"
         +"Uniprot Accession ids for given sequence names?",
         "Find Uniprot Accession Ids",
         JOptionPane.YES_NO_OPTION,
         JOptionPane.QUESTION_MESSAGE);

     if(reply == JOptionPane.YES_OPTION)
     {
       Thread thread = new Thread(new FetchDBRefs());
       thread.start();
     }
     else
      startFetching();
    }
    else
      startFetching();

  /* System.out.println("User selection is "   +
                       ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)
                      + " % Uniprot,  and "+refCount+" / " +sequences.length+" have uniprot accession");
*/
  }

  void startFetching()
  {
    Thread thread = new Thread(this);
    thread.start();
  }

  class FetchDBRefs implements Runnable
  {
    public void run()
    {
      new DBRefFetcher(
             af.getViewport().getAlignment(), af).fetchDBRefs(true);
      startFetching();
    }
  }


  /**
   * 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
		  	// );

	  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 SequenceI 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)
          {
            setThreadsRunning(+1);

          //  int start=seq.getStart(), end = seq.getEnd();
          /*  if(af.getViewport().getSelectionGroup()!=null)
            {
              SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());
              start = tmp.findPosition(
              af.getViewport().getSelectionGroup().getStartRes()
                  );

              end = tmp.findPosition(
                 af.getViewport().getSelectionGroup().getEndRes()
                 );
            }*/

            FeatureThread fetcher = new FeatureThread(id
                                                   //  +  ":" + start + "," + end,
                                                      , source);


            fetcher.addFeatureListener(new FeatureListener()
            {
              public void comeBackLater(FeatureEvent e)
              {
                setThreadsRunning(-1);
                Cache.log.debug("das source " + e.getDasSource().getNickname() +
                                " asked us to come back in " + e.getComeBackLater() +
                                " secs.");
              }

              public void newFeatures(FeatureEvent e)
              {
                setThreadsRunning(-1);
                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());

                      seq.addSequenceFeature(f);
                  }
                }
                else
                {
                  System.out.println("No features found for sequence " +seq.getName()
                                     +" from: "+ e.getDasSource().getNickname());
                }

              }
            }

            );

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

            fetcher.start();
	  }
  }

  synchronized void setThreadsRunning(int i)
  {
    threadsRunning += i;
    if(threadsRunning<1)
    {
      af.setProgressBar("DAS Feature Fetching Complete", startTime);

      if(af.featureSettings!=null)
        af.featureSettings.setTableData();
    }
  }

  /**
   * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
   */
  public void run()
  {
    startTime = System.currentTimeMillis();
    af.setProgressBar("Fetching DAS Sequence Features", startTime);

    DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();

    if(selectedSources==null || selectedSources.size()==0)
    {
      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;
          }
        }
      }
    }

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

    try
    {
      int seqIndex = 0;
      while (seqIndex < sequences.length)
      {
          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
              new String[]  {
              jalview.datamodel.DBRefSource.PDB,
              jalview.datamodel.DBRefSource.UNIPROT});

          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;  j < uprefs.length; j++)
              {

                // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end
                DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
                for (int l=0; l<cs.length; l++)
                {
                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))
                  {
                    Cache.log.debug("Launched fetcher for coordinate system " +
                                    cs[l].getName());


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

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


  public static DasSource[] getDASSources()
  {
    DasSourceReaderImpl reader = new DasSourceReaderImpl();

    String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
        "http://das.sanger.ac.uk/registry/das1/sources/"
      );

    try
    {
      URL url = new URL(registryURL);

      DasSource[] sources = reader.readDasSource(url);

      List das1sources = new ArrayList();
      for (int i = 0; i < sources.length; i++)
      {
        DasSource ds = sources[i];
        if (ds instanceof Das2Source)
        {
          Das2Source d2s = (Das2Source) ds;
          if (d2s.hasDas1Capabilities())
          {
            Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
            das1sources.add(d1s);
          }

        }
        else if (ds instanceof Das1Source)
        {
          das1sources.add( (Das1Source) ds);
        }
      }

      return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
      return null;
    }

  }
}