package jalview.analysis;

import java.io.*;
import java.util.*;
import javax.swing.*;
import jalview.io.*;
import jalview.gui.*;
import jalview.datamodel.*;

public class SequenceFeatureFetcher implements Runnable
{
  AlignmentI align;
  AlignmentPanel ap;
  ArrayList unknownSequences;
  JInternalFrame outputFrame = new JInternalFrame();
  CutAndPasteTransfer output = new CutAndPasteTransfer(false);
  StringBuffer sbuffer = new StringBuffer();

  public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)
  {
    unknownSequences = new ArrayList();
    this.align = align;
    this.ap = ap;
    Thread thread = new Thread(this);
    thread.start();
  }

  public void run()
{

  String cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");

  RandomAccessFile out = null;

  try{
    if (cache == null)
    {
      jalview.bin.Cache.setProperty("UNIPROT_CACHE", System.getProperty("user.home")+"/uniprot.xml");
      cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
    }



    File test = new File(cache);
    if( !test.exists() )
    {
      out = new RandomAccessFile(cache, "rw");
      out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
      out.writeBytes("<UNIPROT_CACHE>\n");
    }
    else
    {
      out = new RandomAccessFile(cache, "rw");
      // open exisiting cache and remove </UNIPROT_CACHE> from the end
      long lastLine = 0;
      String data;
      while ( (data = out.readLine()) != null)
      {
        if (data.indexOf("</entry>") > -1)
          lastLine = out.getFilePointer();

      }
      out.seek(lastLine);
    }

    int seqIndex = 0;
    Vector sequences = align.getSequences();

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

      tryLocalCacheFirst(ids, align);

      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();
         String[] result = ebi.fetchData(remainingIds.toString(), "xml", null);

        if(result!=null)
          ReadUniprotFile(result, out, align);
      }

    }

    if (out != null)
    {
      out.writeBytes("</UNIPROT_CACHE>\n");
      out.close();
    }
  }catch(Exception ex){ex.printStackTrace();}

  ap.RefreshPanels();
  findMissingIds(align);
  if(sbuffer.length()>0)
  {
    output.formatForOutput();
    outputFrame.setContentPane(output);
    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(outputFrame, "Sequence names updated ", 600,300);

  }

  if(unknownSequences.size()>0)
  {
    //ignore for now!!!!!!!!!!
  //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
  }

}

void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)
{
  SequenceI sequence = null;
  Vector features = null;
  String type, description, status, start, end, pdb = null;


  for (int r = 0; r < result.length; r++)
  {
    if(sequence==null && result[r].indexOf("<name>")>-1)
    {
      long filePointer = 0;

      if(out!=null)
      try{
        filePointer=out.getFilePointer();
        out.writeBytes("<entry>\n");
      }catch(Exception ex){}

      String seqName = parseElement( result[r], "<name>" , out);
      sequence = align.findName( seqName ) ;
      if(sequence==null)
      {
        sequence = align.findName( seqName.substring(0, seqName.indexOf('_')));
        if(sequence!=null)
        {
          sbuffer.append("changing "+sequence.getName()+" to "+seqName+"\n");
          sequence.setName(seqName);
        }
      }
      if(sequence==null)
      {
        sbuffer.append("UNIPROT updated suggestion is "+result[r]+"\n");
        sequence = align.findName( result[r] ) ;

        // this entry has been suggested by ebi.
        // doesn't match id in alignment file
        try   { out.setLength(filePointer);  }  catch (Exception ex) {}
        // now skip to next entry
        while( result[r].indexOf("</entry>")==-1)
          r++;
      }

      features = new Vector();
      type=""; start="0"; end="0"; description=""; status=""; pdb="";

    }

    if(sequence==null)
      continue;

     if( result[r].indexOf("<property type=\"pdb accession\"")>-1)
     {
       pdb = parseValue( result[r], "value=" , out);
       sequence.setPDBId(pdb);
     }

     if(result[r].indexOf("feature type")>-1)
     {
       type = parseValue( result[r], "type=" , out);
       description = parseValue( result[r], "description=" , null );
       status = parseValue ( result[r], "status=", null);

       while( result[r].indexOf("position")==-1)
       {
           r++;  //<location>
       }
      // r++;
       if(result[r].indexOf("begin")>-1)
       {
         start = parseValue( result[r], "position=" , out);
         end = parseValue( result[++r], "position=" , out);
       }
       else
       {
         start = parseValue( result[r], "position=" , out);
         end = parseValue(   result[r], "position=" , null);
       }
       int sstart = Integer.parseInt(start);
       int eend = Integer.parseInt(end);
       if(out!=null)
         try{ out.writeBytes("</feature>\n"); }catch(Exception ex){}

         SequenceFeature sf = new SequenceFeature(type,
             sstart,
             eend,
             description,
             status);
         features.add(sf);
     }

     if(result[r].indexOf("<sequence")>-1)
     {
       StringBuffer seqString = new StringBuffer();

       if(out!=null)
         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}

       while(result[++r].indexOf("</sequence>")==-1)
       {
         seqString.append(result[r]);
         if(out!=null)
         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
       }

       if(out!=null)
         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}

       StringBuffer nonGapped = new StringBuffer();
       for (int i = 0; i < sequence.getSequence().length(); i++)
       {
         if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
           nonGapped.append(sequence.getCharAt(i));
       }

       int absStart = seqString.toString().indexOf(nonGapped.toString());
       if(absStart==-1)
       {
         unknownSequences.add(sequence.getName());
         features = null;
         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.setStart(absStart);
       sequence.setEnd(absEnd);

     }

     if(result[r].indexOf("</entry>")>-1)
     {
       if(features!=null)
         sequence.setSequenceFeatures( features );
       features = null;
       sequence = null;
       if(out!=null)
         try{  out.writeBytes("</entry>\n"); }catch(Exception ex){}

     }
  }
}

void findMissingIds(AlignmentI align)
{
  String data;
  ArrayList cachedIds = new ArrayList();

  try
  {
    BufferedReader in = new BufferedReader(
        new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));

    while ( (data = in.readLine()) != null)
    {
      if (data.indexOf("name") > -1)
      {
        String name = parseElement(data, "<name>", null);
        cachedIds.add(name);
      }
    }
  }
  catch (Exception ex)
  {   ex.printStackTrace();  }

  for(int i=0; i<align.getHeight(); i++)
    if( !cachedIds.contains( align.getSequenceAt(i).getName() ) )
      unknownSequences.add( align.getSequenceAt(i).getName() );


}

void tryLocalCacheFirst(ArrayList ids, AlignmentI align)
{
  ArrayList cacheData = new ArrayList();
  try{
    BufferedReader in = new BufferedReader(
          new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));

    // read through cache file, if the cache has sequences we're looking for
    // add the lines to a new String array, Readthis new array and
    // make sure we remove the ids from the list to retrieve from EBI
    String data;
    while( ( data=in.readLine())!=null)
    {
      if(data.indexOf("name")>-1)
      {
        String name = parseElement( data, "<name>" , null) ;
        if(ids.contains( name ) )
        {
          cacheData.add("<entry>");
          cacheData.add(data);
          while( data.indexOf("</entry>")==-1)
          {
            data = in.readLine();
            cacheData.add(data);
          }
          cacheData.add(data);

          ids.remove( name );
        }
      }
    }
  }
  catch(Exception ex){ex.printStackTrace();}

  String [] localData = new String[cacheData.size()];
  cacheData.toArray( localData );
  if(localData!=null && localData.length>0)
    ReadUniprotFile(localData, null, align);
}


String parseValue(String line, String tag, RandomAccessFile out)
{
  if(out!=null)
    try{  out.writeBytes(line+"\n"); }catch(Exception ex){}


  int index = line.indexOf(tag)+tag.length()+1;
  if(index==tag.length())
    return "";

  return line.substring( index, line.indexOf("\"", index+1) );
}


String parseElement(String line, String tag, RandomAccessFile out)
{
  if (out != null)
    try
    {
      out.writeBytes(line + "\n");
    }
    catch (Exception ex)
    {}

  int index = line.indexOf(tag) + tag.length();
  return line.substring(index, line.indexOf("</"));
}


}