/*
* 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 java.io.*;
import java.util.*;
import jalview.schemes.UserColourScheme;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class FeaturesFile extends AlignFile
{
    /**
     * Creates a new FeaturesFile object.
     */
    public FeaturesFile()
    {
    }


    /**
     * Creates a new FeaturesFile object.
     *
     * @param inFile DOCUMENT ME!
     * @param type DOCUMENT ME!
     *
     * @throws IOException DOCUMENT ME!
     */
    public FeaturesFile(String inFile, String type)
       throws IOException
    {
        super(inFile, type);
    }

    /**
     * The Application can render HTML, but the applet will
     * remove HTML tags and replace links with %LINK%
     * Both need to read links in HTML however
     *
     * @throws IOException DOCUMENT ME!
     */
    public boolean parse(AlignmentI align,
                         Hashtable colours,
                         boolean removeHTML)
    {
      return parse(align, colours, null, removeHTML);
    }
    /**
     * The Application can render HTML, but the applet will
     * remove HTML tags and replace links with %LINK%
     * Both need to read links in HTML however
     *
     * @throws IOException DOCUMENT ME!
     */
    public boolean parse(AlignmentI align,
                         Hashtable colours,
                         Hashtable featureLink,
                         boolean removeHTML)
    {
      String line = null;
      try
      {
        SequenceI seq = null;
        String type, desc, token=null;

        int index, start, end;
        float score;
        StringTokenizer st;
        SequenceFeature sf;
        String featureGroup = null, groupLink = null;
        Hashtable typeLink = new Hashtable();

        boolean GFFFile = true;

        while ( (line = nextLine()) != null)
        {
          if(line.startsWith("#"))
            continue;

          st = new StringTokenizer(line, "\t");
          if (st.countTokens()>1 && st.countTokens() < 4 )
          {
            GFFFile = false;
            type = st.nextToken();
            if (type.equalsIgnoreCase("startgroup"))
            {
              featureGroup = st.nextToken();
              if (st.hasMoreElements())
              {
                groupLink = st.nextToken();
                featureLink.put(featureGroup, groupLink);
              }
            }
            else if (type.equalsIgnoreCase("endgroup"))
            {
              //We should check whether this is the current group,
              //but at present theres no way of showing more than 1 group
              st.nextToken();
              featureGroup = null;
              groupLink = null;
            }
            else
            {
              UserColourScheme ucs = new UserColourScheme(st.nextToken());
              colours.put(type, ucs.findColour('A'));
              if (st.hasMoreElements())
              {
                String link = st.nextToken();
                typeLink.put(type, link);
                if(featureLink==null)
                  featureLink = new Hashtable();
                featureLink.put(type, link);
              }

            }
            continue;
          }

          while (st.hasMoreElements())
          {

            if(GFFFile)
            {
              // Still possible this is an old Jalview file,
              // which does not have type colours at the beginning
              token = st.nextToken();
              seq = align.findName(token);
              if(seq != null)
              {
                desc = st.nextToken();
                type = st.nextToken();
                start = Integer.parseInt(st.nextToken());
                end = Integer.parseInt(st.nextToken());
                try
                {
                  score =  new Float(st.nextToken()).floatValue();
                }
                catch (NumberFormatException ex)
                {
                  score = 0;
                }

                sf = new SequenceFeature(type, desc, start, end, score, null);

                try
                {
                  sf.setValue("STRAND", st.nextToken());
                  sf.setValue("FRAME", st.nextToken());
                }
                catch (Exception ex)
                {}

                if(st.hasMoreTokens())
                {
                  StringBuffer attributes = new StringBuffer();
                  while (st.hasMoreTokens())
                  {
                    attributes.append("\t"+st.nextElement());
                  }
                  sf.setValue("ATTRIBUTES", attributes.toString());
                }

                seq.addSequenceFeature(sf);

                break;
              }
            }

            if(GFFFile && seq==null)
            {
              desc = token;
            }
            else
              desc = st.nextToken();


            token = st.nextToken();
            if (!token.equals("ID_NOT_SPECIFIED"))
            {
              seq = align.findName(token);
              st.nextToken();
            }
            else
            {
              try{
                index = Integer.parseInt(st.nextToken());
                seq = align.getSequenceAt(index);
              }
              catch(NumberFormatException ex)
              {
                seq = null;
              }
            }

            if(seq==null)
            {
              System.out.println("Sequence not found: "+line);
              break;
            }

            start = Integer.parseInt(st.nextToken());
            end = Integer.parseInt(st.nextToken());

            type = st.nextToken();

            if (!colours.containsKey(type))
            {
              // Probably the old style groups file
              UserColourScheme ucs = new UserColourScheme(type);
              colours.put(type, ucs.findColour('A'));
            }

            sf = new SequenceFeature(type, desc, "", start, end, featureGroup);

            seq.addSequenceFeature(sf);

            if(groupLink!=null && removeHTML)
            {
              sf.addLink(groupLink);
              sf.description += "%LINK%";
            }
            if(typeLink.containsKey(type) && removeHTML)
            {
              sf.addLink(typeLink.get(type).toString());
              sf.description += "%LINK%";
            }

            parseDescriptionHTML(sf, removeHTML);

            //If we got here, its not a GFFFile
            GFFFile = false;
          }
        }
      }
      catch (Exception ex)
      {
        System.out.println(line);
        System.out.println("Error parsing feature file: " + ex +"\n"+line);
        return false;
      }

      return true;
    }

    public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
    {
      if(sf.getDescription()==null)
        return;

      if(removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>")==-1)
        removeHTML = false;

      StringBuffer sb = new StringBuffer();
      StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
      String token,  link;
      int startTag;
      String tag=null;
      while(st.hasMoreElements())
      {
        token = st.nextToken("&>");
        if(token.equalsIgnoreCase("html") || token.startsWith("/"))
        {
          continue;
        }

        tag = null;
        startTag = token.indexOf("<");

        if (startTag > -1)
        {
          tag = token.substring(startTag+1);
          token = token.substring(0, startTag);
        }

        if (tag != null && tag.toUpperCase().startsWith("A HREF="))
        {
          if(token.length()>0)
            sb.append(token);
          link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);
          String label = st.nextToken("<>");
          sf.addLink(label + "|" + link);
          sb.append(label + "%LINK%");
        }
        else if (tag != null && tag.equalsIgnoreCase("br"))
          sb.append("\n");
        else if (token.startsWith("lt;"))
          sb.append("<" + token.substring(3));
        else if (token.startsWith("gt;"))
          sb.append(">" + token.substring(3));
        else if (token.startsWith("amp;"))
          sb.append("&" + token.substring(4));
        else
        {
          sb.append(token);
        }
      }

      if(removeHTML)
        sf.description = sb.toString();

  }

    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     * @param len DOCUMENT ME!
     * @param gaps DOCUMENT ME!
     * @param displayId DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String printJalviewFormat(SequenceI [] seqs,
                                     Hashtable visible)
    {
        StringBuffer out = new StringBuffer();
        SequenceFeature [] next;

        if(visible==null || visible.size()<1)
          return "No Features Visible";

        Enumeration en = visible.keys();
        String type;
        int color;
        while( en.hasMoreElements() )
        {
          type = en.nextElement().toString();
          color = Integer.parseInt( visible.get(type).toString() );
          out.append(type + "\t"
                     + jalview.util.Format.getHexString(
                         new java.awt.Color(color)  )
                     +"\n");
        }

        //Work out which groups are both present and visible
        Vector groups = new Vector();
        int groupIndex = 0;

        for(int i=0; i<seqs.length; i++)
        {
          next = seqs[i].getSequenceFeatures();
          if(next!=null)
          {
            for(int j=0; j<next.length; j++)
            {
              if (!visible.containsKey(next[j].type))
                continue;

              if (    next[j].featureGroup != null
                  && !groups.contains(next[j].featureGroup))
                groups.addElement(next[j].featureGroup);
            }
          }
        }

        String group = null;

        do
        {


          if (groups.size() > 0 && groupIndex < groups.size())
          {
            group = groups.elementAt(groupIndex).toString();
            out.append("\nSTARTGROUP\t" + group + "\n");
          }
          else
            group = null;

          for (int i = 0; i < seqs.length; i++)
          {
            next = seqs[i].getSequenceFeatures();
            if (next != null)
            {
              for (int j = 0; j < next.length; j++)
              {
                if (!visible.containsKey(next[j].type))
                  continue;

                if (group != null
                    && (next[j].featureGroup==null
                        || !next[j].featureGroup.equals(group))
                  )
                  continue;

                if(group==null && next[j].featureGroup!=null)
                  continue;

                if(next[j].description==null || next[j].description.equals(""))
                  out.append(next[j].type+"\t");
                else
                {
                  if(next[j].links!=null
                     && next[j].getDescription().indexOf("<html>")==-1)
                    out.append("<html>");

                  out.append(next[j].description+" ");
                  if(next[j].links!=null)
                    {
                      for(int l=0; l<next[j].links.size(); l++)
                      {
                        String label = next[j].links.elementAt(l).toString();
                        String href = label.substring(label.indexOf("|")+1);
                        label = label.substring(0, label.indexOf("|"));

                        if(next[j].description.indexOf(href)==-1)
                        {
                          out.append("<a href=\""
                                     + href
                                     + "\">"
                                     + label
                                     + "</a>");
                        }
                      }

                      if (next[j].getDescription().indexOf("</html>") == -1)
                        out.append("</html>");
                    }


                   out.append("\t");
                }


                out.append(  seqs[i].getName() + "\t-1\t"
                           + next[j].begin + "\t"
                           + next[j].end + "\t"
                           + next[j].type + "\n"
                    );
              }
            }
          }

          if(group!=null)
          {
            out.append("ENDGROUP\t"+group+"\n");
            groupIndex++;
          }
          else
            break;

        }
        while(groupIndex < groups.size()+1);


      return out.toString();
    }

    public String printGFFFormat(SequenceI [] seqs, Hashtable visible)
    {
      StringBuffer out = new StringBuffer();
      SequenceFeature [] next;
      String source;

      for(int i=0; i<seqs.length; i++)
      {
        if(seqs[i].getSequenceFeatures()!=null)
        {
          next = seqs[i].getSequenceFeatures();
          for(int j=0; j<next.length; j++)
          {
            if(!visible.containsKey(next[j].type))
              continue;

            source = next[j].featureGroup;
            if(source==null)
              source = next[j].getDescription();

            out.append(seqs[i].getName() + "\t"
                       + source + "\t"
                       + next[j].type  + "\t"
                       + next[j].begin + "\t"
                       + next[j].end   + "\t"
                       + next[j].score + "\t"
                      );

            if(next[j].getValue("STRAND")!=null)
              out.append(next[j].getValue("STRAND")+"\t");
            else
              out.append(".\t");

            if(next[j].getValue("FRAME")!=null)
              out.append(next[j].getValue("FRAME"));
            else
              out.append(".");

            if(next[j].getValue("ATTRIBUTES")!=null)
              out.append(next[j].getValue("ATTRIBUTES"));

            out.append("\n");

          }
        }
      }

      return out.toString();
    }

    public void parse()
    {
      //IGNORED
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String print()
    {
        return "USE printGFFFormat() or printJalviewFormat()";
    }
}