/*
 * 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 java.io.*;
import java.util.*;

import jalview.datamodel.*;
import jalview.util.*;

public class PfamFile
    extends AlignFile
{
  Vector ids;

  public PfamFile()
  {
  }

  public PfamFile(String inStr)
  {
    super(inStr);
  }

  public PfamFile(String inFile, String type)
      throws IOException
  {
    super(inFile, type);
  }

  public void initData()
  {
    super.initData();
    ids = new Vector();
  }

  public void parse()
      throws IOException
  {
    int i = 0;
    String line;

    Hashtable seqhash = new Hashtable();
    Vector headers = new Vector();

    while ( (line = nextLine()) != null)
    {
      if (line.indexOf(" ") != 0)
      {
        if (line.indexOf("#") != 0)
        {
          StringTokenizer str = new StringTokenizer(line, " ");
          String id = "";

          if (str.hasMoreTokens())
          {
            id = str.nextToken();

            StringBuffer tempseq;

            if (seqhash.containsKey(id))
            {
              tempseq = (StringBuffer) seqhash.get(id);
            }
            else
            {
              tempseq = new StringBuffer();
              seqhash.put(id, tempseq);
            }

            if (! (headers.contains(id)))
            {
              headers.addElement(id);
            }

            tempseq.append(str.nextToken());
          }
        }
      }
    }

    this.noSeqs = headers.size();

    if (noSeqs < 1)
    {
      throw new IOException("No sequences found (PFAM input)");
    }

    for (i = 0; i < headers.size(); i++)
    {
      if (seqhash.get(headers.elementAt(i)) != null)
      {
        if (maxLength < seqhash.get(headers.elementAt(i)).toString()
            .length())
        {
          maxLength = seqhash.get(headers.elementAt(i)).toString()
              .length();
        }

        String head = headers.elementAt(i).toString();
        int start = 1;
        int end = seqhash.get(headers.elementAt(i)).toString().length();

        if (head.indexOf("/") > 0)
        {
          StringTokenizer st = new StringTokenizer(head, "/");

          if (st.countTokens() == 2)
          {
            ids.addElement(st.nextToken());

            String tmp = st.nextToken();
            st = new StringTokenizer(tmp, "-");

            if (st.countTokens() == 2)
            {
              start = Integer.valueOf(st.nextToken()).intValue();
              end = Integer.valueOf(st.nextToken()).intValue();
            }
            else
            {
              start = -1;
              end = -1;
            }
          }
          else
          {
            ids.addElement(headers.elementAt(i));
          }
        }
        else
        {
          ids.addElement(headers.elementAt(i));
        }

        Sequence newSeq = null;

        if ( (start != -1) && (end != -1))
        {
          newSeq = new Sequence(ids.elementAt(i).toString(),
                                seqhash.get(headers.elementAt(i).toString())
                                .toString(), start, end);
          seqs.addElement(newSeq);
        }
        else
        {
          newSeq = new Sequence(ids.elementAt(i).toString(),
                                seqhash.get(headers.elementAt(i).toString())
                                .toString(), 1,
                                seqhash.get(headers.elementAt(i).toString())
                                .toString().length());
          seqs.addElement(newSeq);
        }

        if (!isValidProteinSequence(newSeq.getSequence()))
        {
          throw new IOException(
              "Not a valid protein sequence - (PFAM input)");
        }
      }
      else
      {
        System.err.println("PFAM File reader: Can't find sequence for " +
                           headers.elementAt(i));
      }
    }
  }

  public static String print(SequenceI[] s)
  {
    StringBuffer out = new StringBuffer("");

    int max = 0;
    int maxid = 0;

    int i = 0;

    while ( (i < s.length) && (s[i] != null))
    {
      String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +
          s[i].getEnd();

      if (s[i].getSequence().length() > max)
      {
        max = s[i].getSequence().length();
      }

      if (tmp.length() > maxid)
      {
        maxid = tmp.length();
      }

      i++;
    }

    if (maxid < 15)
    {
      maxid = 15;
    }

    int j = 0;

    while ( (j < s.length) && (s[j] != null))
    {
      out.append(new Format("%-" + maxid + "s").form(s[j].getName() +
          "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");

      out.append(s[j].getSequence() + "\n");
      j++;
    }

    out.append("\n");

    return out.toString();
  }

  public String print()
  {
    return print(getSeqsAsArray());
  }
}