/*
* 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.*;


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

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

    /**
     * DOCUMENT ME!
     *
     * @throws IOException DOCUMENT ME!
     */
    public void parse() throws IOException
    {
        StringBuffer sb = new StringBuffer();
        boolean firstLine = true;

        String line;
        Sequence seq = null;

        boolean annotation = false;

        while ((line = nextLine()) != null)
        {
            line = line.trim();
            if (line.length() > 0)
            {
              if (line.charAt(0)=='>')
                {
                  if (line.startsWith(">#_"))
                  {
                    if (annotation)
                    {
                      Annotation[] anots = new Annotation[sb.length()];
                      for (int i = 0; i < sb.length(); i++)
                      {
                        anots[i] = new Annotation(sb.substring(i, i+1),
                                                  null,
                                                  ' ', 0);
                      }
                      AlignmentAnnotation aa = new AlignmentAnnotation(
                          seq.getName().substring(2), seq.getDescription(),
                          anots);

                      annotations.add(aa);
                    }
                    annotation = true;
                  }
                  else
                    annotation = false;

                    if (!firstLine)
                    {
                      if (!annotation && !isValidProteinSequence(sb.toString().toCharArray()))
                      {
                        throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
                                              +" : "+seq.getName()
                                              +" : "+invalidCharacter);
                      }

                       seq.setSequence(sb.toString());

                       if (!annotation)
                         seqs.addElement(seq);
                    }

                    seq = parseId(line.substring(1));
                    firstLine = false;

                    sb = new StringBuffer();
                }
                else
                {
                    sb.append(line);
                }
            }
        }

        if (annotation)
        {
          Annotation[] anots = new Annotation[sb.length()];
          for (int i = 0; i < sb.length(); i++)
          {
            anots[i] = new Annotation(sb.substring(i, i + 1),
                                      null,
                                      ' ', 0);
          }
          AlignmentAnnotation aa = new AlignmentAnnotation(
              seq.getName().substring(2), seq.getDescription(),
              anots);

          annotations.add(aa);
        }

        else if (!firstLine)
        {

            if (!isValidProteinSequence(sb.toString().toCharArray()))
            {
                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
                                      +" : "+seq.getName()
                                      +" : "+invalidCharacter);
            }

            seq.setSequence(sb.toString());
            seqs.addElement(seq);
        }
    }


    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     * @param len DOCUMENT ME!
     * @param gaps DOCUMENT ME!
     * @param displayId DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String print(SequenceI[] s)
    {
        int len = 72;
        StringBuffer out = new StringBuffer();
        int i = 0;

        while ((i < s.length) && (s[i] != null))
        {
            out.append(">" + printId(s[i]));
            if(s[i].getDescription()!=null)
              out.append(" "+s[i].getDescription());

            out.append("\n");

            int nochunks = (s[i].getLength() / len) + 1;

            for (int j = 0; j < nochunks; j++)
            {
                int start = j * len;
                int end = start + len;

                if (end < s[i].getLength())
                {
                    out.append(s[i].getSequenceAsString(start, end) + "\n");
                }
                else if (start < s[i].getLength())
                {
                    out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
                }
            }

            i++;
        }

        return out.toString();
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String print()
    {
        return print(getSeqsAsArray());
    }
}