/*
* 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 jalview.datamodel.*;

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

public abstract class AlignFile extends FileParse {
  int noSeqs    = 0;
  int maxLength = 0;

  Vector    seqs;
  Vector    headers;

  long start;
  long end;

  public AlignFile()
  {}

  public AlignFile(String inStr) {
    initData();
System.out.println("is this ever called??");
    try{
      parse();
    }catch(Exception ex){}
  }

/**
 * Constructor which parses the data from a file of some specified type.
 * @param inFile Filename to read from.
 * @param type   What type of file to read from (File, URL)
 */
  public AlignFile(String inFile, String type) throws IOException {
    super(inFile,type);

    initData();

    parse();

  }

/**
 * Return the seqs Vector
 */
  public Vector getSeqs() {
    return seqs;
  }

/**
 * Return the Sequences in the seqs Vector as an array of Sequences
 */
  public SequenceI [] getSeqsAsArray() {
    SequenceI [] s = new SequenceI[seqs.size()];
    for (int i=0;i < seqs.size();i++) {
      s[i] = (SequenceI)seqs.elementAt(i);
    }
    return s;
  }


/**
 * Initialise objects to store sequence data in.
 */
  protected void initData() {
    seqs    = new Vector();
    headers = new Vector();
  }

  protected void setSeqs(SequenceI [] s) {
    seqs = new Vector();
    for (int i=0; i<s.length; i++) {
      seqs.addElement(s[i]);
    }
  }

  // Checks whether sequence is valid aa characters
  protected boolean isValidProteinSequence(String sequence)
  {
    for (int i = 0; i < sequence.length(); i++)
      if (!jalview.schemes.ResidueProperties.aaHash.containsKey(String.valueOf(sequence.charAt(i))))
        return false;

    return true;
  }


/**
 * This method must be implemented to parse the contents of the file.
 */
  public abstract void parse() throws IOException;


/**
 * Print out in alignment file format the Sequences in the seqs Vector.
 */
  public abstract String print();
}