/* Sequence.java
 *
 * created: Mon Oct 12 1998
 *
 * This file is part of Artemis
 * 
 * Copyright (C) 1998,1999,2000  Genome Research Limited
 * 
 * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 * $Header: /nfs/disk222/yeastpub/Repository/powmap/uk/ac/sanger/pathogens/embl/Sequence.java,v 1.3 2000/04/17 15:26:21 kmr Exp $
 */

package uk.ac.sanger.pathogens.embl;

import uk.ac.sanger.pathogens.ReadOnlyException;

/**
 *  Sequence interface
 *
 *  @author Kim Rutherford
 *  @version $Id: Sequence.java,v 1.3 2000/04/17 15:26:21 kmr Exp $
 *
 */

public interface Sequence {
  /**
   *  Return a the given range of bases as a String.
   *  @param start The start base of the range.
   *  @param end The end base of the range.
   **/
  public String getSubSequence (int start, int end);

  /**
   *  Set this sequence to hold the bases in the given String.
   *  @exception ReadOnlyException If this Sequence cannot be changed.
   **/
  public void setFromString (final String new_sequence)
      throws ReadOnlyException;

  /**
   *  Return an identifier for this sequence.  This will most likely be a
   *  discription (eg. from a FASTA header).  Returns null if there is no
   *  identifier for the sequence.
   **/
  public String getIdentifier ();

  /**
   *  Returns the length of the sequence in bases.
   **/
  public int length ();

  /**
   *  Return the count of c bases in the whole sequence.
   **/
  public int getCCount ();

  /**
   *  Return the count of g bases in the whole sequence.
   **/
  public int getGCount ();

  /**
   *  Return the count of a bases in the whole sequence.
   **/
  public int getACount ();

  /**
   *  Return the count of t bases in the whole sequence.
   **/
  public int getTCount ();

  /**
   *  Return the count of non-g,c,t,a bases in the whole sequence.
   **/
  public int getOtherCount ();
}
