Sequence.java

// $Id: Sequence.java,v 1.2 2010/10/13 03:52:57 cmzmasek Exp $
//
// forester -- software libraries and applications
// for genomics and evolutionary biology research.
//
// Copyright (C) 2010 Christian M Zmasek
// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
// All rights reserved
// 
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library 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
// Lesser General Public License for more details.
// 
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester

package org.forester.sequence;

public interface Sequence {
    
    public static final char    UNSPECIFIED_AA  = 'X';
    public static final char    UNSPECIFIED_NUC = 'N';
    public static final char    GAP             = '-';
    public static final String  GAP_STR         = Character.toString( GAP );
    public static final char    TERMINATE       = '*';
     static final String AA_REGEXP       = "[^ARNDBCQEZGHILKMFPSTWYVXU\\-\\*]";
    static final String DNA_REGEXP      = "[^ACGTRYMKWSN\\-\\*]";
     static final String RNA_REGEXP      = "[^ACGURYMKWSN\\-\\*]";

    public abstract Object getIdentifier();

    public abstract int getLength();

    public abstract char[] getMolecularSequence();

    public abstract char getResidueAt( final int position );

    public abstract TYPE getType();

    public enum TYPE {
        RNA, DNA, AA;
    }
}