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Alignment.h

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00001 /*                               -*- Mode: C++ -*- 
00002  * Alignment.h
00003  * Copyright © 2003 Laboratoire de Biologie Informatique et Théorique
00004  *                  Université de Montréal.
00005  * Author           : Patrick Charbonneau
00006  * Created On       : Wed Sep 12 16:48:15 2003
00007  * $Revision: 1.2 $
00008  * $Id: Alignment.h,v 1.2 2003/10/18 00:19:54 larosem Exp $
00009  *
00010  * This file is part of xmlcpg.
00011  *
00012  * xmlcpg is free software; you can redistribute it and/or modify it under
00013  * the terms of the GNU Lesser General Public License as published by the Free
00014  * Software Foundation; either version 2 of the License, or (at your option)
00015  * any later version.
00016  *
00017  * xmlcpg is distributed in the hope that it will be useful, but WITHOUT ANY
00018  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
00019  * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for
00020  * more details.
00021  *
00022  * You should have received a copy of the GNU Lesser General Public License
00023  * along with xmlcpg; if not, write to the Free Software Foundation, Inc.,
00024  * 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
00025  */
00026 
00027 
00028 #ifndef _rnaml_Alignment_h_
00029 #define _rnaml_Alignment_h_
00030 
00031 #include <vector>
00032 
00033 extern "C" {
00034 #include "alignment.h"
00035 }
00036 
00037 #include "Object.h"
00038 
00039 
00040 
00041 namespace rnaml
00042 {
00043   class AliSequence;
00044 
00045 
00046   
00047   class Alignment : public Object
00048   {
00052     std::vector< AliSequence* > aliSequences;
00053 
00054   public:
00055 
00056     // LIFECYCLE ------------------------------------------------------------
00057 
00061     Alignment () : Object ((rnamlObject*) rnamlnewAlignment ()) { }
00062 
00067     Alignment (const Alignment &right);
00068 
00073     Alignment* clone () const { return new Alignment (*this); }
00074 
00078     virtual ~Alignment ();
00079 
00080     // OPERATORS ------------------------------------------------------------
00081 
00087     Alignment& operator= (const Alignment &right);
00088 
00089     // ACCESS ---------------------------------------------------------------
00090 
00095     const char* getId () const { return rnamlgetAlignmentId ((const rnamlAlignment*) getCStructure ()); }
00096 
00101     void setId (const char *id) { rnamlsetAlignmentId ((rnamlAlignment*) getCStructure (), id); }
00102 
00107     std::vector< AliSequence* >& getAliSequences () { return aliSequences; }
00108 
00113     void addAliSequence (AliSequence* aliSequence);
00114 
00119     virtual void setCStructure (rnamlObject *obj);
00120 
00121     // METHODS --------------------------------------------------------------
00122 
00123     // I/O  -----------------------------------------------------------------
00124 
00125   };
00126 }
00127 
00128 #endif

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