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Molecule.h

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00001 /*                               -*- Mode: C++ -*- 
00002  * Molecule.h
00003  * Copyright © 2002-03 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: 1.11 $
00008  * $Id: Molecule.h,v 1.11 2003/10/18 00:23:34 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_Molecule_h_
00029 #define _rnaml_Molecule_h_
00030 
00031 #include <vector>
00032 
00033 extern "C" {
00034 #include "molecule.h"
00035 #include "object.h"
00036 }
00037 
00038 #include "Object.h"
00039 
00040 
00041 
00042 namespace rnaml
00043 {
00044   class Identity;
00045   class Sequence;
00046   class Structure;
00047 
00048 
00049 
00050   class Molecule : public Object
00051   {
00055     std::vector< Sequence* > sequences;
00056 
00057   public:
00058 
00059     // LIFECYCLE ------------------------------------------------------------
00060 
00064     Molecule () : Object ((rnamlObject*) rnamlnewMolecule ()) { }
00065 
00070     Molecule (const Molecule &right);
00071 
00076     Molecule* clone () const { return new Molecule (*this); }
00077 
00081     virtual ~Molecule ();
00082 
00083     // OPERATORS ------------------------------------------------------------
00084 
00090     Molecule& operator= (const Molecule &right);
00091 
00092     // ACCESS ---------------------------------------------------------------
00093 
00098     const char* getId () const { return rnamlgetMoleculeId ((const rnamlMolecule*) getCStructure ()); }
00099 
00104     void setId (const char *id) { rnamlsetMoleculeId ((rnamlMolecule*) getCStructure (), id); }
00105 
00110     const char* getType () const { return rnamlgetMoleculeType ((const rnamlMolecule*) getCStructure ()); }
00111 
00116     void setType (const char *type) { rnamlsetMoleculeType ((rnamlMolecule*) getCStructure (), type); }
00117 
00122     Identity* getIdentity () const;
00123 
00128     void setIdentity (Identity *identity);
00129 
00134     std::vector< Sequence* >& getSequences () { return sequences; }
00135 
00140     void addSequence (Sequence* sequence);
00141 
00146     Structure* getStructure () const;
00147 
00152     void setStructure (Structure *structure);
00153 
00158     virtual void setCStructure (rnamlObject *obj);
00159 
00160     // METHODS --------------------------------------------------------------
00161 
00162     // I/O  -----------------------------------------------------------------
00163 
00164   };
00165 }
00166 
00167 #endif

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