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