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Base.h

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00001 /*                               -*- Mode: C++ -*- 
00002  * Base.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: 1.7 $
00008  * $Id: Base.h,v 1.7 2003/10/18 00:20:28 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_Base_h_
00029 #define _rnaml_Base_h_
00030 
00031 extern "C"{
00032 #include "base.h"
00033 #include "object.h"
00034 }
00035 
00036 #include <vector>
00037 
00038 #include "Object.h"
00039 
00040 
00041 
00042 namespace rnaml
00043 {
00044   class Atom;
00045 
00046 
00047 
00048   class Base : public Object
00049   {
00053     std::vector< Atom* > atoms;
00054 
00055   public:
00056 
00057     // LIFECYCLE ------------------------------------------------------------
00058 
00062     Base () : Object ((rnamlObject*) rnamlnewBase ()) { }
00063 
00068     Base (const Base &right);
00069 
00074     Base* clone () const { return new Base (*this); }
00075 
00079     virtual ~Base ();
00080 
00081     // OPERATORS ------------------------------------------------------------
00082 
00088     Base& operator= (const Base &right);
00089 
00090     // ACCESS ---------------------------------------------------------------
00091 
00096     const char* getStrand () const { return rnamlgetBaseStrand ((const rnamlBase*) getCStructure ()); }
00097 
00102     void setStrand (const char *strand) { rnamlsetBaseStrand ((rnamlBase*) getCStructure (), strand); }
00103 
00108     int getPosition () const { return rnamlgetBasePosition ((const rnamlBase*) getCStructure ()); }
00109 
00114     void setPosition (int position) { rnamlsetBasePosition ((rnamlBase*) getCStructure (), position); }
00115 
00120     const char* getBaseType () const { return rnamlgetBaseBaseType ((const rnamlBase*) getCStructure ()); }
00121 
00126     void setBaseType (const char *baseType) { rnamlsetBaseBaseType ((rnamlBase*) getCStructure (), baseType); }
00127 
00132     char getAltLoc () const { return rnamlgetBaseAltLoc ((const rnamlBase*) getCStructure ()); }
00133 
00138     void setAltLoc (char altLoc) { rnamlsetBaseAltLoc ((rnamlBase*) getCStructure (), altLoc); }
00139 
00144     char getInsertion () const { return rnamlgetBaseInsertion ((const rnamlBase*) getCStructure ()); }
00145 
00150     void setInsertion (char insertion) { rnamlsetBaseInsertion ((rnamlBase*) getCStructure (), insertion); }
00151 
00156     std::vector< Atom* >& getAtoms () { return atoms; }
00157 
00162     void addAtom (Atom* atom);
00163 
00168     virtual void setCStructure (rnamlObject *obj);
00169 
00170     // METHODS --------------------------------------------------------------
00171 
00172     // I/O  -----------------------------------------------------------------
00173 
00174   };
00175 }
00176 
00177 #endif

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