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Sequence.h

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00001 /*                               -*- Mode: C++ -*- 
00002  * Sequence.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: 1.13 $
00008  * $Id: Sequence.h,v 1.13 2003/10/18 00:25:19 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_Sequence_h_
00029 #define _rnaml_Sequence_h_
00030 
00031 #include <vector>
00032 
00033 extern "C" {
00034 #include "object.h"
00035 #include "sequence.h"
00036 }
00037 
00038 #include "Object.h"
00039 
00040 
00041 
00042 namespace rnaml
00043 {
00044   class NumberingSystem;
00045   class SeqData;
00046   class SeqAnnotation;
00047 
00048 
00049 
00050   class Sequence : public Object
00051   {
00055     std::vector< NumberingSystem* > numberingSystems;
00056 
00057   public:
00058 
00059     // LIFECYCLE ------------------------------------------------------------
00060 
00064     Sequence () : Object ((rnamlObject*) rnamlnewSequence ()) { }
00065 
00070     Sequence (const Sequence &right);
00071 
00076     Sequence* clone () const { return new Sequence (*this); }
00077 
00081     virtual ~Sequence ();
00082 
00083     // OPERATORS ------------------------------------------------------------
00084 
00090     Sequence& operator= (const Sequence &right);
00091 
00092     // ACCESS ---------------------------------------------------------------
00093 
00098     const char* getStrand () const { return rnamlgetSequenceStrand ((const rnamlSequence*) getCStructure ()); }
00099 
00104     void setStrand (const char *strand) { rnamlsetSequenceStrand ((rnamlSequence*) getCStructure (), strand); }
00105 
00110     int getLength () const { return rnamlgetSequenceLength ((const rnamlSequence*) getCStructure ()); }
00111 
00116     void setLength (int length) { rnamlsetSequenceLength ((rnamlSequence*) getCStructure (), length); }
00117 
00122     bool getCircular () const;
00123 
00128     void setCircular (bool circular);
00129 
00134     std::vector< NumberingSystem* >& getNumberingSystems () { return numberingSystems; }
00135 
00140     void addNumberingSystem (NumberingSystem* numberingSystem);
00141 
00146     SeqData* getSeqData () const;
00147 
00152     void setSeqData (SeqData *seqData);
00153 
00158     SeqAnnotation* getSeqAnnotation () const;
00159 
00164     void setSeqAnnotation (SeqAnnotation *seqAnnotation);
00165 
00170     virtual void setCStructure (rnamlObject *obj);
00171 
00172     // METHODS --------------------------------------------------------------
00173 
00174     // I/O  -----------------------------------------------------------------
00175 
00176   };
00177 }
00178 
00179 #endif

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