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