00001 /* -*- Mode: C++ -*- 00002 * Alignment.h 00003 * Copyright © 2003 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: 1.2 $ 00008 * $Id: Alignment.h,v 1.2 2003/10/18 00:19:54 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_Alignment_h_ 00029 #define _rnaml_Alignment_h_ 00030 00031 #include <vector> 00032 00033 extern "C" { 00034 #include "alignment.h" 00035 } 00036 00037 #include "Object.h" 00038 00039 00040 00041 namespace rnaml 00042 { 00043 class AliSequence; 00044 00045 00046 00047 class Alignment : public Object 00048 { 00052 std::vector< AliSequence* > aliSequences; 00053 00054 public: 00055 00056 // LIFECYCLE ------------------------------------------------------------ 00057 00061 Alignment () : Object ((rnamlObject*) rnamlnewAlignment ()) { } 00062 00067 Alignment (const Alignment &right); 00068 00073 Alignment* clone () const { return new Alignment (*this); } 00074 00078 virtual ~Alignment (); 00079 00080 // OPERATORS ------------------------------------------------------------ 00081 00087 Alignment& operator= (const Alignment &right); 00088 00089 // ACCESS --------------------------------------------------------------- 00090 00095 const char* getId () const { return rnamlgetAlignmentId ((const rnamlAlignment*) getCStructure ()); } 00096 00101 void setId (const char *id) { rnamlsetAlignmentId ((rnamlAlignment*) getCStructure (), id); } 00102 00107 std::vector< AliSequence* >& getAliSequences () { return aliSequences; } 00108 00113 void addAliSequence (AliSequence* aliSequence); 00114 00119 virtual void setCStructure (rnamlObject *obj); 00120 00121 // METHODS -------------------------------------------------------------- 00122 00123 // I/O ----------------------------------------------------------------- 00124 00125 }; 00126 } 00127 00128 #endif