00001 /* -*- Mode: C -*- 00002 * alignment.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: 1.1 $ 00008 * $Id: alignment.h,v 1.1 2003/10/01 13:05:10 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 "alisequence.h" 00032 #include "object.h" 00033 #include "xmlcpg.h" 00034 00035 00036 00040 typedef struct rnamlALIGNMENT rnamlAlignment; 00041 00046 rnamlAlignment* rnamlnewAlignment (); 00047 00053 rnamlAlignment* rnamlcloneAlignment (const rnamlAlignment *alignment); 00054 00059 void rnamldeleteAlignment (rnamlAlignment *alignment); 00060 00066 int rnamlisAlignment (const rnamlObject *obj); 00067 00074 int rnamlequalsAlignment (const rnamlAlignment *left, const rnamlAlignment *right); 00075 00082 const char* rnamlgetAlignmentId (const rnamlAlignment *alignment); 00083 00090 void rnamlsetAlignmentId (rnamlAlignment *alignment, const char *id); 00091 00097 void rnamladdAlignmentAliSequence (rnamlAlignment *alignment, rnamlAliSequence *aliSequence); 00098 00104 xmlcpgList* rnamlgetAlignmentAliSequences (rnamlAlignment *alignment); 00105 00112 xmlcpgObject* rnamltoXMLAlignment (const rnamlAlignment *alignment); 00113 00114 #endif 00115