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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: 1.7 $
00008  * $Id: sequence.h,v 1.7 2003/10/18 00:19:38 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 "numberingsystem.h"
00032 #include "seqdata.h"
00033 #include "seqannotation.h"
00034 #include "object.h"
00035 #include "xmlcpg.h"
00036 
00037 
00038 
00042 typedef struct rnamlSEQUENCE rnamlSequence;
00043 
00048 rnamlSequence* rnamlnewSequence ();
00049 
00055 rnamlSequence* rnamlcloneSequence (const rnamlSequence *sequence);
00056 
00061 void rnamldeleteSequence (rnamlSequence *sequence);
00062 
00068 int rnamlisSequence (const rnamlObject *obj);
00069 
00076 int rnamlequalsSequence (const rnamlSequence *left, const rnamlSequence *right);
00077 
00084 const char* rnamlgetSequenceStrand (const rnamlSequence *sequence);
00085 
00092 void rnamlsetSequenceStrand (rnamlSequence *sequence, const char *strand);
00093 
00099 int rnamlgetSequenceLength (const rnamlSequence *sequence);
00100 
00106 void rnamlsetSequenceLength (rnamlSequence *sequence, int length);
00107 
00114 int rnamlgetSequenceCircular (const rnamlSequence *sequence);
00115 
00121 void rnamlsetSequenceCircular (rnamlSequence *sequence, int circular);
00122 
00128 void rnamladdSequenceNumberingSystem (rnamlSequence *sequence, rnamlNumberingSystem *numberingSystem);
00129 
00135 xmlcpgList* rnamlgetSequenceNumberingSystems (rnamlSequence *sequence);
00136 
00143 rnamlSeqData* rnamlgetSequenceSeqData (rnamlSequence *sequence);
00144 
00150 void rnamlsetSequenceSeqData (rnamlSequence *sequence, rnamlSeqData *seqData);
00151 
00158 rnamlSeqAnnotation* rnamlgetSequenceSeqAnnotation (rnamlSequence *sequence);
00159 
00165 void rnamlsetSequenceSeqAnnotation (rnamlSequence *sequence, rnamlSeqAnnotation *seqAnnotation);
00166 
00173 xmlcpgObject* rnamltoXMLSequence (const rnamlSequence *sequence);
00174 
00175 #endif
00176 

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