/*  File: blxparser.h
 *  Author: Gemma Barson, 2010-09-02
 *  Copyright (c) 2010 - 2012 Genome Research Ltd
 * ---------------------------------------------------------------------------
 * SeqTools is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 3
 * of the License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
 * ---------------------------------------------------------------------------
 * This file is part of the SeqTools sequence analysis package, 
 * written by
 *      Gemma Barson      (Sanger Institute, UK)  <gb10@sanger.ac.uk>
 * 
 * based on original code by
 *      Erik Sonnhammer   (SBC, Sweden)           <Erik.Sonnhammer@sbc.su.se>
 * 
 * and utilizing code taken from the AceDB and ZMap packages, written by
 *      Richard Durbin    (Sanger Institute, UK)  <rd@sanger.ac.uk>
 *      Jean Thierry-Mieg (CRBM du CNRS, France)  <mieg@kaa.crbm.cnrs-mop.fr>
 *      Ed Griffiths      (Sanger Institute, UK)  <edgrif@sanger.ac.uk>
 *      Roy Storey        (Sanger Institute, UK)  <rds@sanger.ac.uk>
 *      Malcolm Hinsley   (Sanger Institute, UK)  <mh17@sanger.ac.uk>
 *
 *  Description: Parser for Blixem and Dotter feature input files.
 *               
 *               GFF v3 is the preferred input file format. This parser also
 *               includes code to parse the old exblx or feature-series file
 *               types (e.g. as output from the MSPcrunch program). 
 *----------------------------------------------------------------------------
 */

void           parseFS(MSP **MSPlist, FILE *file, BlxBlastMode *blastMode, GArray* featureLists[], GList **seqList, GList *columnList, GSList *supportedTypes, GSList *styles,
		       char **seq1, char *seq1name, IntRange *seq1Range, char **seq2, char *seq2name, GKeyFile *keyFile, GHashTable *lookupTable, GError **error) ;

void           parseBuffer(MSP **MSPlist, const char *buffer_in, BlxBlastMode *blastMode, GArray* featureLists[], GList **seqList, GList *columnList, GSList *supportedTypes, GSList *styles,
                           char **seq1, char *seq1name, IntRange *seq1Range, char **seq2, char *seq2name, GKeyFile *keyFile, GHashTable *lookupTable, GError **error) ;
gboolean       blxParseGaps(char **text, MSP *msp, const gboolean hasGapsTag);