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/* 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, GHashTable *fetchMethods, 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);
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