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/* File: blxGff3parser.h
* Author: Gemma Barson
* 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: GFF v3 file format parser.
*----------------------------------------------------------------------------
*/
#ifndef BLX_GFF_P_H
#define BLX_GFF_P_H
#include <gtk/gtk.h>
#include <seqtoolsUtils/blxmsp.hpp>
/* We follow glib convention in error domain naming:
* "The error domain is called <NAMESPACE>_<MODULE>_ERROR" */
#define BLX_GFF_ERROR "BLX_GFF_ERROR"
/* This struct contains info about a GFF type: its name and SO id, and the blixem
* type that it corresponds to */
typedef struct _BlxGffType
{
char *name; /* the type name as given in the GFF file, e.g. nucleotide_match */
char *soId; /* the type's SO Id, as given in the GFF file, e.g. SO:0000347 */
BlxMspType blxType; /* the Blixem object type that the GFF type corresponds to */
} BlxGffType;
/* This enum is to record the type of data currently being parsed by the parser. An input file can
* contain multiple types of data. The start of a new section of data is indicated by a header
* line beginning with a hash and a known type name, e.g. "# exblx_x" or "##gff-version 3"
*
* FS and SFS (Feature Series) data type names have "FS" or "SFS" followed by a specific format
* type, e.g. "# SFS type=SEG".
*
* For some data types, additional data is included in the header line(s) as well as in the 'body'
* section below it. For these, there are two data types in the enum, one postfixed with _HEADER
* and one with _BODY. When the header line is detected the initial type is set to the _HEADER enum,
* and when we are finished processing the header information it is set to _BODY, so that we go on
* to process the body of the data on the next loop through. For types with no information in the
* header, there is only a _BODY enum.
*/
typedef enum
{
PARSER_START, /* indicates that we haven't started processing yet */
PARSER_ERROR, /* indiates an error state */
GFF_3_HEADER, /* GFF 3 header */
GFF_3_BODY, /* GFF 3 data */
FASTA_SEQ_HEADER, /* FASTA sequence header */
FASTA_SEQ_BODY, /* Sequence data in FASTA format */
FASTA_SEQ_IGNORE, /* A FASTA sequence we're not interested in */
EXBLX_BODY, /* Old style sequence entries. */
SEQBL_BODY, /* Old style sequence entries. */
EXBLX_X_BODY, /* New style sequence entries with gaps and match strand. (_X stands for eXtended.) */
SEQBL_X_BODY, /* New style sequence entries with gaps and match strand. (_X stands for eXtended.) */
FS_HSP_BODY, /* feature-series HSP data */
FS_GSP_HEADER, /* feature-series GSP data header */
FS_GSP_BODY, /* feature-series GSP data */
FS_GFF_BODY, /* feature-series GFF data */
FS_SEG_BODY, /* feature-series segment data */
FS_XY_HEADER, /* feature-series XY data header */
FS_XY_BODY, /* feature-series XY data */
FS_SEQ_HEADER, /* feature-series sequence data header */
FS_SEQ_BODY /* feature-series sequence data */
} BlxParserState ;
/* External functions */
void parseGff3Header(const int lineNum,
MSP **lastMsp,
MSP **mspList,
BlxParserState *parserState,
GString *line_string,
GList **seqList,
char *refSeqName,
IntRange *refSeqRange,
GError **error);
void parseGff3Body(const int lineNum,
GArray* featureLists[],
MSP **lastMsp,
MSP **mspList,
BlxParserState *parserState,
GString *line_string,
GList **seqList,
GList *columnList,
GSList *supportedTypes,
GSList *styles,
const int resFactor,
GKeyFile *keyFile,
const IntRange* const refSeqRange,
GHashTable *lookupTable,
GHashTable *fetchMethods);
void parseFastaSeqHeader(char *line, const int lineNum,
char **refSeq, char *refSeqName, IntRange *refSeqRange,
char ***readSeq, int *readSeqLen, int *readSeqMaxLen,
BlxParserState *parserState);
GSList* blxCreateSupportedGffTypeList(const BlxSeqType seqType);
void blxDestroyGffTypeList(GSList **supportedTypes);
BlxDataType* getBlxDataType(GQuark dataType, const char *source, GKeyFile *keyFile, GError **error);
#endif /* BLX_GFF_P_H */
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