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/* File: seqtoolsFetch.hpp
* Author: Gemma Guest, 2015-12-21
* Copyright (c) 2015 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: Utility structs for sequence-fetching code
*----------------------------------------------------------------------------
*/
#ifndef DEF_SEQTOOLS_FETCH_HPP
#define DEF_SEQTOOLS_FETCH_HPP
#include <glib.h>
/* These are the supported fetch modes. ***If you add anything here, also add it in fetchModeStr*** */
typedef enum
{
#ifdef PFETCH_HTML
BLXFETCH_MODE_HTTP,
BLXFETCH_MODE_PIPE,
#endif
BLXFETCH_MODE_SOCKET,
BLXFETCH_MODE_WWW,
BLXFETCH_MODE_SQLITE,
BLXFETCH_MODE_COMMAND,
BLXFETCH_MODE_INTERNAL,
BLXFETCH_MODE_NONE,
BLXFETCH_NUM_MODES /* must be last in list */
} BlxFetchMode;
/* output types for fetch modes. *** if you add anything here, also add it in outputTypeStr *** */
typedef enum
{
BLXFETCH_OUTPUT_INVALID,
BLXFETCH_OUTPUT_RAW, /* raw sequence data, separated by newlines */
BLXFETCH_OUTPUT_FASTA, /* sequence data in FASTA format */
BLXFETCH_OUTPUT_EMBL, /* the sequence's EMBL entry */
BLXFETCH_OUTPUT_LIST, /* a list of named columns is returned */
BLXFETCH_OUTPUT_GFF, /* a new gff for re-parsing is returned */
BLXFETCH_NUM_OUTPUT_TYPES
} BlxFetchOutputType;
/* struct to hold info about a fetch method */
typedef struct _BlxFetchMethod
{
GQuark name; /* fetch method name */
BlxFetchMode mode; /* the type of fetch method */
char *location; /* e.g. url, script, command, db location etc. */
char *node; /* for socket fetch mode */
int port; /* for socket and http/pipe fetch modes */
char *cookie_jar; /* for http/pipe fetch mode */
char *proxy; /* for http/pipe fetch mode */
char *args; /* arguments/query/request */
GArray *columns; /* for db-fetch, the list of columns the query will populate */
char *separator; /* separator when combining multiple sequence names into a list */
GArray *errors; /* array of messages (as GQuarks) that indicate that an error occurred, e.g. "no match" */
BlxFetchOutputType outputType; /* the output format to expect from the fetch command */
} BlxFetchMethod;
#endif /* DEF_SEQTOOLS_FETCH_HPP */
BlxFetchMethod* createBlxFetchMethod(const char *fetchName);
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