initial version of GFF v2 parser

src/zmapGFF/README

+================================================================================   
+ZMapGFF
+
+
+This directory contains the code that parses GFF lines and constructs ZMapFeature's
+from the lines. The intention is that the code will eventually parse either GFF
+v2 or v3. Currently the code only does v2 as this is the supported version of
+GFF and v3 format is still in the melting pot.
+
+The GFF parser needs to handed lines to parse, it deliberately does not deal with
+issues of data sources, this is so that is can be coupled to any source and large
+GFF documents can be parsed a line at a time.

src/zmapGFF/zmapGFF_P.h

+/*  File: zmapGFF_P.h
+ *  Author: Ed Griffiths (edgrif@sanger.ac.uk)
+ *  Copyright (c) Sanger Institute, 2004
+ *-------------------------------------------------------------------
+ * ZMap 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 2
+ * 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 ZMap genome database package
+ * originated by
+ * 	Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
+ *      Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
+ *
+ * Description: 
+ * Exported functions: See XXXXXXXXXXXXX.h
+ * HISTORY:
+ * Last edited: Jun 15 15:29 2004 (edgrif)
+ * Created: Sat May 29 13:18:32 2004 (edgrif)
+ * CVS info:   $Id: zmapGFF_P.h,v 1.1 2004-06-15 14:37:35 edgrif Exp $
+ *-------------------------------------------------------------------
+ */
+#ifndef ZMAP_GFF_P_H
+#define ZMAP_GFF_P_H
+
+#include <ZMap/zmapGFF.h>
+
+
+
+/* Some defines for parsing stuff....my need v2 and v3 versions of these. */
+enum {GFF_MANDATORY_FIELDS = 8, GFF_MAX_FIELD_CHARS = 50, GFF_MAX_FREETEXT_CHARS = 1000} ;
+
+
+
+/* possible states for parsing GFF file, rather trivial in fact.... */
+typedef enum {ZMAPGFF_PARSE_HEADER, ZMAPGFF_PARSE_BODY, ZMAPGFF_PARSE_ERROR} ZMapGFFParseState ;
+
+
+/* We follow glib convention in error domain naming:
+ *          "The error domain is called <NAMESPACE>_<MODULE>_ERROR" */
+#define ZMAP_GFF_ERROR "ZMAP_GFF_ERROR"
+
+typedef enum
+{
+  ZMAP_GFF_ERROR_HEADER,				    /* Error in GFF header section. */
+  ZMAP_GFF_ERROR_BODY,					    /* Error in GFF body section. */
+  ZMAP_GFF_ERROR_FAILED					    /* Other fatal failure, error->message
+							       should explain. */
+} ZMapGFFError ;
+
+
+
+
+/* For each set of features that come from a single source, we keep an array of those features
+ * but also a list of features that need to be built up from several GFF lines. */
+typedef struct ZMapGFFParserFeatureSetStruct_
+{
+  char *source ;					    /* Name of feature set source. */
+
+  GArray *features ;					    /* All features in this feature set. */
+
+  GData *multiline_features ;				    /* Features in this feature set that
+							       must be built up from multiple
+							       lines. */
+  ZMapGFFParser parser ;				    /* Self reference forced on us because
+							       GData destroy func. does not have a
+							       user_data parameter. */
+
+} ZMapGFFParserFeatureSetStruct, *ZMapGFFParserFeatureSet ;
+
+
+
+
+/* this struct will need to hold the buffers for the parsing, the hash tables for referencing
+ * features etc. etc....... */
+typedef struct ZMapGFFParserStruct_
+{
+  ZMapGFFParseState state ;
+  GError *error ;					    /* Holds recoverable error. */
+  GQuark error_domain ;
+
+  /* Header data, need to find all this for parsing to be valid. */
+  gboolean done_version ;
+  int gff_version ;
+
+  gboolean done_source ;				    /* Not sure if we need this... */
+  char *source_name ;
+  char *source_version ;
+
+  gboolean done_sequence_region ;
+  char *sequence_name ;
+  int sequence_start, sequence_end ;
+
+
+
+
+  /* Some features need to be built up from multiple GFF lines so we keep associations
+   * of these features in arrays. The arrays are indexed via sources. These arrays are only used
+   * while building up the final arrays of features. */
+  GData *feature_sets ;					    /* A list of arrays of features, the
+							       arrays are indexed via their
+							       "source". Hence each array contains
+							       features from a single source. */
+
+  gboolean free_on_destroy ;				    /* TRUE => free all feature arrays
+							       when parser is destroyed. */
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+  /* Let's not worry about this for now.........we could even just return the array of arrays
+   * dynamically by zooming through the sources and extracting all the sources.... */
+
+  /* The final array of arrays of features. Each sub-array contains features that all have the
+   * same source. */
+  GArray *feature_sets ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+
+} ZMapGFFParserStruct ;
+
+
+
+
+
+
+
+
+#endif /* ZMAP_GFF_P_H */