From 5b4b6c9121a7488525f5243690ff7bfb9c0613ef Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Mon, 30 Nov 2009 10:46:59 +0000
Subject: [PATCH] add code to allow separate parsing of sequence from file.
---
src/zmapGFF/zmapGFF_P.h | 46 +++++++++++++++++++++++++++--------------
1 file changed, 30 insertions(+), 16 deletions(-)
diff --git a/src/zmapGFF/zmapGFF_P.h b/src/zmapGFF/zmapGFF_P.h
index 815e86074..d08fe6253 100755
--- a/src/zmapGFF/zmapGFF_P.h
+++ b/src/zmapGFF/zmapGFF_P.h
@@ -25,9 +25,9 @@
* Description: Internal types, functions etc. for the GFF parser,
* currently this parser only does GFF v2.
* HISTORY:
- * Last edited: Jul 2 12:06 2009 (rds)
+ * Last edited: Nov 20 18:14 2009 (edgrif)
* Created: Sat May 29 13:18:32 2004 (edgrif)
- * CVS info: $Id: zmapGFF_P.h,v 1.19 2009-07-02 22:22:08 rds Exp $
+ * CVS info: $Id: zmapGFF_P.h,v 1.20 2009-11-30 10:46:59 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_GFF_P_H
@@ -43,7 +43,8 @@ enum {GFF_MANDATORY_FIELDS = 8, GFF_MAX_FIELD_CHARS = 50, GFF_MAX_FREETEXT_CHARS
/* possible states for parsing GFF file, rather trivial in fact.... */
-typedef enum {ZMAPGFF_PARSE_HEADER, ZMAPGFF_PARSE_BODY, ZMAPGFF_PARSE_ERROR} ZMapGFFParseState ;
+typedef enum {ZMAPGFF_PARSE_HEADER, ZMAPGFF_PARSE_BODY,
+ ZMAPGFF_PARSE_SEQUENCE, ZMAPGFF_PARSE_ERROR} ZMapGFFParseState ;
/* We follow glib convention in error domain naming:
@@ -106,20 +107,30 @@ typedef struct ZMapGFFParserStruct_
int clip_start, clip_end ; /* Coords used for clipping. */
- /* Header data, need to find all this for parsing to be valid. */
- gboolean done_header ;
- gboolean done_version ;
+ /* Parsing header data, need to find all this for parsing to be valid. */
+ struct
+ {
+ unsigned int done_header : 1 ;
+ unsigned int done_version : 1 ;
+ unsigned int done_source : 1 ;
+ unsigned int done_date : 1 ;
+ unsigned int done_type : 1 ;
+ unsigned int done_sequence_region : 1 ;
+ } header_flags ;
+
int gff_version ;
- gboolean done_source ; /* Not sure if we need this... */
char *source_name ;
char *source_version ;
- gboolean done_sequence_region ;
+ char *date ;
+
char *sequence_name ;
int features_start, features_end ;
+
+ /* Parsing feature data. */
ZMapFeatureTypeStyle locus_set_style ; /* cached locus style. */
GQuark locus_set_id ; /* If not zero then make a locus set from
locus tags in sequence objects. */
@@ -128,26 +139,29 @@ typedef struct ZMapGFFParserStruct_
GFF records with a source from this
list. */
-
GData *feature_sets ; /* A list of ZMapGFFParserFeatureSetStruct.
There is one of these structs per
"source". The struct contains among
other things an array of all
features for that source. */
-
/* These two are used for holding the attributes and comments fields of a GFF line,
* these can be very long so need dynamic allocation. */
GString *attributes_str ;
GString *comments_str ;
- struct
+
+
+ /* Parsing DNA sequence data, used when DNA sequence is embedded in the file. */
+ struct
{
- GString *raw_line_data;
- ZMapSequenceStruct seq_data;
- unsigned int in_sequence_block : 1;
- unsigned int finished :1;
- }parsed_sequence;
+ unsigned int done_start : 1 ;
+ unsigned int in_sequence_block : 1 ;
+ unsigned int done_finished :1 ;
+ } sequence_flags ;
+ GString *raw_line_data ;
+ ZMapSequenceStruct seq_data ;
+
} ZMapGFFParserStruct ;
--
GitLab