change styles to be a dataset not a list.

src/zmapControl/zmapControlRemoteXML.c

@@ -27,9 +27,9 @@
  *
  * Exported functions: See XXXXXXXXXXXXX.h
  * HISTORY:
- * Last edited: Feb 19 13:22 2007 (rds)
+ * Last edited: Feb 26 08:50 2007 (edgrif)
  * Created: Thu Feb  1 00:12:49 2007 (rds)
- * CVS info:   $Id: zmapControlRemoteXML.c,v 1.7 2007-02-20 12:53:44 rds Exp $
+ * CVS info:   $Id: zmapControlRemoteXML.c,v 1.8 2007-03-01 09:22:26 edgrif Exp $
  *-------------------------------------------------------------------
  */
 
@@ -37,7 +37,7 @@
 #include <ZMap/zmapGLibUtils.h>
 
 static gboolean setupStyles(ZMapFeatureSet set, ZMapFeature feature, 
-                            GList *styles,      GQuark style_id);
+                            GData *styles, GQuark style_id) ;
 /* xml event callbacks ... */
 /* starts */
 static gboolean xml_zmap_start_cb(gpointer user_data, ZMapXMLElement zmap_element, 
@@ -127,7 +127,7 @@ ZMapXMLParser zmapControlRemoteXMLInitialise(void *data)
 /* INTERNALS */
 
 static gboolean setupStyles(ZMapFeatureSet set, ZMapFeature feature, 
-                            GList *styles,      GQuark style_id)
+                            GData *styles, GQuark style_id)
 {
   ZMapFeatureTypeStyle style, set_style;
   gboolean got_style = TRUE;

src/zmapControl/zmapControlRemote_P.h

@@ -27,9 +27,9 @@
  *
  * Exported functions: See XXXXXXXXXXXXX.h
  * HISTORY:
- * Last edited: Feb  1 08:57 2007 (rds)
+ * Last edited: Feb 19 10:32 2007 (edgrif)
  * Created: Thu Feb  1 00:29:43 2007 (rds)
- * CVS info:   $Id: zmapControlRemote_P.h,v 1.1 2007-02-06 11:00:15 rds Exp $
+ * CVS info:   $Id: zmapControlRemote_P.h,v 1.2 2007-03-01 09:22:26 edgrif Exp $
  *-------------------------------------------------------------------
  */
 
@@ -103,7 +103,7 @@ typedef struct {
 
   controlClientObj  client;
 
-  GList *styles;                /* These should be ZMapFeatureTypeStyle */
+  GData *styles;                /* These should be ZMapFeatureTypeStyle */
   GList *locations;             /* This is just a list of ZMapSpan Structs */
 
   ViewConnectDataStruct new_view;

src/zmapGFF/gffparser.c

@@ -27,9 +27,9 @@
  *
  * Exported functions: See XXXXXXXXXXXXX.h
  * HISTORY:
- * Last edited: Jan 11 16:02 2006 (rds)
+ * Last edited: Feb 19 13:56 2007 (edgrif)
  * Created: Wed Jan 11 11:30:39 2006 (rds)
- * CVS info:   $Id: gffparser.c,v 1.2 2006-11-08 09:24:15 edgrif Exp $
+ * CVS info:   $Id: gffparser.c,v 1.3 2007-03-01 09:20:51 edgrif Exp $
  *-------------------------------------------------------------------
  */
 
@@ -197,7 +197,7 @@ static gboolean readFeatures(parserFile data)
   return result;
 }
 
-static int parseFile(char *filename, GList *styles)
+static int parseFile(char *filename, GData *styles)
 {
   parserFileStruct data = {NULL};
 
@@ -218,7 +218,7 @@ static int parseFile(char *filename, GList *styles)
 int main(int argc, char *argv[])
 {
   int main_rc ;
-  GList *styles = NULL;
+  GData *styles = NULL;
   
   styles  = zMapFeatureTypeGetFromFile("ZMapTypes");
   main_rc = parseFile("huge.gff", styles);

src/zmapGFF/zmapGFF2Dumper.c

@@ -26,9 +26,9 @@
  *
  * Exported functions: See ZMap/zmapGFF.h
  * HISTORY:
- * Last edited: Feb  6 17:55 2007 (rds)
+ * Last edited: Feb 26 11:20 2007 (edgrif)
  * Created: Mon Nov 14 13:21:14 2005 (edgrif)
- * CVS info:   $Id: zmapGFF2Dumper.c,v 1.7 2007-02-06 17:55:58 rds Exp $
+ * CVS info:   $Id: zmapGFF2Dumper.c,v 1.8 2007-03-01 09:20:51 edgrif Exp $
  *-------------------------------------------------------------------
  */
 
@@ -280,7 +280,7 @@ static gboolean dumpFeature(GIOChannel *file, gpointer user_data,
   GIOStatus status ;
   gsize bytes_written ;
   GString *buffer = (GString *)user_data ;
-  const char *gff_source = NULL, *gff_feature = NULL ;
+  const char *gff_source, *gff_feature ;
 
 
   /* Don't dump some features...this will go when dna is not longer a feature... */
@@ -289,10 +289,8 @@ static gboolean dumpFeature(GIOChannel *file, gpointer user_data,
 
 
   /* Set up GFF output specials from style. */
-  if (style->gff_source)
-    gff_source = g_quark_to_string(style->gff_source) ;
-  if (style->gff_feature)
-    gff_feature = g_quark_to_string(style->gff_feature) ;
+  gff_source = zMapStyleGetGFFSource(style) ;
+  gff_feature = zMapStyleGetGFFFeature(style) ;
 
   /* Fields are: <seqname> <source> <feature> <start> <end> <score> <strand> <frame> */
 

src/zmapGFF/zmapGFF2parser.c

@@ -26,9 +26,9 @@
  *              
  * Exported functions: See ZMap/zmapGFF.h
  * HISTORY:
- * Last edited: Jan  5 10:05 2007 (rds)
+ * Last edited: Mar  1 09:20 2007 (edgrif)
  * Created: Fri May 28 14:25:12 2004 (edgrif)
- * CVS info:   $Id: zmapGFF2parser.c,v 1.69 2007-01-05 22:26:23 rds Exp $
+ * CVS info:   $Id: zmapGFF2parser.c,v 1.70 2007-03-01 09:20:51 edgrif Exp $
  *-------------------------------------------------------------------
  */
 
@@ -82,23 +82,12 @@ static void destroyFeatureArray(gpointer data) ;
 static void printSource(GQuark key_id, gpointer data, gpointer user_data) ;
 #endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
 
-
 static gboolean loadGaps(char *currentPos, GArray *gaps);
 
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static int sortGapsByTarget(gconstpointer a, gconstpointer b);
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-static void initSources(GData **datalist, GList *sources);
-
-
-
 #ifdef ED_G_NEVER_INCLUDE_THIS_CODE
 static void stylePrintCB(gpointer data, gpointer user_data) ;
 #endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
 
-
 static void mungeFeatureType(char *source, ZMapFeatureType *type_inout);
 static gboolean getNameFromNote(char *attributes, char **name) ;
 
@@ -112,7 +101,7 @@ static gboolean getNameFromNote(char *attributes, char **name) ;
  * _not_ create any features. This means the parser can be tested/used on huge datasets
  * without having to have huge amounts of memory to hold the feature structs.
  * You can only set parse_only when you create the parser, it cannot be set later. */
-ZMapGFFParser zMapGFFCreateParser(GList *sources, gboolean parse_only)
+ZMapGFFParser zMapGFFCreateParser(GData *sources, gboolean parse_only)
 {
   ZMapGFFParser parser ;
   GQuark locus_id ;
@@ -144,14 +133,11 @@ ZMapGFFParser zMapGFFCreateParser(GList *sources, gboolean parse_only)
   parser->done_sequence_region = FALSE ;
   parser->sequence_name = NULL ;
   parser->features_start = parser->features_end = 0 ;
-
-  initSources(&(parser->sources), sources);
+  parser->sources = sources ;
 
   /* Check for Locus as one of the sources as this needs to be constructed as we go along. */
   locus_id = zMapStyleCreateID(ZMAP_FIXED_STYLE_LOCUS_NAME) ;
-  if (!(parser->locus_set_style = zMapFindStyle(g_datalist_id_get_data(&(parser->sources),
-								       locus_id), 
-						locus_id)))
+  if (!(parser->locus_set_style = zMapFindStyle(parser->sources, locus_id)))
     {
       zMapLogWarning("Locus set will not be created, "
 		     "could not find style \"%s\" for feature set \"%s\".",
@@ -547,9 +533,6 @@ void zMapGFFDestroyParser(ZMapGFFParser parser)
   if (!parser->parse_only && parser->feature_sets)
     g_datalist_clear(&(parser->feature_sets)) ;
 
-  if(parser->sources)
-    g_datalist_clear(&(parser->sources));
-
   g_free(parser) ;
 
   return ;
@@ -972,9 +955,7 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
 
   /* If a feature set style or a feature style is missing then we can't carry on.
    * NOTE the feature sets style has the same name as the feature set. */
-  if (!(feature_set_style = zMapFindStyle(g_datalist_id_get_data(&(parser->sources),
-								 feature_set_style_id), 
-					  feature_set_style_id)))
+  if (!(feature_set_style = zMapFindStyle(parser->sources, feature_set_style_id)))
     {
       *err_text = g_strdup_printf("feature ignored, could not find style \"%s\" for feature set \"%s\".",
 				  feature_set_name, feature_set_name) ;
@@ -983,9 +964,7 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
       return result ;
     }
 
-  if (!(feature_style = zMapFindStyle(g_datalist_id_get_data(&(parser->sources),
-							     feature_style_id), 
-				      feature_style_id)))
+  if (!(feature_style = zMapFindStyle(parser->sources, feature_style_id)))
     {
       *err_text = g_strdup_printf("feature ignored, could not find its style \"%s\".",
 				  g_quark_to_string(feature_style_id)) ;
@@ -1142,7 +1121,7 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
      else if (feature_type == ZMAPFEATURE_ALIGNMENT)
        {
 	 /* I am not sure if we ever have target_strand, target_phase from GFF output.... */
-         if(feature_style->opts.parse_gaps && 
+         if(zMapStyleIsParseGaps(feature_style) && 
             ((gaps_onwards = strstr(attributes, "\tGaps ")) != NULL)) 
            {
              gaps = g_array_new(FALSE, FALSE, sizeof(ZMapAlignBlockStruct));
@@ -1431,32 +1410,6 @@ static gboolean getFeatureName(NameFindType name_find, char *sequence, char *att
   return has_name ;
 }
 
-/* This should speed things up a little as the look up will be quicker.
- * We store the actual list item at the moment.  This is deliberate so
- * we can use the zMapFindStyle function with the list that we get
- * from our g_dataset_id_get lookup...
- */
-static void initSources(GData **datalist, GList *sources)
-{
-  GList *list = NULL;
-
-  list = g_list_first(sources);
-
-  g_datalist_init(datalist);
-
-  while(list)
-    {
-      g_datalist_id_set_data_full(datalist, 
-				  ((ZMapFeatureTypeStyle)list->data)->unique_id, 
-				  list,
-				  NULL); /* MUST NOT Destroy when g_dataset_clear called */
-      list = list->next;
-    }
-
-  return ;
-}
-
-
 
 /* Format of column group attribute section is:
  * 

src/zmapServer/file/fileServer.c

@@ -30,9 +30,9 @@
  *              
  * Exported functions: See ZMap/zmapServerPrototype.h
  * HISTORY:
- * Last edited: Feb  6 18:15 2007 (rds)
+ * Last edited: Feb 19 14:05 2007 (edgrif)
  * Created: Fri Sep 10 18:29:18 2004 (edgrif)
- * CVS info:   $Id: fileServer.c,v 1.25 2007-02-06 18:15:47 rds Exp $
+ * CVS info:   $Id: fileServer.c,v 1.26 2007-03-01 09:23:34 edgrif Exp $
  *-------------------------------------------------------------------
  */
 
@@ -72,7 +72,7 @@ static gboolean createConnection(void **server_out,
                                  char *version_str, int timeout) ;
 
 static ZMapServerResponseType openConnection(void *server) ;
-static ZMapServerResponseType getStyles(void *server, GList **styles_out) ;
+static ZMapServerResponseType getStyles(void *server, GData **styles_out) ;
 static ZMapServerResponseType getFeatureSets(void *server, GList **feature_sets_out) ;
 static ZMapServerResponseType setContext(void *server,  ZMapFeatureContext feature_context) ;
 static ZMapFeatureContext copyContext(void *server_conn) ;
@@ -213,7 +213,7 @@ static ZMapServerResponseType openConnection(void *server_in)
  * something has gone wrong.
  * 
  *  */
-static ZMapServerResponseType getStyles(void *server_in, GList **styles_out)
+static ZMapServerResponseType getStyles(void *server_in, GData **styles_out)
 {
   ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
   FileServer server = (FileServer)server_in ;