redundant file....should have been removed ages ago...

src/zmapWindow/GFF_scaffold.c

-/*  Last edited: Sep  9 14:32 2005 (edgrif) */
-/* This is a temporary file only to help with testing....it will go once GFF code is combined
- * into the threads etc. code proper.... */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <glib.h>
-#include <ZMap/zmapGFF.h>
-#include <ZMap/zmapConfig.h>
-
-
-static ZMapFeatureContext parseGFF(char *filename) ;
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void testfunc(GQuark key_id, gpointer data, gpointer user_data);
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-ZMapFeatureContext testGetGFF(void)
-{
-  ZMapFeatureContext features = NULL ;
-  ZMapConfig config ;
-  char *GFF_file = NULL ;
-
-  if ((config = zMapConfigCreate()))
-    {
-      ZMapConfigStanzaSet GFF_list = NULL ;
-      ZMapConfigStanza GFF_stanza ;
-      char *GFF_stanza_name = "GFF" ;
-      ZMapConfigStanzaElementStruct GFF_elements[] = {{"filename", ZMAPCONFIG_STRING, {NULL}},
-						      {NULL, -1, {NULL}}} ;
-
-      GFF_stanza = zMapConfigMakeStanza(GFF_stanza_name, GFF_elements) ;
-
-      if (zMapConfigFindStanzas(config, GFF_stanza, &GFF_list))
-	{
-	  ZMapConfigStanza next_log ;
-	  
-	  /* Get the first GFF stanza found, we will ignore any others. */
-	  next_log = zMapConfigGetNextStanza(GFF_list, NULL) ;
-	  
-	  if ((GFF_file = zMapConfigGetElementString(next_log, "filename")))
-	    GFF_file = g_strdup(GFF_file) ;
-	  
-	  zMapConfigDeleteStanzaSet(GFF_list) ;		    /* Not needed anymore. */
-	}
-      
-      zMapConfigDestroyStanza(GFF_stanza) ;
-      
-      zMapConfigDestroy(config) ;
-    }
-
-
-  if (GFF_file)
-    {
-      features = parseGFF(GFF_file) ;
-      g_free(GFF_file) ;
-    }
-
-  return features ;
-}
-
-
-
-static ZMapFeatureContext parseGFF(char *filename)
-{
-  ZMapFeatureContext feature_context = NULL ;
-  GIOChannel* gff_file ;
-  GError *gff_file_err = NULL ;
-
-
-  if ((gff_file = g_io_channel_new_file(filename, "r", &gff_file_err)))
-    {
-      ZMapGFFParser parser ;
-      GString* gff_line ;
-      GIOStatus status ;
-      gsize terminator_pos = 0 ;
-      gboolean free_arrays = FALSE, parse_only = FALSE ;
-
-
-      gff_line = g_string_sized_new(2000) ;		    /* Probably not many lines will be >
-							       2k chars. */
-
-      parser = zMapGFFCreateParser(NULL, parse_only) ;
-
-      while ((status = g_io_channel_read_line_string(gff_file, gff_line, &terminator_pos,
-						     &gff_file_err)) == G_IO_STATUS_NORMAL)
-	{
-
-	  *(gff_line->str + terminator_pos) = '\0' ;	    /* Remove terminating newline. */
-
-
-	  if (!zMapGFFParseLine(parser, gff_line->str))
-	    {
-	      GError *error = zMapGFFGetError(parser) ;
-
-	      if (!error)
-		{
-		  printf("WARNING: zMapGFFParseLine() failed with no GError for line %d: %s\n",
-			 zMapGFFGetLineNumber(parser), gff_line->str) ;
-		}
-	      else
-		printf("%s\n", (zMapGFFGetError(parser))->message) ;
-	    }
-	  
-	  
-	  gff_line = g_string_truncate(gff_line, 0) ;   /* Reset line to empty. */
-
-	}
-
-
-      /* Try getting the features. */
-      feature_context = g_new0(ZMapFeatureContextStruct, 1) ;
-      zmapGFFGetFeatures(parser, feature_context) ;	    /* we ignore success/failure of call... */
-
-      zMapGFFSetFreeOnDestroy(parser, free_arrays) ;
-      zMapGFFDestroyParser(parser) ;
-            
-      if (status == G_IO_STATUS_EOF)
-	{
-	  if (g_io_channel_shutdown(gff_file, FALSE, &gff_file_err) != G_IO_STATUS_NORMAL)
-	    {
-	      printf("Could not close gff file\n") ;
-	      exit(-1) ;
-	    }
-	}
-      else
-	{
-	  printf("Error reading lines from gff file\n") ;
-	  exit(-1) ;
-	}
-      
-    }
-
-  return feature_context ;
-}
-
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void testfunc(GQuark key_id, gpointer data, gpointer user_data)
-{
-  ZMapFeatureSet zMapFeatureSet = (ZMapFeatureSet)data;
-  ZMapFeature zMapFeature;
-  int i; 
-
-    printf("GFF_scaffold.c; call %s\n", (char*)user_data);
-
-  for (i=0; i<zMapFeatureSet->features->len; i++)
-    {
-      zMapFeature = &g_array_index(zMapFeatureSet->features, ZMapFeatureStruct, i);
-      printf("processing %s, x1 is %d, x2 is %d\n", zMapFeature->name, zMapFeature->x1, zMapFeature->x2);
-    }
-  return;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-