[gt-users] gff3 parser

[Gordon Gremme]

> i'm doing something wrong with the make_unique_id function because
> when it's called it does turn 'name' into 'name.1'
> but it prints out ascii characters as well.
> any feedback on that and in general?

The make_id_unique() procedure is flawed, see below:

+static void make_unique_id_string(GtStr *current_id, unsigned long counter)
+{
+    /* name => name.1 */
+    gt_str_append_char(current_id, '.');
+    gt_str_append_ulong(current_id, counter);
+}
+
+static void make_id_unique(GtGFF3Visitor *gff3_visitor, GtStr *id)
+{
+
+  GtCstrTable *used_ids = gff3_visitor->gt_used_ids;
+  unsigned long i = 0;
+  const char *id_string = gt_str_get(id);

id_string now contains a _pointer_ to the internal memory of the GtStr id.


+  while ( gt_cstr_table_get(used_ids, gt_str_get(id) )) {
+    /* TODO: add warning */
+    make_unique_id_string(id, ++i);

This call modifies id which means the iternal memory might be resized
and therefore might be moved around in memory.
Therefore, id_string has to be considered invalid at this point.

+    gt_str_set(id, id_string);

Now you reset id to the content of id_string (which might be invalid).
What are you trying to do here?
If you want to reset id for the next iteration, you have to do it
differently, because now you would get into an infinite loop (you
haven't called gt_cstr_table_get() with the modified id yet).

+  }
+  /* update table with the new id */
+  gt_cstr_table_add(used_ids, gt_str_get(id));
+
+}
+

Hope that helps,

Gordon