Changeset 8301 for branches/stable_5.0/AWT

Timestamp:

13/12/11 13:30:13 (6 months ago)

Author:

westram

Message:

• fixed some realigner bugs
  • when species did not contain transl_table and codon_start, the realigner inserted only codon_start.
    • the next realignment/translation failed since it expected BOTH or NONE of the two fields.
    • now the realigner
      • either writes both fields (if used transl_table is well-defined)
      • deletes both fields
  • when some/all species did not contain data in source and/or destination alignment, the realigner silently skipped them
    • now prints a message about skipped species
  • errors during realignment (e.g. protection errors) were not shown

Note: grml .. similar patch was already in trunk as [6600]

Location:

branches/stable_5.0/AWT

Files:

• AWT_translate.cxx (modified) (1 diff)
• awt_codon_table.hxx (modified) (1 diff)
• awt_translate.hxx (modified) (1 diff)

branches/stable_5.0/AWT/AWT_translate.cxx

@@ -28 +28 @@
     GB_ERROR error    = GBT_write_string(gb_species, "transl_table", GBS_global_string("%i", embl_transl_table));
     if (!error) error = GBT_write_string(gb_species, "codon_start",  GBS_global_string("%i", codon_start+1));
+
+    return error;
+}
+
+GB_ERROR AWT_removeTranslationInfo(GBDATA *gb_species) {
+    GB_ERROR error = NULL;
+
+    GBDATA *gb_transl_table    = GB_entry(gb_species, "transl_table");
+    if (gb_transl_table) error = GB_delete(gb_transl_table);
+
+    if (!error) {
+        GBDATA *gb_codon_start    = GB_entry(gb_species, "codon_start");
+        if (gb_codon_start) error = GB_delete(gb_codon_start);
+    }
 
     return error;

branches/stable_5.0/AWT/awt_codon_table.hxx

@@ -71 +71 @@
         }
     }
+
+    int explicit_table() const {
+        // return explicit table number (or -1 if not exactly 1 table is allowed)
+        int table = -1;
+        for (int i = 0; i<AWT_CODON_TABLES; ++i) {
+            if (allowed[i]) {
+                if (table != -1) return -1;
+                table = i;
+            }
+        }
+        return table;
+    }
 };
 

branches/stable_5.0/AWT/awt_translate.hxx

@@ -14 +14 @@
 GB_ERROR AWT_getTranslationInfo(GBDATA *gb_species, int& arb_transl_table, int &codon_start);
 GB_ERROR AWT_saveTranslationInfo(GBDATA *gb_species, int arb_transl_table, int codon_start);
+GB_ERROR AWT_removeTranslationInfo(GBDATA *gb_species);
 
 int AWT_pro_a_nucs_convert(int arb_code_nr, char *data, size_t size, size_t pos, bool translate_all, bool create_start_codon, bool append_stop_codon, int *translatedSize);