Changeset 8301

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

Files:

• AWT/AWT_translate.cxx (modified) (1 diff)
• AWT/awt_codon_table.hxx (modified) (1 diff)
• AWT/awt_translate.hxx (modified) (1 diff)
• NTREE/ad_transpro.cxx (modified) (6 diffs)

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);

branches/stable_5.0/NTREE/ad_transpro.cxx

@@ -341 +341 @@
 // before deciding "X was realigned correctly"
 
-GB_ERROR arb_transdna(GBDATA *gb_main, char *ali_source, char *ali_dest, long *neededLength)
-{
+static GB_ERROR arb_transdna(GBDATA *gb_main, char *ali_source, char *ali_dest, long *neededLength) {
     AWT_initialize_codon_tables();
 
@@ -353 +352 @@
 
     aw_openstatus("Re-aligner");
-    
+
     int no_of_marked_species    = GBT_count_marked_species(gb_main);
     int no_of_realigned_species = 0;
@@ -642 +641 @@
 
             // re-alignment successful
-            error             = GB_write_string(gb_dest_data, buffer);
-            if (!error) error = GBT_write_string(gb_species, "codon_start", "1"); // after re-alignment codon_start is always 1
+            error = GB_write_string(gb_dest_data, buffer);
+
+            if (!error) {
+                int explicit_table_known = allowed_code.explicit_table();
+
+                if (explicit_table_known >= 0) { // we know the exact code -> write codon_start and transl_table
+                    const int codon_start  = 1; // by definition (after realignment)
+                    error = AWT_saveTranslationInfo(gb_species, explicit_table_known, codon_start);
+                }
+                else { // we dont know the exact code -> delete codon_start and transl_table
+                    error = AWT_removeTranslationInfo(gb_species);
+                }
+            }
         }
 
@@ -656 +666 @@
     aw_closestatus();
 
-    if (max_wanted_ali_len>0) {
-        if (neededLength) *neededLength = max_wanted_ali_len;
-    }
-
-    if (error) {
-        return error;
-    }
-
-    error = GBT_check_data(gb_main,ali_dest);
-
+    *neededLength = max_wanted_ali_len;
+
+    if (!error) {
+        int not_realigned = no_of_marked_species - no_of_realigned_species;
+        if (not_realigned>0) {
+            aw_message(GBS_global_string("Did not try to realign %i species (source/dest alignment missing?)", not_realigned));
+        }
+    }
+
+    if (!error) error = GBT_check_data(gb_main,ali_dest);
     return error;
 }
@@ -685 +695 @@
         error = GB_end_transaction(GLOBAL_gb_main, error);
 
-        if (neededLength) {
+        if (!error && neededLength>0) {
             if (retrying || !aw_ask_sure(GBS_global_string("Increase length of '%s' to %li?", ali_dest, neededLength))) {
                 error = GBS_global_string("Missing %li columns in alignment '%s'", neededLength, ali_dest);
@@ -698 +708 @@
                                                  "running re-aligner again!",
                                                  ali_dest, neededLength));
-                    retrying = true;
+                    retrying     = true;
+                    neededLength = -1;
                 }
             }