Changeset 8302 for trunk

Timestamp:

13/12/11 14:01:48 (6 months ago)

Author:

westram

Message:

• merges [8301] from stable and fixes conflicts with partly duplicate [6600]

Location:

trunk

Files:

• NTREE/ad_transpro.cxx (modified) (6 diffs)
• SL/PRONUC/AP_codon_table.hxx (modified) (1 diff)
• SL/TRANSLATE/Translate.cxx (modified) (1 diff)
• SL/TRANSLATE/Translate.hxx (modified) (1 diff)

trunk/NTREE/ad_transpro.cxx

@@ -338 +338 @@
 // 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) {
     AP_initialize_codon_tables();
 
     GBDATA *gb_source = GBT_get_alignment(gb_main, ali_source); if (!gb_source) return "Please select a valid source alignment";
-    GBDATA *gb_dest   = GBT_get_alignment(gb_main, ali_dest);  if (!gb_dest)   return "Please select a valid destination alignment";
+    GBDATA *gb_dest   = GBT_get_alignment(gb_main, ali_dest);   if (!gb_dest)   return "Please select a valid destination alignment";
 
     long     ali_len            = GBT_get_alignment_len(gb_main, ali_dest);
@@ -349 +348 @@
     GB_ERROR error              = 0;
 
-    arb_progress progress("Re-aligner", GBT_count_marked_species(gb_main));
+    long no_of_marked_species    = GBT_count_marked_species(gb_main);
+    long no_of_realigned_species = 0;
+
+    arb_progress progress("Re-aligner", no_of_marked_species);
     progress.auto_subtitles("Re-aligning species");
 
@@ -637 +639 @@
             // re-alignment successful
             error = GB_write_string(gb_dest_data, buffer);
+
             if (!error) {
-                int writeTableNr = -1;
-                if (allowed_code.strictly_defined(writeTableNr)) {
-                    error = AWT_saveTranslationInfo(gb_species, writeTableNr, 1); // after re-alignment codon_start is always 1
+                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);
                 }
             }
@@ -651 +659 @@
 
         progress.inc_and_check_user_abort(error);
-    }
-
-    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);
+        no_of_realigned_species++;
+    }
+
+    *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;
@@ -682 +692 @@
         error = GB_end_transaction(GLOBAL_gb_main, error);
 
-        if (neededLength > 0) {
+        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);
@@ -695 +705 @@
                                                  "running re-aligner again!",
                                                  ali_dest, neededLength));
-                    retrying = true;
+                    retrying     = true;
+                    neededLength = -1;
                 }
             }

trunk/SL/PRONUC/AP_codon_table.hxx

@@ -72 +72 @@
     }
 
-    bool strictly_defined(int& nr) {
-        nr = -1;
-        for (int table = 0; table<AWT_CODON_TABLES; ++table) {
-            if (is_allowed(table)) {
-                if (nr != -1) return false;
-                nr = table;
+    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 true;
+        return table;
     }
 };

trunk/SL/TRANSLATE/Translate.cxx

@@ -26 +26 @@
     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;

trunk/SL/TRANSLATE/Translate.hxx

@@ -20 +20 @@
 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);