Only create one shared version of each ambiguous table, rather than o…

…ne copy for each different name of the table

Bio/Data/CodonTable.py

@@ -673,56 +673,47 @@ def _sort(x, y, table = self.ambiguous_protein):
         self._cache[codon] = x
         return x
 
-
+#Prepare the ambiguous tables for DNA, RNA and Generic (DNA or RNA)
 ambiguous_dna_by_name = {}
-for key, val in unambiguous_dna_by_name.items():
-    ambiguous_dna_by_name[key] = AmbiguousCodonTable(val,
-                                     IUPAC.ambiguous_dna,
-                                     IUPACData.ambiguous_dna_values,
-                                     IUPAC.extended_protein,
-                                     IUPACData.extended_protein_values)
 ambiguous_dna_by_id = {}
 for key, val in unambiguous_dna_by_id.items():
     ambiguous_dna_by_id[key] = AmbiguousCodonTable(val,
                                      IUPAC.ambiguous_dna,
                                      IUPACData.ambiguous_dna_values,
                                      IUPAC.extended_protein,
                                      IUPACData.extended_protein_values)
+    for name in unambiguous_dna_by_name:
+        ambiguous_dna_by_name[name] = ambiguous_dna_by_id[key]
 
 ambiguous_rna_by_name = {}
-for key, val in unambiguous_rna_by_name.items():
-    ambiguous_rna_by_name[key] = AmbiguousCodonTable(val,
-                                     IUPAC.ambiguous_rna,
-                                     IUPACData.ambiguous_rna_values,
-                                     IUPAC.extended_protein,
-                                     IUPACData.extended_protein_values)
 ambiguous_rna_by_id = {}
 for key, val in unambiguous_rna_by_id.items():
     ambiguous_rna_by_id[key] = AmbiguousCodonTable(val,
                                      IUPAC.ambiguous_rna,
                                      IUPACData.ambiguous_rna_values,
                                      IUPAC.extended_protein,
                                      IUPACData.extended_protein_values)
+    for name in unambiguous_rna_by_name:
+        ambiguous_rna_by_name[name] = ambiguous_rna_by_id[key]
 
 #The following isn't very elegant, but seems to work nicely.
 _merged_values = dict(IUPACData.ambiguous_rna_values.iteritems())
 _merged_values["T"] = "U"
 
-for key, val in generic_by_name.items():
-    ambiguous_generic_by_name[key] = AmbiguousCodonTable(val,
-                                     Alphabet.NucleotideAlphabet(),
-                                     _merged_values,
-                                     IUPAC.extended_protein,
-                                     IUPACData.extended_protein_values)
-
 for key, val in generic_by_id.items():
     ambiguous_generic_by_id[key] = AmbiguousCodonTable(val,
                                      Alphabet.NucleotideAlphabet(),
                                      _merged_values,
                                      IUPAC.extended_protein,
                                      IUPACData.extended_protein_values)
+    for name in generic_by_name:
+        ambiguous_generic_by_name[name] = ambiguous_generic_by_id[key]
+
+#Basic sanity tests,
+assert len(ambiguous_dna_by_name.keys()) == len(unambiguous_dna_by_name.keys())
+assert len(ambiguous_rna_by_name.keys()) == len(unambiguous_rna_by_name.keys())
+assert len(ambiguous_generic_by_name.keys()) == len(generic_by_name.keys())
 
-#Basic sanity test,
 for id in ambiguous_generic_by_id.keys() :
     assert ambiguous_rna_by_id[id].forward_table["GUU"] == "V"
     assert ambiguous_rna_by_id[id].forward_table["GUN"] == "V"