Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and Missi…

…ngTable classes which are all dead code after the removal of the Bio.SeqUtils.translate function

Bio/SeqUtils/__init__.py

@@ -221,13 +221,18 @@ def nt_search(seq, subseq):
 # should be moved to ???
 
 class ProteinX(Alphabet.ProteinAlphabet):
+    """Variant of the extended IUPAC extended protein alphabet (DEPRECATED)."""
     letters = IUPACData.extended_protein_letters + "X"
 
+#Can't add a deprecation warning to the class due to the following line:
 proteinX = ProteinX()
 
 class MissingTable:
     def __init__(self, table):
         self._table = table
+        import warnings
+        warnings.warn("Function Bio.SeqUtils.makeTableX() and related classes ProteinX "
+                      "and MissingTable are deprecated.", DeprecationWarning)
     def get(self, codon, stop_symbol):
         try:
             return self._table.get(codon, stop_symbol)

DEPRECATED

@@ -309,6 +309,10 @@ in Release 1.31, and removed in Release 1.43.  Function 'translate' was
 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
 and methods in Bio.Seq instead.
 
+Function makeTableX and classes ProteinX and MissingTable were deprecated
+in Release 1.54. These were remnants of the removed translate function,
+and no longer served any useful purpose.
+
 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, instead
 just use the string's slice method with a step of minus one.