1.1 --- a/allpy/base.py	Fri Jan 21 15:28:00 2011 +0300
     1.2 +++ b/allpy/base.py	Fri Jan 21 15:28:26 2011 +0300
     1.3 @@ -2,7 +2,6 @@
     1.4  
     1.5  import util
     1.6  import fasta
     1.7 -import data.codes
     1.8  
     1.9  default_gaps = set((".", "-", "~"))
    1.10  """Set of characters to recoginze as gaps when parsing alignment."""
    1.11 @@ -45,7 +44,7 @@
    1.12          Monomer.by_name[name] = TheMonomer
    1.13  
    1.14      @classmethod
    1.15 -    def _initialize(cls, codes=data.codes.codes):
    1.16 +    def _initialize(cls, codes=None):
    1.17          """Create all relevant subclasses of Monomer."""
    1.18          # NB. The table uses letters d, r, p for types,
    1.19          # while we use full words; hence, we compare by first letter