1.1 --- a/allpy/base.py	Sun Jun 10 15:20:37 2012 +0400
     1.2 +++ b/allpy/base.py	Sun Jun 10 16:08:47 2012 +0400
     1.3 @@ -29,9 +29,6 @@
     1.4      by_name = {}
     1.5      """A mapping from full monomer name to Monomer subclass."""
     1.6  
     1.7 -    sequence = None
     1.8 -    """A sequence the monomer belongs to."""
     1.9 -
    1.10      @classmethod
    1.11      def _subclass(cls, name='', code1='', code3='', is_modified=False):
    1.12          """Create new subclass of Monomer for given monomer type."""
    1.13 @@ -70,6 +67,32 @@
    1.14          for code1, is_modified, code3, name in codes:
    1.15              cls._subclass(name, code1, code3, is_modified)
    1.16  
    1.17 +    @classmethod
    1.18 +    def from_code1(cls, code1):
    1.19 +        """Create new monomer from 1-letter code."""
    1.20 +        deprecated(
    1.21 +            "Monomer.from_code1(...) is deprecated in favor of Sequence.append_monomer(code1=...)"
    1.22 +        )
    1.23 +        monomer = cls.by_code1[code1.upper()]()
    1.24 +        monomer.input_code1 = code1
    1.25 +        return monomer
    1.26 +
    1.27 +    @classmethod
    1.28 +    def from_code3(cls, code3):
    1.29 +        """Create new monomer from 3-letter code."""
    1.30 +        deprecated(
    1.31 +            "Monomer.from_code3(...) is deprecated in favor of Sequence.append_monomer(code3=...)"
    1.32 +        )
    1.33 +        return cls.by_code3[code3.upper()]()
    1.34 +
    1.35 +    @classmethod
    1.36 +    def from_name(cls, name):
    1.37 +        """Create new monomer from full name."""
    1.38 +        deprecated(
    1.39 +            "Monomer.from_name(...) is deprecated in favor of Sequence.append_monomer(name=...)"
    1.40 +        )
    1.41 +        return cls.by_name[name.strip().capitalize()]()
    1.42 +
    1.43      def __repr__(self):
    1.44          return "<Monomer %s>"  % str(self.code1)
    1.45  
    1.46 @@ -87,30 +110,6 @@
    1.47      def __ne__(self, other):
    1.48          return not (self == other)
    1.49  
    1.50 -    def __getstate__(self):
    1.51 -        """Overcome difficulties with pickle.
    1.52 -
    1.53 -        Pickle is unable to store `set`s/`dict`s that have objects referencing
    1.54 -        back the `set`/`dict` itself, which `sequence` in monomer does.
    1.55 -        ( http://bugs.python.org/issue9269 )
    1.56 -
    1.57 -        To sidestep the bug we store the monomer WITHOUT `sequence` attribute.
    1.58 -
    1.59 -        See also `Sequence.__setstate__`.
    1.60 -        """
    1.61 -        state = {}
    1.62 -        state.update(vars(self))
    1.63 -        if 'sequence' in state:
    1.64 -            del state['sequence']
    1.65 -        return state
    1.66 -
    1.67 -    def _obsolete_method(cls, *args, **kws):
    1.68 -        """OBSOLETE"""
    1.69 -        raise AttributeError("Call to obsolete method.")
    1.70 -    from_code1 = classmethod(_obsolete_method)
    1.71 -    from_code3 = classmethod(_obsolete_method)
    1.72 -    from_name = classmethod(_obsolete_method)
    1.73 -
    1.74  class MarkupContainerMixin(object):
    1.75      """Common functions for alignment and sequence for dealing with markups.
    1.76      """
    1.77 @@ -199,12 +198,19 @@
    1.78          elif name:
    1.79              cls = self.types.Monomer.by_name[name.strip().capitalize()]
    1.80          monomer = cls()
    1.81 -        monomer.sequence = self
    1.82          monomer.input_code1 = code1
    1.83          self.append(monomer)
    1.84          return monomer
    1.85  
    1.86      @classmethod
    1.87 +    def from_monomers(cls, monomers=[], name='', description='', source=''):
    1.88 +        """Create sequence from a list of monomer objecst."""
    1.89 +        deprecated(
    1.90 +            "Sequence.from_monomers(...) is deprecated in favor of Sequence(...)"
    1.91 +        )
    1.92 +        return cls(monomers, name, description, source)
    1.93 +
    1.94 +    @classmethod
    1.95      def from_string(cls, string, name='', description='', source=''):
    1.96          """Create sequences from string of one-letter codes."""
    1.97          self = cls([], name=name, description=description, source=source)
    1.98 @@ -226,26 +232,6 @@
    1.99          """Hash sequence by identity."""
   1.100          return id(self)
   1.101  
   1.102 -    def __setstate__(self, state):
   1.103 -        """Overcome difficulties with pickle: add `monomer.sequence` after loading.
   1.104 -
   1.105 -        Pickle is unable to store `set`s/`dict`s that have objects referencing
   1.106 -        back the `set`/`dict` itself, which `sequence` in monomer does.
   1.107 -        ( http://bugs.python.org/issue9269 )
   1.108 -
   1.109 -        To sidestep the bug we store the monomer WITHOUT `sequence` attribute.
   1.110 -
   1.111 -        See also `Monomer.__getstate__`.
   1.112 -        """
   1.113 -        vars(self).update(state)
   1.114 -        for monomer in self:
   1.115 -            monomer.sequence = self
   1.116 -
   1.117 -    @classmethod
   1.118 -    def from_monomers(cls, *args, **kws):
   1.119 -        """OBSOLETE."""
   1.120 -        raise AttributeError("Sequence.from_monomers is obsolete")
   1.121 -
   1.122  class Alignment(MarkupContainerMixin):
   1.123      """Alignment. It is a list of Columns."""
   1.124  

     2.1 --- a/test/test_pickle.py	Sun Jun 10 15:20:37 2012 +0400
     2.2 +++ b/test/test_pickle.py	Sun Jun 10 16:08:47 2012 +0400
     2.3 @@ -18,6 +18,5 @@
     2.4      s = pickle.load(file)
     2.5      assert s.name == 'sequence'
     2.6      assert str(s) == 'SEQVENCE'
     2.7 -    assert s[0].sequence is s
     2.8  
     2.9  # vim: set et ts=4 sts=4 sw=4: