1.1 --- a/allpy/base.py	Sat Jul 02 15:29:06 2011 +0400
     1.2 +++ b/allpy/base.py	Sat Jul 02 15:42:49 2011 +0400
     1.3 @@ -117,6 +117,10 @@
     1.4      description = ''
     1.5      source = ''
     1.6  
     1.7 +    def __init__(self, *args):
     1.8 +        self.markups = {}
     1.9 +        list.__init__(self, *args)
    1.10 +
    1.11      @classmethod
    1.12      def from_monomers(cls, monomers=[], name=None, description=None, source=None):
    1.13          """Create sequence from a list of monomer objecst."""
    1.14 @@ -164,6 +168,7 @@
    1.15          """Initialize empty alignment."""
    1.16          self.sequences = []
    1.17          self.columns = []
    1.18 +        self.markups = {}
    1.19  
    1.20      # Alignment grow & IO methods
    1.21      # ==============================
    1.22 @@ -496,9 +501,9 @@
    1.23          if name:
    1.24              self.name = name
    1.25          assert self.name is not None
    1.26 -        assert name not in sequence.markups
    1.27 +        assert self.name not in sequence.markups
    1.28          self.sequence = sequence
    1.29 -        sequence.markups[name] = self
    1.30 +        sequence.markups[self.name] = self
    1.31          self.refresh()
    1.32  
    1.33      def refresh(self):
    1.34 @@ -521,10 +526,10 @@
    1.35      def __init__(self, alignment, name=None):
    1.36          if name:
    1.37              self.name = name
    1.38 -        assert name is not None
    1.39 -        assert name not in alignment.markups
    1.40 +        assert self.name is not None
    1.41 +        assert self.name not in alignment.markups
    1.42          self.alignment = alignment
    1.43 -        alignment.markups[name] = self
    1.44 +        alignment.markups[self.name] = self
    1.45          self.refresh()
    1.46  
    1.47      def refresh(self):