1.1 --- a/allpy/base.py	Tue Feb 01 00:20:24 2011 +0300
     1.2 +++ b/allpy/base.py	Tue Feb 01 17:11:33 2011 +0300
     1.3 @@ -49,9 +49,8 @@
     1.4          """Create all relevant subclasses of Monomer."""
     1.5          # NB. The table uses letters d, r, p for types,
     1.6          # while we use full words; hence, we compare by first letter
     1.7 -        for type, code1, is_modified, code3, name in codes:
     1.8 -            if type[0] == cls.type[0]:
     1.9 -                cls._subclass(name, code1, code3, is_modified)
    1.10 +        for code1, is_modified, code3, name in codes:
    1.11 +            cls._subclass(name, code1, code3, is_modified)
    1.12  
    1.13      @classmethod
    1.14      def from_code1(cls, code1):
    1.15 @@ -107,7 +106,7 @@
    1.16      @classmethod
    1.17      def from_monomers(cls, monomers=[], name=None, description=None, source=None):
    1.18          """Create sequence from a list of monomer objecst."""
    1.19 -        result = cls()
    1.20 +        result = cls(monomers)
    1.21          if name:
    1.22              result.name = name
    1.23          if description:
    1.24 @@ -194,7 +193,7 @@
    1.25          """
    1.26          assert format == 'fasta', "We don't support other formats yet"
    1.27          for (name, description, body) in fasta.parse_file(file):
    1.28 -            self.append_row(body, name, description, file.name, gaps)
    1.29 +            self.append_row_from_string(body, name, description, file.name, gaps)
    1.30          return self
    1.31  
    1.32      def to_file(self, file, format='fasta'):
    1.33 @@ -314,7 +313,7 @@
    1.34      def _wipe(self):
    1.35          """Make all positions gaps (but keep sequences intact)."""
    1.36          for column in self.columns:
    1.37 -            for sequence in column:
    1.38 +            for sequence in list(column.keys()):
    1.39                  del column[sequence]
    1.40  
    1.41      def _merge(self, dst, new, merge):
    1.42 @@ -358,7 +357,7 @@
    1.43          """Replace alignment contents with those of other alignment."""
    1.44          if copy_contents:
    1.45              self._replace_sequence_contents(new, copy_descriptions)
    1.46 -        self._replace_column_conents(new)
    1.47 +        self._replace_column_contents(new)
    1.48  
    1.49      def process(self, function, copy_descriptions=True, copy_contents=True):
    1.50          """Apply function to the alignment (or block); inject results back.