1.1 --- a/allpy/base.py	Wed Feb 02 16:42:23 2011 +0300
     1.2 +++ b/allpy/base.py	Wed Feb 02 21:28:55 2011 +0300
     1.3 @@ -158,34 +158,31 @@
     1.4          If sequence is too short, pad it with gaps on the right.
     1.5          """
     1.6          self.sequences.append(sequence)
     1.7 -        for i, monomer in enumerate(sequence):
     1.8 -            self._column_at(i)[sequence] = monomer
     1.9 +        self._pad_to_width(len(sequence))
    1.10 +        for column, monomer in zip(self.columns, sequence):
    1.11 +            column[sequence] = monomer
    1.12          return self
    1.13  
    1.14      def append_row_from_string(self, string,
    1.15              name='', description='', source='', gaps=default_gaps):
    1.16          """Add row from a string of one-letter codes and gaps. Return self."""
    1.17          Sequence = self.types.Sequence
    1.18 -        not_gap = lambda (i, char): char not in gaps
    1.19          without_gaps = util.remove_each(string, gaps)
    1.20          sequence = Sequence.from_string(without_gaps, name, description, source)
    1.21 -        # The following line has some simple magic:
    1.22 -        # 1. attach natural numbers to monomers
    1.23 -        # 2. delete gaps
    1.24 -        # 3. attach numbers again
    1.25 -        # This way we have a pair of numbers attached to monomer:
    1.26 -        # - it's position in alignment (the first attached number, j)
    1.27 -        # - it's position in sequence (the second attached number, i)
    1.28 -        for i, (j, char) in enumerate(filter(not_gap, enumerate(string))):
    1.29 -            self._column_at(j)[sequence] = sequence[i]
    1.30 +        self._pad_to_width(len(string))
    1.31 +        non_gap_columns = [column
    1.32 +            for column, char in zip(self.coumns, string)
    1.33 +            if char not in gaps
    1.34 +        ]
    1.35 +        for monomer, column in zip(sequence, non_gap_columns):
    1.36 +            column[sequence] = monomer
    1.37          self.sequences.append(sequence)
    1.38          return self
    1.39  
    1.40 -    def _column_at(self, n):
    1.41 -        """Return column by index. Create new columns if required."""
    1.42 -        for i in range(len(self.columns), n + 1):
    1.43 +    def _pad_to_width(self, n):
    1.44 +        """Pad alignment with empty columns on the right to width n."""
    1.45 +        for i in range(len(self.columns), n):
    1.46              self.columns.append(Column())
    1.47 -        return self.columns[n]
    1.48  
    1.49      def append_file(self, file, format='fasta', gaps=default_gaps):
    1.50          """Append sequences from file to alignment. Return self.
    1.51 @@ -351,9 +348,12 @@
    1.52          not_gap = lambda (a,b): a != None
    1.53          for sequence, new_row in zip(self.sequences, new.rows_as_lists()):
    1.54              assert len(sequence) == len(new_row.sequence)
    1.55 -            zipped = zip(sequence, filter(not_gap, enumerate(new_row)))
    1.56 -            for monomer, (i, _) in zipped:
    1.57 -                self._column_at(i)[sequence] = monomer
    1.58 +            non_gap_columns = [column
    1.59 +                for column, monomer in zip(self.columns, new_row)
    1.60 +                if monomer
    1.61 +            ]
    1.62 +            for monomer, column in zip(sequence, non_gap_columns):
    1.63 +                column[sequence] = monomer
    1.64  
    1.65      def _replace_contents(self, new, copy_descriptions, copy_contents):
    1.66          """Replace alignment contents with those of other alignment."""