1.1 --- a/allpy/base.py	Mon Feb 28 19:24:28 2011 +0300
     1.2 +++ b/allpy/base.py	Mon Feb 28 21:17:41 2011 +0300
     1.3 @@ -180,6 +180,15 @@
     1.4          self.sequences.append(sequence)
     1.5          return self
     1.6  
     1.7 +    def append_row_with_gaps(self, row, sequence):
     1.8 +        """Add row from row_as_list representation and sequence. Return self."""
     1.9 +        self.sequences.append(sequence)
    1.10 +        self._pad_to_width(len(row))
    1.11 +        for column, monomer in zip(self.columns, row):
    1.12 +            if monomer:
    1.13 +                column[sequence] = monomer
    1.14 +        return self
    1.15 +
    1.16      def _pad_to_width(self, n):
    1.17          """Pad alignment with empty columns on the right to width n."""
    1.18          for i in range(len(self.columns), n):
    1.19 @@ -285,35 +294,20 @@
    1.20      # Alignment / Block editing methods
    1.21      # =================================
    1.22  
    1.23 -    def _flush_row(self, row, whence='left'):
    1.24 -        """Helper for `flush`: flush to one side all monomers in one row."""
    1.25 -        row = filter(None, row)
    1.26 -        padding = [None] * len(self.columns)
    1.27 -        if whence == 'left':
    1.28 -            return row + padding
    1.29 -        if whence == 'right':
    1.30 -            return padding + row
    1.31 -        if whence == 'center':
    1.32 -            pad_len = (len(self.columns) - len(row)) // 2
    1.33 -            # vvv fix padding for case when length is odd: better have more
    1.34 -            pad_len += len(self.columns) - 2 * pad_len
    1.35 -            padding = [None] * pad_len
    1.36 -            return padding + row + padding
    1.37 -        assert True, "whence must be either 'left' or 'right' or 'center'"
    1.38 -
    1.39      def flush(self, whence='left'):
    1.40          """Remove all gaps from alignment and flush results to one side.
    1.41  
    1.42          `whence` must be one of 'left', 'right' or 'center'
    1.43          """
    1.44 -        for row in self.rows_as_lists():
    1.45 -            sequence = row.sequence
    1.46 -            row = self._flush_row(row, whence)
    1.47 -            for monomer, column in zip(row, self.columns):
    1.48 -                if monomer:
    1.49 -                    column[sequence] = monomer
    1.50 -                elif sequence in column:
    1.51 -                    del column[sequence]
    1.52 +        if whence == 'left':
    1.53 +            from processors import Left as Flush
    1.54 +        elif whence == 'right':
    1.55 +            from processors import Right as Flush
    1.56 +        elif whence == 'center':
    1.57 +            from processors import Center as Flush
    1.58 +        else:
    1.59 +            raise AssertionError, "Whence must be left, right or center"
    1.60 +        self.realign(Flush())
    1.61  
    1.62      def remove_gap_columns(self):
    1.63          """Remove all empty columns."""
    1.64 @@ -391,6 +385,17 @@
    1.65              copy_contents = function.copy_contents
    1.66          self._replace_contents(new, copy_descriptions, copy_contents)
    1.67  
    1.68 +    def realign(self, function):
    1.69 +        """Realign self.
    1.70 +
    1.71 +        I.e.: apply function to self to produce a new alignment, then update
    1.72 +        self to have the same gap patterns as the new alignment.
    1.73 +
    1.74 +        This is the same as process(function, False, False)
    1.75 +        """
    1.76 +        new = function(self)
    1.77 +        self._replace_column_contents(new)
    1.78 +
    1.79  class Column(dict):
    1.80      """Column of alignment.
    1.81