1.1 --- a/allpy/base.py	Wed Jan 26 21:03:23 2011 +0300
     1.2 +++ b/allpy/base.py	Wed Jan 26 21:17:01 2011 +0300
     1.3 @@ -272,6 +272,39 @@
     1.4              columns.append(col)
     1.5          return columns
     1.6  
     1.7 +    # Alignment / Block editing methods
     1.8 +    # =================================
     1.9 +
    1.10 +    def _flush_row(self, row, whence='left'):
    1.11 +        """Helper for `flush`: flush to one side all monomers in one row."""
    1.12 +        row = filter(None, row)
    1.13 +        padding = [None] * len(self.columns)
    1.14 +        if whence == 'left':
    1.15 +            return row + padding
    1.16 +        if whence == 'right':
    1.17 +            return padding + row
    1.18 +        if whence == 'center':
    1.19 +            pad_len = (len(self.columns) - len(row)) // 2
    1.20 +            # vvv fix padding for case when length is odd: better have more
    1.21 +            pad_len += len(self.columns) - 2 * pad_len
    1.22 +            padding = [None] * pad_len
    1.23 +            return padding + row + padding
    1.24 +        assert True, "whence must be either 'left' or 'right' or 'center'"
    1.25 +
    1.26 +    def flush(self, whence='left'):
    1.27 +        """Remove all gaps from alignment and flush results to one side.
    1.28 +
    1.29 +        `whence` must be one of 'left', 'right' or 'center'
    1.30 +        """
    1.31 +        for row in self.rows_as_lists():
    1.32 +            sequence = row.sequence
    1.33 +            row = self._flush_row(row, whence)
    1.34 +            for monomer, column in zip(row, self.columns):
    1.35 +                if monomer:
    1.36 +                    column[sequence] = monomer
    1.37 +                elif sequence in column:
    1.38 +                    del column[sequence]
    1.39 +
    1.40  class Column(dict):
    1.41      """Column of alignment.
    1.42  
    1.43 @@ -323,17 +356,4 @@
    1.44          block.columns = columns
    1.45          return block
    1.46  
    1.47 -    def flush_left(self):
    1.48 -        """Move all monomers to the left, gaps to the right within block."""
    1.49 -        padding = [None] * len(self.columns)
    1.50 -        for row in self.rows_as_lists():
    1.51 -            sequence = row.sequence
    1.52 -            row = filter(None, row) + padding
    1.53 -            for monomer, column in zip(row, self.columns):
    1.54 -                if monomer:
    1.55 -                    column[sequence] = monomer
    1.56 -                elif sequence in column:
    1.57 -                    del column[sequence]
    1.58 -
    1.59 -
    1.60  # vim: set ts=4 sts=4 sw=4 et: