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  

     2.1 --- a/allpy/processors.py	Mon Feb 28 19:24:28 2011 +0300
     2.2 +++ b/allpy/processors.py	Mon Feb 28 21:17:41 2011 +0300
     2.3 @@ -67,4 +67,31 @@
     2.4          new_block = ExternalCommand.__call__(self, block)
     2.5          return fix_ordering(block, fix_missing(block, new_block))
     2.6  
     2.7 +class Flush(object):
     2.8 +    """Flush all non-gap monomers to one side."""
     2.9 +    def __call__(self, alignment):
    2.10 +        result = alignment.types.Alignment()
    2.11 +        for row in alignment.rows_as_lists():
    2.12 +            sequence = row.sequence
    2.13 +            no_gaps = filter(None, row)
    2.14 +            llen, rlen = self._padding_sizes(len(row) - len(no_gaps))
    2.15 +            row = [None] * llen + no_gaps + [None] * rlen
    2.16 +            result.append_row_with_gaps(row, sequence)
    2.17 +        return result
    2.18 +
    2.19 +class Left(Flush):
    2.20 +    """Flush all non-gap monomers to the left."""
    2.21 +    def _padding_sizes(self, n_gaps):
    2.22 +        return 0, n_gaps
    2.23 +
    2.24 +class Right(Flush):
    2.25 +    """Flush all non-gap monomers to the right."""
    2.26 +    def _padding_sizes(self, n_gaps):
    2.27 +        return n_gaps, 0
    2.28 +
    2.29 +class Center(Flush):
    2.30 +    """Center all non-gap monomers in alignment."""
    2.31 +    def _padding_sizes(self, n_gaps):
    2.32 +        return n_gaps // 2, (n_gaps + 1) // 2
    2.33 +
    2.34  # vim: set et ts=4 sts=4 sw=4:

     3.1 --- a/test/test_base.py	Mon Feb 28 19:24:28 2011 +0300
     3.2 +++ b/test/test_base.py	Mon Feb 28 21:17:41 2011 +0300
     3.3 @@ -1,5 +1,6 @@
     3.4  import allpy.base as b
     3.5  import allpy.protein as p
     3.6 +from allpy import processors
     3.7  from StringIO import StringIO
     3.8  
     3.9  def test_new_monomers():
    3.10 @@ -42,21 +43,21 @@
    3.11          "-------------RST",
    3.12      )
    3.13  
    3.14 -    a.flush("left")
    3.15 +    a.process(processors.Left())
    3.16      assert_alignment(a,
    3.17          "ACDEF-----------",
    3.18          "GHIKLMPQ--------",
    3.19          "RST-------------",
    3.20      )
    3.21  
    3.22 -    a.flush("center")
    3.23 +    a.process(processors.Center())
    3.24      assert_alignment(a,
    3.25          "-----ACDEF------",
    3.26          "----GHIKLMPQ----",
    3.27          "------RST-------",
    3.28      )
    3.29  
    3.30 -    a.flush("right")
    3.31 +    a.process(processors.Right())
    3.32      assert_alignment(a,
    3.33          "-----------ACDEF",
    3.34          "--------GHIKLMPQ",