1.1 --- a/allpy/base.py	Wed Jan 26 21:34:36 2011 +0300
     1.2 +++ b/allpy/base.py	Wed Jan 26 22:25:13 2011 +0300
     1.3 @@ -311,6 +311,64 @@
     1.4              if column == {}:
     1.5                  self.columns[n:n+1] = []
     1.6  
     1.7 +    def _wipe(self):
     1.8 +        """Make all positions gaps (but keep sequences intact)."""
     1.9 +        for column in self.columns:
    1.10 +            for sequence in column:
    1.11 +                del column[sequence]
    1.12 +
    1.13 +    def _append_row_from_list(self, new):
    1.14 +        sequence = new.sequence
    1.15 +        self.sequences.append(sequence)
    1.16 +        for i, monomer in enumerate(new):
    1.17 +            if monomer:
    1.18 +                self._column_at(i)[sequence] = monomer
    1.19 +
    1.20 +    def _replace_sequence_contents(self, new):
    1.21 +        """Replace contents of sequences with those of new alignment."""
    1.22 +        # XXX: we manually copy sequence contents here
    1.23 +        # XXX: we do not copy all sequence contents, only overlapping parts
    1.24 +        # XXX: if sequence shortens, we leave some monomers unmodified (!!!)
    1.25 +        for sequence, new_sequence in zip(self.sequences, new.sequences):
    1.26 +            sequence.name = new_sequence.name
    1.27 +            sequence.description = new_sequence.desription
    1.28 +            sequence.source = new_sequence.source
    1.29 +            for monomer, new_monomer in zip(sequence, new_sequence):
    1.30 +                monomer.__class__ = new_monomer.__class__
    1.31 +            for i in range(len(sequence), len(new_sequence)):
    1.32 +                sequence.append(new_sequence[i])
    1.33 +        for i in range(len(self.sequences), len(new.sequences)):
    1.34 +            self._append_row_from_list(new.rows_as_lists()[i])
    1.35 +
    1.36 +    def _replace_column_contents(self, new):
    1.37 +        """Replace column contents with those of new alignment.
    1.38 +
    1.39 +        This requires that self.sequences and new.sequences have same length
    1.40 +        and same contents. (If sequences have same length but different
    1.41 +        contents, this effectively copies gap patterns. If sequences have
    1.42 +        different length, the results are meaningless and dumb).
    1.43 +        """
    1.44 +        self._wipe()
    1.45 +        not_gap = lambda (a,b): a != None
    1.46 +        for sequence, new_row in zip(self.sequences, new.rows_as_lists()):
    1.47 +            assert len(sequence) == len(new_row.sequence)
    1.48 +            zipped = zip(sequence, filter(not_gap, enumerate(new_row)))
    1.49 +            for monomer, (i, _) in zipped:
    1.50 +                self._column_at(i)[sequence] = monomer
    1.51 +
    1.52 +    def _replace_contents(self, new):
    1.53 +        """Replace alignment contents with those of other alignment."""
    1.54 +        self._replace_sequence_contents(new)
    1.55 +        self._replace_column_conents(new)
    1.56 +
    1.57 +    def process(self, function):
    1.58 +        """Apply function to the alignment (or block); inject results back.
    1.59 +
    1.60 +        function(block) must return block with same line order.
    1.61 +        """
    1.62 +        new = function(self)
    1.63 +        self.replace_contents(new)
    1.64 +
    1.65  class Column(dict):
    1.66      """Column of alignment.
    1.67