1.1 --- a/allpy/base.py	Wed Jan 26 22:25:13 2011 +0300
     1.2 +++ b/allpy/base.py	Mon Jan 31 18:44:23 2011 +0300
     1.3 @@ -317,36 +317,33 @@
     1.4              for sequence in column:
     1.5                  del column[sequence]
     1.6  
     1.7 -    def _append_row_from_list(self, new):
     1.8 -        sequence = new.sequence
     1.9 -        self.sequences.append(sequence)
    1.10 -        for i, monomer in enumerate(new):
    1.11 -            if monomer:
    1.12 -                self._column_at(i)[sequence] = monomer
    1.13 +    def _merge(self, dst, new, merge):
    1.14 +        """Replace contents of dst with those of new.
    1.15 +
    1.16 +        Replace contents of elements using function `merge(dst_el, new_le)`.
    1.17 +        """
    1.18 +        for el, new_el in zip(dst, new):
    1.19 +            merge(el, new_el)
    1.20 +        dst[len(dst):] = new[len(dst):]
    1.21 +        del dst[len(new):]
    1.22  
    1.23      def _replace_sequence_contents(self, new):
    1.24          """Replace contents of sequences with those of new alignment."""
    1.25          # XXX: we manually copy sequence contents here
    1.26 -        # XXX: we do not copy all sequence contents, only overlapping parts
    1.27 -        # XXX: if sequence shortens, we leave some monomers unmodified (!!!)
    1.28 -        for sequence, new_sequence in zip(self.sequences, new.sequences):
    1.29 -            sequence.name = new_sequence.name
    1.30 -            sequence.description = new_sequence.desription
    1.31 -            sequence.source = new_sequence.source
    1.32 -            for monomer, new_monomer in zip(sequence, new_sequence):
    1.33 -                monomer.__class__ = new_monomer.__class__
    1.34 -            for i in range(len(sequence), len(new_sequence)):
    1.35 -                sequence.append(new_sequence[i])
    1.36 -        for i in range(len(self.sequences), len(new.sequences)):
    1.37 -            self._append_row_from_list(new.rows_as_lists()[i])
    1.38 +        # XXX: we only copy, overlapping parts and link to the rest
    1.39 +        def merge_monomers(dst, new):
    1.40 +            dst.__class__ = new.__class__
    1.41 +        def merge_sequences(dst, new):
    1.42 +            vars(dst).update(vars(new))
    1.43 +            self._merge(dst, new, merge_monomers)
    1.44 +        self._merge(self.sequences, new.sequences, merge_sequences)
    1.45  
    1.46      def _replace_column_contents(self, new):
    1.47          """Replace column contents with those of new alignment.
    1.48  
    1.49 -        This requires that self.sequences and new.sequences have same length
    1.50 -        and same contents. (If sequences have same length but different
    1.51 -        contents, this effectively copies gap patterns. If sequences have
    1.52 -        different length, the results are meaningless and dumb).
    1.53 +        Synonym: copy gap patterns from new to self.
    1.54 +
    1.55 +        self.sequences and new.sequences should have the same contents.
    1.56          """
    1.57          self._wipe()
    1.58          not_gap = lambda (a,b): a != None
    1.59 @@ -367,7 +364,7 @@
    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 +        self._replace_contents(new)
    1.65  
    1.66  class Column(dict):
    1.67      """Column of alignment.