1.1 --- a/allpy/base.py	Wed May 30 13:38:41 2012 +0400
     1.2 +++ b/allpy/base.py	Wed May 30 13:38:27 2012 +0400
     1.3 @@ -415,28 +415,6 @@
     1.4              if sequence in column:
     1.5                  del column[sequence]
     1.6  
     1.7 -    def _merge(self, dst, new, merge):
     1.8 -        """Replace contents of `dst` with those of `new`.
     1.9 -
    1.10 -        Replace contents of elements using function `merge(dst_el, new_le)`.
    1.11 -        """
    1.12 -        for el, new_el in zip(dst, new):
    1.13 -            merge(el, new_el)
    1.14 -        dst[len(dst):] = new[len(dst):]
    1.15 -        del dst[len(new):]
    1.16 -
    1.17 -    def _replace_sequence_contents(self, new, copy_descriptions):
    1.18 -        """Replace contents of sequences with those of `new` alignment."""
    1.19 -        # XXX: we manually copy sequence contents here
    1.20 -        # XXX: we only copy, overlapping parts and link to the rest
    1.21 -        def merge_monomers(dst, new):
    1.22 -            dst.__class__ = new.__class__
    1.23 -        def merge_sequences(dst, new):
    1.24 -            if copy_descriptions:
    1.25 -                vars(dst).update(vars(new))
    1.26 -            self._merge(dst, new, merge_monomers)
    1.27 -        self._merge(self.sequences, new.sequences, merge_sequences)
    1.28 -
    1.29      def _replace_column_contents(self, new):
    1.30          """Replace column contents with those of `new` alignment.
    1.31  
    1.32 @@ -458,41 +436,11 @@
    1.33              for monomer, column in zip(monomers, non_gap_columns):
    1.34                  column[sequence] = monomer
    1.35  
    1.36 -    def _replace_contents(self, new, copy_descriptions, copy_contents):
    1.37 -        """Replace alignment contents with those of other alignment."""
    1.38 -        if copy_contents:
    1.39 -            self._replace_sequence_contents(new, copy_descriptions)
    1.40 -        self._replace_column_contents(new)
    1.41 -
    1.42 -    def process(self, function, copy_descriptions=True, copy_contents=True):
    1.43 -        """Apply function to the alignment (or block); inject results back.
    1.44 -
    1.45 -        - `function(block)` must return block with same line order.
    1.46 -        - if `copy_descriptions` is False, ignore new sequence names.
    1.47 -        - if `copy_contents` is False, don't copy sequence contents too.
    1.48 -
    1.49 -        `function` (object) may have attributes `copy_descriptions` and
    1.50 -        `copy_contents`, which override the same named arguments.
    1.51 -        """
    1.52 -        deprecated(
    1.53 -            "aln.process() is deprecated and may cause damage to your"
    1.54 -            " alignment! It will be removed from 1.4.1 realease."
    1.55 -            " Use aln.realign() instead."
    1.56 -        )
    1.57 -        new = function(self)
    1.58 -        if hasattr(function, 'copy_descriptions'):
    1.59 -            copy_descriptions = function.copy_descriptions
    1.60 -        if hasattr(function, 'copy_contents'):
    1.61 -            copy_contents = function.copy_contents
    1.62 -        self._replace_contents(new, copy_descriptions, copy_contents)
    1.63 -
    1.64      def realign(self, function):
    1.65          """Realign self.
    1.66  
    1.67 -        I.e.: apply function to self to produce a new alignment, then update
    1.68 -        self to have the same gap patterns as the new alignment.
    1.69 -
    1.70 -        This is the same as process(function, False, False)
    1.71 +        * apply function to self to produce a new alignment,
    1.72 +        * update self to have the same gap patterns as the new alignment.
    1.73          """
    1.74          new = function(self)
    1.75          self._replace_column_contents(new)