1.1 --- a/allpy/base.py	Thu Dec 16 18:35:25 2010 +0300
     1.2 +++ b/allpy/base.py	Thu Dec 16 18:35:56 2010 +0300
     1.3 @@ -286,31 +286,6 @@
     1.4                  line.append(all_columns[position].get(aa))
     1.5          return self.identity_percentages
     1.6  
     1.7 -    def column(self, sequence=None, sequences=None, original=None):
     1.8 -        """ returns list of columns of alignment
     1.9 -
    1.10 -        sequence or sequences:
    1.11 -            * if sequence is given, then column is (original_monomer, monomer)
    1.12 -            * if sequences is given, then column is (original_monomer, {sequence: monomer})
    1.13 -            * if both of them are given, it is an error
    1.14 -
    1.15 -        original (Sequence type):
    1.16 -            * if given, this filters only columns represented by original sequence
    1.17 -        """
    1.18 -        if sequence and sequences:
    1.19 -            raise Exception("Wrong usage. read help")
    1.20 -        indexes = dict([(v, k) for( k, v) in enumerate(self.sequences)])
    1.21 -        alignment = self.body.items()
    1.22 -        alignment.sort(key=lambda i: indexes[i[0]])
    1.23 -        alignment = [monomers for seq, monomers in alignment]
    1.24 -        for column in zip(*alignment):
    1.25 -            if not original or column[indexes[original]]:
    1.26 -                if sequence:
    1.27 -                    yield (column[indexes[original]], column[indexes[sequence]])
    1.28 -                else:
    1.29 -                    yield (column[indexes[original]],
    1.30 -                    dict([(s, column[indexes[s]]) for s in sequences]))
    1.31 -
    1.32  class Block(object):
    1.33      """ Block of alignment
    1.34