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Sourcecode: python-biopython version File versions

def Bio::Align::AlignInfo::SummaryInfo::_get_all_letters (   self  )  [private]

Returns a string containing the expected letters in the alignment.

Definition at line 308 of file AlignInfo.py.

00308                               :
        """Returns a string containing the expected letters in the alignment."""
        all_letters = self.alignment._alphabet.letters
        if all_letters is None \
        or (isinstance(self.alignment._alphabet, Alphabet.Gapped) \
        and all_letters == self.alignment._alphabet.gap_char):
            #We are dealing with a generic alphabet class where the
            #letters are not defined!  We must build a list of the
            #letters used...
            set_letters = set()
            for record in self.alignment :
                #Note the built in set does not have a union_update
                #which was provided by the sets module's Set
                set_letters = set_letters.union(record.seq)
            list_letters = list(set_letters)
            all_letters = "".join(list_letters)
        return all_letters

    def _get_base_replacements(self, skip_items = []):

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