def graftm_package_is_protein(graftm_package):
        '''Return true if this package is an Amino Acid alignment package, otherwise
        False i.e. it is a nucleotide package. In general it is best to use
        'is_protein_package' instead.

        '''
        found = None
        with open(graftm_package.alignment_hmm_path()) as f:
            r = f.read().split("\n")
        for line in r:
            if line=='ALPH  DNA':
                found = False
                break
            elif line=='ALPH  amino':
                found = True
                break
        if found is None:
            raise Exception("Unable to determine whether the HMM was amino acid or dna")
        return found
Return true if this package is an Amino Acid alignment package, otherwise
        False i.e. it is a nucleotide package. In general it is best to use
        'is_protein_package' instead.