def replacement(self, template, e):
r = dna_type()
base_to_string = str.__str__
for t in template:
tt = type(t)
if tt is Base:
r.append(base_to_string(t))
elif tt is Reference:
if t.n < len(e):
begin, end = e[t.n]
else:
begin, end = 0, 0
if t.level == 0:
r.extend(self.dna[begin:end])
else:
p = protect(self.dna[begin:end], t.level)
self.cost += len(p)
r.extend(p)
elif tt is Length:
if t < len(e):
begin, end = e[t]
else:
begin, end = 0, 0
r.extend(asnat(end - begin))
return r
def __init__(self, dna):
#assert all(c in 'ICFP' for c in dna)
self.pattern_freqs = defaultdict(int)
self.template_freqs = defaultdict(int)
self.codon_len_freqs = defaultdict(int)
self.freqs = [self.pattern_freqs, self.template_freqs, self.codon_len_freqs]
self.explicit_rna_items = False
self.dna = dna_type(dna)
self.parser = DNA_parser(self.dna, self.freqs)
self.item_starts = []
self.rna = []
self.cost = 0
self.debug = False
self.iteration = 0
