def step(self):
if self.debug:
print 'iteration', self.iteration
print 'dna =', limit_string(self.dna)
try:
p = self.pattern()
if self.debug:
print 'pattern ', ''.join(map(str, p))
t = self.template()
if self.debug:
print 'template', ''.join(map(str, t))
for pp in p:
self.pattern_freqs[type(pp)] += 1
for tt in t:
self.template_freqs[type(tt)] += 1
finally:
index = self.parser.index
self.cost += index
self.parser = None
self.item_starts = []
del self.dna[:index]
self.matchreplace(p, t)
self.parser = DNA_parser(self.dna, self.freqs)
self.iteration += 1
if self.debug:
print 'len(rna) =', len(self.rna)
print
def matchreplace(self, pattern, template):
e = []
i = 0
c = []
dna = self.dna
for p in pattern:
tp = type(p)
if tp is Base:
self.cost += 1
if dna[i] == p:
i += 1
else:
if self.debug:
print 'failed match (base)'
return
elif tp is Skip:
i += p
if i > len(dna):
if self.debug:
print 'failed match (skip)'
return
elif tp is Search:
j = next(kmp.find(dna, p, start=i), None)
if j is not None:
self.cost += j + len(p) - i
i = j + len(p)
else:
self.cost += len(dna) - i
if self.debug:
print 'failed match (search)'
return
elif tp is OpenParen:
c.append(i)
elif tp is CloseParen:
e.append((c.pop(), i))
else:
assert False, 'unknown pattern element'
if self.debug:
print 'succesful match of length', i
for j, ee in enumerate(e):
print 'e[{0}] = {1}'.format(j, limit_string(dna[ee[0]: ee[1]]))
r = self.replacement(template, e)
dna[:i] = r
