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 __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
class Executor(object):
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
def obtain_rna(self):
try:
while True:
self.step()
for r in self.rna:
yield r
self.rna = []
except FinishException:
pass
for r in self.rna:
yield r
self.rna = []
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 pattern(self):
result = []
lvl = 0
parser = self.parser
while True:
self.item_starts.append(parser.index)
a = parser.read_codon()
base = Base.decode.get(a)
if base is not None:
result.append(base)
elif a == 'IP':
result.append(Skip(self.nat()))
elif a == 'IF':
parser.read_base() # that's right
result.append(Search(self.consts()))
elif a == 'IIP':
lvl += 1
result.append(open_paren)
elif a == 'IIC' or a == 'IIF':
if lvl == 0:
return result
lvl -= 1
result.append(close_paren)
elif a == 'III':
command = ''
for i in range(7):
command += parser.read_base()
if self.explicit_rna_items:
result.append(RNA_Item(command))
else:
self.rna.append(command)
else:
raise FinishException()
def nat(self):
result = 0
power = 1
while True:
a = self.parser.read_base()
if a == '' or a == 'P':
break
if a == 'C':
result += power
power *= 2
return result
def consts(self):
result = []
while True:
a = self.parser.read_codon()
if a == 'C':
result.append('I')
elif a == 'F':
result.append('C')
elif a == 'P':
result.append('F')
elif a == 'IC':
result.append('P')
else:
self.parser.unread_codon(a) #it will be later consumed in pattern()
break
return ''.join(result)
def template(self):
result = []
parser = self.parser
while True:
self.item_starts.append(parser.index)
a = parser.read_codon()
base = Base.decode.get(a)
if base is not None:
result.append(base)
elif a == 'IF' or a == 'IP':
level = self.nat()
n = self.nat()
result.append(Reference(n, level))
elif a == 'IIC' or a == 'IIF':
return result
elif a == 'IIP':
result.append(Length(self.nat()))
elif a == 'III':
command = ''
for i in range(7):
command += parser.read_base()
if self.explicit_rna_items:
result.append(RNA_Item(command))
else:
self.rna.append(command)
else:
raise FinishException(a)
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
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
