def BMMethod(tDNA, eDNA):
calc = 0
jamptable = table(eDNA)
n1 = len(tDNA)
n2 = len(eDNA)
hit_ind = list()
#index DNA1
indDNA1 = n2 - 1
while indDNA1 < n1:
#number of match
num_mt = -2
if tDNA[indDNA1] == eDNA[-1]:
for indDNA2 in range(-2, (-1 * n2 -1), -1):
if tDNA[indDNA1 + indDNA2 + 1] == eDNA[indDNA2]:
num_mt = num_mt - 1
if num_mt == (-1 * n2 - 1):
hit_ind.append(indDNA1)
else:
jampnum = jamptable[num_mt]
calc = calc + 1
break
indDNA1 = jampnum + indDNA1
else:
indDNA1 = indDNA1 + 1
calc = calc + 1
return [hit_ind, calc]
num_mt = num_mt - 1
if num_mt == (-1 * n2 - 1):
hit_ind.append(indDNA1)
else:
jampnum = jamptable[num_mt]
calc = calc + 1
break
indDNA1 = jampnum + indDNA1
else:
indDNA1 = indDNA1 + 1
calc = calc + 1
return [hit_ind, calc]
if __name__ == '__main__':
from MakeDNA import SimpleDNA
tDNA = SimpleDNA(10).getDNA()
eDNA = SimpleDNA(10).getDNA()
#print tDNA
print table(eDNA)
print eDNA
[matchp1, count1] = SimpleSearch(tDNA, eDNA)
print matchp1
print count1
[matchp2, count2] = BMMethod(tDNA, eDNA)
print matchp2
print count2