def load(self, handler):
# type: (BinaryIO) -> None
for s in handler.readlines():
s = s.split()
if len(s) == 0:
continue
if s[0] == "mat":
self.sMatch[basic.letterToIndex(
s[1])] = -math.log10(float(s[2]))
elif s[0] == "mis":
self.sMM[basic.letterToIndex(s[1][0])][basic.letterToIndex(
s[1][-1])] = -math.log10(float(s[2]))
elif s[0] == "del":
self.sDel[basic.letterToIndex(s[1])] = -math.log10(float(s[2]))
self.sHomo[basic.letterToIndex(
s[1])] = -math.log10(float(s[2])) / 3
elif s[0] == "ins":
self.sIns[basic.letterToIndex(s[1])] = -math.log10(float(s[2]))
def scoreIns(self, char):
return self.sIns[basic.letterToIndex(char)]
def scoreMatch(self, char):
return self.sMatch[basic.letterToIndex(char)]
def scoreHomo(self, char):
return self.sHomo[basic.letterToIndex(char)]
def scoreMM(self, char1, char2):
return self.sMM[basic.letterToIndex(char1)][basic.letterToIndex(char2)]
def scoreDel(self, char):
return self.sDel[basic.letterToIndex(char)]