How do I properly use getline() to turn strings to ints? - c++

Question

I have an input txt file that looks like so:
3 2
ATCGATTGA
GACTATACG
I'm using fstream, and creating it as a string. I'm then able to turn 3 and 2 into their own separate ints, but want to also turn the next two lines into ints as well. I'm trying to use getline() because I am told that would be the most efficient, but can't figure out how to create the lower two as their own ints. Any help on how to get that to work?

Answer 1

getline isn't going to convert a string to an int. Just not what it's intended to do.
If you want to convert ATCGATTGA to an int, the obvious approach would be to treat the input as base 4. If memory serves, the "order" is usually given as A-T-C-G. Assuming that's correct, you'd treat them as A=0, T=1, C=2, G=3, and convert the sequences accordingly (but note that for our purposes, the order you choose doesn't really matter, as long as you use the same order for both encoding and decoding).
int cvt_amino(std::string const &amino) {
int result = 0;
for (char c : amino) {
result *= 4;
switch(c) {
case 'a':
case 'A':
result += 0;
break;
case 't':
case 'T':
result += 1;
break;
case 'c':
case 'C':
result += 2;
break;
case 'g':
case 'G':
result += 3;
break;
default:
throw std::runtime_error("Error: bad argument");
}
}
return result;
}
The result is a unique number for each sequence (up to the maximum that will fit in an int). Modulo bugs (I haven't tested this code) you should be able to convert a result back to the original sequence that generated it.
That does assume that the length of each original sequence is known/fixed. If lengths might vary, you won't know the number of leading 'A's to include. In such a case, you probably want to switch to base 5, and change the mapping to A=1, T=2, C=3, G=4. This removes the ambiguity with respect to variable-length inputs (but reduces the maximum length that will fit in a given variable size).
As far as reading data from the file goes, it seems pretty trivial, at least assuming we know the input format. For the format you've given above, you might use something like this:
int a, b;
your_file >> a >> b; // read the 3 and 2
// We'll assume an arbitrary number of space-separated sequences after that:
std::string input;
std:vector<int> values;
while (your_file >> input)
values.push_back(cvt_amino(input));