Question

C++ Programming help, please include comments to help me understand the code. Thank you for helping.

Task C: Substitution and Hamming Distance

For this task, we will explore mutations that occur by substitution. Your task is to write a program called hamming.cpp that calculates the Hamming distance between two strings. Given two strings of equal length, the Hamming distance is the number of positions at which the two strings differ. e. g.: Hamming("aactgc", "atcaga") would output 3. Notice that certain amino acids are encoded by multiple codons. Therefore, not all substitutions result in a change of protein structure. The file mutations.txt contains an even number of lines (zero-indexed). The even-numbered lines contain the original DNA sequence, and the odd-numbered lines contain that same sequence with substitution mutations. For each pair in mutations.txt, output to the console the Hamming distance followed by “yes” or “no” whether the substitution caused a change in structure. Example:

$ ./hamming
0 no
17 yes
4 yes

Remember that translation to proteins does not begin until the first “Start” codon, and stops at the first “Stop” codon, and unlike the “Start” codon, the “Stop” codon is not included in the protein chain translation; it simply signifies the end of translation.

Answer 1

I have coded assuming the input is taken only from the file and it is in this format;

mutations.txt

aactgc
atcaga
gctata
gctata

and the file will be in the same folder as hamming.cpp and is not empty.

hamming.cpp

#include <iostream>

#include <fstream>

#include <string>

using namespace std;

int main()

{

//file handling using ifstream class object to read the file

ifstream file("mutations.txt");

//String to hold string for comparision

string ham1, ham2;

//To keep count of hamming distance

int hamming_dist = 0;

  //execute the loop if file is not empty

while (getline(file, ham1))   //using getline to read each odd line

{   

//hamming_dist is initialize to zero with each iteration

//so as not to add to previous iteration.

hamming_dist = 0;

  //using getline to read each even line

getline(file, ham2);

  //iterate through both string comparing

for (int i = 0; i < ham1.length(); i++)

{

  //increasing hamming distance by 1 when characters of strings don't match

if (ham1[i] != ham2[i])

++hamming_dist;

}

if (hamming_dist == 0)

cout << "0"<< " "<< "no\n";

else

cout << hamming_dist << " "<< "yes\n";

}

}