Bit Operation For Finding String Difference

Question

The following string of mine tried to find difference between two strings. But it's horribly slow as it iterate the length of string:

#include <string>
#include <vector>
#include <iostream>
using namespace std;


int hd(string s1, string s2) {
    // hd stands for "Hamming Distance"
    int dif = 0;

    for (unsigned i = 0; i < s1.size(); i++ ) {
        string b1 = s1.substr(i,1);
        string b2 = s2.substr(i,1);

        if (b1 != b2) {
            dif++;
        }
    }  

    return dif;
}

int main() {

    string string1 = "AAAAA";
    string string2 = "ATATT";
    string string3 = "AAAAA";

    int theHD12 = hd(string1,string2);
    cout << theHD12 << endl;

    int theHD13 = hd(string1,string3);
    cout << theHD13 << endl;
}

Is there a fast alternative to do that? In Perl we can have the following approach:

sub hd {
    return ($_[0] ^ $_[1]) =~ tr/\001-\255//;
}

which is much2 faster than iterating the position.

I wonder what's the equivalent of it in C++?

Answer 1

Try to replace the for loop by:

for (unsigned i = 0; i < s1.size(); i++ ) {
    if (b1[i] != b2[i]) {
            dif++;
    }
}  

This should be a lot faster because no new strings are created.

Answer 2

Fun with the STL:

#include <numeric>    //inner_product
#include <functional> //plus, equal_to, not2
#include <string>   
#include <stdexcept>

unsigned int 
hd(const std::string& s1, const std::string& s2)
{
    // TODO: What should we do if s1.size() != s2.size()?
    if (s1.size() != s2.size()){
      throw std::invalid_argument(
          "Strings passed to hd() must have the same lenght"
      );
    }

    return std::inner_product(
        s1.begin(), s1.end(), s2.begin(), 
        0, std::plus<unsigned int>(),
        std::not2(std::equal_to<std::string::value_type>())
    );
}

Answer 3

Use iterators:

int GetHammingDistance(const std::string &a, const std::string &b)
{
    // Hamming distance is not defined for strings of different lengths.
    ASSERT(a.length() == b.length());

    std::string::const_iterator a_it = a.begin();
    std::string::const_iterator b_it = b.begin();

    std::string::const_iterator a_end = a.end();
    std::string::const_iterator b_end = b.end();

    int distance = 0;
    while (a_it != a_end && b_it != b_end)
    {
        if (*a_it != *b_it) ++distance;
        ++a_it; ++b_it;
    }

    return distance;
}

Answer 4

Choice 1: Modify your original code to be as effecient as possable.

int hd(string const& s1, string const& s2)
{
    // hd stands for "Hamming Distance"
    int dif = 0;

    for (std::string::size_type i = 0; i < s1.size(); i++ )
    {
        char b1 = s1[i];
        char b2 = s2[i];

        dif += (b1 != b2)?1:0;
    }  

    return dif;
}

Second option use some of the STL algorithms to do the heavy lifting.

struct HammingFunc
{
    inline int operator()(char s1,char s2)
    {
        return s1 == s2?0:1;
    }
};

int hd(string const& s1, string const& s2)
{
    int diff = std::inner_product(s1.begin(),s1.end(),
                                  s2.begin(),
                                  0,
                                  std::plus<int>(),HammingFunc()
                                 );
    return diff;
}

Answer 5

Some obvious points that might make it faster:

1. Pass the strings as const references, not by value
2. Use the indexing operator [] to get characters, not a method call
3. Compile with optimization on