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  1. #include <iostream>
  2. #include <string>
  3. #include <cstdlib>
  4. #include <ctime>
  5. #include <vector>
  6. #include <assert.h>
  7. #include <iomanip>
  8.  
  9. // demo for SO answer at http://stackoverflow.com/a/38491405/2932052
  10. using namespace std;
  11.  
  12. const string CODE = "ATCG";
  13. vector<unsigned> buildRMap()
  14. {
  15.     vector<unsigned> result(256, 0);
  16.         for (size_t i=0; i<CODE.size(); ++i) {
  17.         result[CODE[i]]= i;
  18.     }
  19.     return result;
  20. }
  21. const vector<unsigned> RMAP = buildRMap();
  22.  
  23. enum { SEQ_LEN = 16 };
  24.  
  25. string randomDna()
  26. {
  27.     string result(SEQ_LEN, ' ');
  28.     for (size_t i=0; i<SEQ_LEN; ++i ){
  29.         result[i] = CODE[rand() & 3];
  30.     }
  31.     return result;
  32. }
  33.  
  34. int distS(const char* const a, const char* const b)
  35. {
  36.     int result = 0;
  37.     for (size_t i=0; i<SEQ_LEN; ++i) {
  38.         result += a[i] != b[i];
  39.     }
  40.     return result;
  41. }
  42.  
  43. unsigned encodeV(const string& atcg)
  44. {
  45.     assert(atcg.size() == SEQ_LEN);
  46.     unsigned result = 0;
  47.     for (size_t i=0; i<SEQ_LEN; ++i) {
  48.         result |= RMAP[atcg[i]] << (i << 1);
  49.     }
  50.     return result;
  51. }
  52.  
  53. int distV(const unsigned va, const unsigned vb)
  54. {
  55.     const unsigned x = va ^ vb;
  56.     const unsigned bn = ((x & 0xaaaaaaaa) >> 1 ) | (x & 0x55555555);
  57.     return __builtin_popcount(bn);
  58. }
  59.  
  60. int main()
  61. {
  62.     srand(time(0));
  63.     const string a = randomDna();
  64.     const unsigned va = encodeV(a);
  65.     cout << a << " -> V: 0x" << setfill('0') << setw(8) << hex << va << endl;
  66.     const string b = randomDna();
  67.     const unsigned vb = encodeV(b);
  68.     cout << b << " -> V: 0x" << setfill('0') << setw(8) << hex << vb << endl;
  69.     cout << "dS=" << dec << distS(a.c_str(), b.c_str()) << endl;
  70.     cout << "dV=" << dec << distV(va, vb) << endl;
  71.     return 0;
  72. }
  73.  
Success #stdin #stdout 0s 2820KB
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stdin
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Standard input is empty
stdout
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GTATCTGTTGACCGGA -> V: 0x3e8d7647
AATAATTTAGACAATG -> V: 0xd08c5410
dS=11
dV=11
https://ideone.com/FdrWll
language:
C++ 4.3.2 (gcc-4.3.2)
created:
9 years ago
visibility:
public

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