test.cpp

#include <iostream>
#include <fstream>
#include <string>
#include <set>
#include <stdlib.h>

using namespace std;

int main(int argc, char** argv) {
  if(argc != 2) {
    cout << "Usage: ./parse <filename.txt>" << endl;
    return 255;
  }

  string line;
  ifstream f(argv[1]);
  if(!f.is_open()) {
    cout << "The file you specified could not be read." << endl;
    return 1;
  }

  while(!f.eof()) {
    getline(f, line);
    if(line == "" || line[0] == '#') continue;

    char *ptr, *buf;
    buf = new char[line.size() + 1];
    strcpy(buf, line.c_str());

    // Peptide values
    double mass;
    char* sequence;
    int numK;
    int numPTS;
    int numM;
    set<int> parents;

    mass     = strtod(strtok(buf, " "), NULL);
    sequence = strtok(NULL, " ");
    numK     = strtol(strtok(NULL, " "), NULL, 10);
    numPTS   = strtol(strtok(NULL, " "), NULL, 10);
    numM     = strtol(strtok(NULL, " "), NULL, 10);
    while(ptr = strtok(NULL, " "))
      parents.insert(strtol(ptr, NULL, 10));

    //cout << "mass: " << mass << endl
    //     << "sequence: " << sequence << endl
    //     << "numK: " << numK << endl
    //     << "numPTS: " << numPTS << endl
    //     << "numM: " << numM << endl
    //     << "parents:" << endl;

    //set<int>::iterator it;
    //for(it = parents.begin(); it != parents.end(); it++)
    //  cout << "\t- " << *it << endl;
  }
  f.close();

  return 0;
}