PolyARules.h

   1 #ifndef POLYARULES
   2 #define POLYARULES
   3
   4 #include<cstdio>
   5 #include<cstdlib>
   6 #include<cassert>
   7 #include<set>
   8 #include<cstring>
   9 #include<fstream>
  10
  11 /**
  12 Isoform id starts from 1 !
  13 */
  14
  15 class PolyARules {
  16 public:
  17         PolyARules() {
  18                 polyAChoice = 0;
  19                 polyALen = 0;
  20                 exceptionList.clear();
  21         }
  22
  23         //Assume parameters are valid here
  24         PolyARules(int polyAChoice, int polyALen, char* exceptionF) {
  25                 this->polyAChoice = polyAChoice;
  26                 this->polyALen =  polyALen;
  27
  28                 if (polyAChoice == 2) {
  29                         exceptionList.clear();
  30
  31                         std::string transcript_id;
  32                         std::ifstream fin(exceptionF);
  33                         if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", exceptionF); exit(-1); }
  34
  35                         while (fin>> transcript_id) {
  36                                 exceptionList.insert(transcript_id);
  37                         }
  38
  39                         fin.close();
  40                 }
  41         }
  42
  43         //get the length of padding poly As
  44         int getLenAt(const std::string& transcript_id) {
  45                 switch(polyAChoice) {
  46                 case 0 : return polyALen;
  47                 case 1 : return 0;
  48                 case 2 : iter = exceptionList.find(transcript_id);
  49                                  return (iter == exceptionList.end() ? polyALen : 0);
  50                 default : assert(false);
  51                 }
  52         }
  53
  54 private:
  55         int polyAChoice; // 0, pad; 1, do not pad; 2 pad all but those in exceptionList
  56         int polyALen;
  57         std::set<std::string> exceptionList; // exception list of transcript_ids
  58         std::set<std::string>::iterator iter;
  59 };
  60
  61 #endif