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#ifndef POLYARULES
#define POLYARULES
#include<cstdio>
#include<cstdlib>
#include<cassert>
#include<set>
#include<cstring>
#include<fstream>
/**
Isoform id starts from 1 !
*/
class PolyARules {
public:
PolyARules() {
polyAChoice = 0;
polyALen = 0;
exceptionList.clear();
}
//Assume parameters are valid here
PolyARules(int polyAChoice, int polyALen, char* exceptionF) {
this->polyAChoice = polyAChoice;
this->polyALen = polyALen;
if (polyAChoice == 2) {
exceptionList.clear();
std::string transcript_id;
std::ifstream fin(exceptionF);
if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", exceptionF); exit(-1); }
while (fin>> transcript_id) {
exceptionList.insert(transcript_id);
}
fin.close();
}
}
//get the length of padding poly As
int getLenAt(const std::string& transcript_id) {
switch(polyAChoice) {
case 0 : return polyALen;
case 1 : return 0;
case 2 : iter = exceptionList.find(transcript_id);
return (iter == exceptionList.end() ? polyALen : 0);
default : assert(false);
}
}
private:
int polyAChoice; // 0, pad; 1, do not pad; 2 pad all but those in exceptionList
int polyALen;
std::set<std::string> exceptionList; // exception list of transcript_ids
std::set<std::string>::iterator iter;
};
#endif
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