};
struct linePair {
- unsigned long int start;
- unsigned long int end;
- linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
linePair(){}
};
public:
- Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
+ Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; byGroup = false; }
virtual ~Chimera(){ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } for (int i = 0; i < filteredTemplateSeqs.size(); i++) { delete filteredTemplateSeqs[i]; } };
virtual bool getUnaligned() { return unaligned; }
virtual int getLength() { return length; }
vector<Sequence*> templateSeqs;
vector<Sequence*> filteredTemplateSeqs;
- bool filter, unaligned;
+ bool filter, unaligned, byGroup;
int length;
string seqMask, filterString, outputDir, templateFileName;
Sequence* getSequence(string); //find sequence from name