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; }
#ifdef USE_MPI
virtual Sequence print(MPI_File&, MPI_File&){ Sequence temp; return temp; }
- virtual Sequence print(MPI_File&, MPI_File&, data_results, data_results){ Sequence temp; return temp; }
+ virtual Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&){ Sequence temp; return temp; }
virtual int print(MPI_File&, MPI_File&, string){ return 0; }
#endif
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