1 // 2 // optimatrix.h 3 // Mothur 4 // 5 // Created by Sarah Westcott on 4/20/16. 6 // Copyright (c) 2016 Schloss Lab. All rights reserved. 7 // 8 9 #ifndef __Mothur__optimatrix__ 10 #define __Mothur__optimatrix__ 11 12 #include "optidata.hpp" 13 14 15 class OptiMatrix : public OptiData { 16 17 18 public: 19 20 #ifdef UNIT_TEST OptiMatrix()21 OptiMatrix() : OptiData(0.03) {}; 22 #endif 23 24 OptiMatrix(vector< set<long long> >, vector<string>, vector<string>, double); //closeness, namemap, singleton, cutoff 25 OptiMatrix(string, string, string, string, double, bool); //distfile, dupsFile, dupsFormat, distFormat, cutoff, sim ~OptiMatrix()26 ~OptiMatrix(){} 27 28 protected: 29 30 string distFile, namefile, countfile, format, distFormat; 31 bool sim; 32 33 int readPhylip(); 34 int readColumn(); 35 }; 36 37 38 #endif /* defined(__Mothur__optimatrix__) */ 39