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