#include "mothur.h"
#include "groupmap.h"
-#include "globaldata.hpp"
#include "progress.hpp"
class FullMatrix {
public:
- FullMatrix(){};
- FullMatrix(ifstream&);
+ //FullMatrix(){ m = MothurOut::getInstance(); }
+ FullMatrix(ifstream&, GroupMap*, bool);
~FullMatrix(){};
int getNumSeqs();
private:
vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
- void readSquareMatrix(ifstream&);
- void readLTMatrix(ifstream&);
+ int readSquareMatrix(ifstream&);
+ int readLTMatrix(ifstream&);
vector<Names> index; // row in vector, sequence group. need to know this so when we sort it can be updated.
vector<int> sizes;
vector<string> groups;
int numSeqs;
int numGroups;
int numUserGroups;
- GlobalData* globaldata;
+ bool sim;
+ MothurOut* m;
};
#endif