#include "mothur.h"
#include "groupmap.h"
+#include "globaldata.hpp"
+#include "progress.hpp"
+
+using namespace std;
+
+struct Names {
+ string groupname;
+ string seqName;
+};
+
class FullMatrix {
-public:
- FullMatrix(){};
- FullMatrix(ifstream&);
- ~FullMatrix();
+ public:
+ FullMatrix(){};
+ FullMatrix(ifstream&);
+ ~FullMatrix(){};
- int getNumSeqs();
+ int getNumSeqs();
+ void printMatrix(ostream&);
-private:
- void sortGroups(); //this function sorts the sequences within the matrix.
- vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
- GroupMap* groupmap; //maps sequences to groups they belong to.
- int numSeqs;
+ private:
+ void sortGroups(int, int); //this function sorts the sequences within the matrix.
+ void readSquareMatrix(ifstream&);
+ void readLTMatrix(ifstream&);
+ vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
+ map<int, Names> index; // row in vector, sequence group. need to know this so when we sort it can be updated.
+ GroupMap* groupmap; //maps sequences to groups they belong to.
+ GlobalData* globaldata;
+ int numSeqs;
+ bool square;
};