- private:
- void sortGroups(); //this function sorts the sequences within the matrix.
- void quicksort(int, int, int);//row of matrix, low, high and row number
- 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, string> 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;
-
+private:
+ vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
+ 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;
+
+ void sortGroups(int, int); //this function sorts the sequences within the matrix.
+ void swapRows(int, int);
+
+ GroupMap* groupmap; //maps sequences to groups they belong to.
+ int numSeqs;
+ int numGroups;
+ int numUserGroups;
+ bool sim;
+ MothurOut* m;