private:
MothurOut* m;
- int row, column, numPermutations;
+ int row, column, numPermutations, secondGroupingStart;
double threshold;
-
+
+ vector<double> permuted_pvalues(vector< vector<double> >&, vector<double>&, vector< vector<double> >&);
+ vector<double> permute_and_calc_ts(vector< vector<double> >&);
+
int start(vector<double>&, int, vector<double>&, vector< vector<double> >&); //Find the initial values for the matrix
int meanvar(vector<double>&, int, vector<double>&);
int testp(vector<double>&, vector<double>&, vector<double>&, int, vector<double>&, vector<double>&);
int permute_matrix(vector<double>&, vector<double>&, int, vector<double>&, vector<double>&, vector<double>&);
int permute_array(vector<int>&);
int calc_twosample_ts(vector<double>&, int, vector<double>&, vector<double>&, vector<double>&);
+ double smoothSpline(vector<double>&, vector<double>&, int);
+ vector<double> calc_qvalues(vector<double>&);
+ vector<double> sknot1(double*, int);
+ int nkn(int);
+ int OrderPValues(int, int, vector<double>&, vector<int>&);
+ int swapElements(int, int, vector<double>&, vector<int>&);
+ vector<int> getSequence(int, int, int);
+
};
#endif