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);
+
};
- //void testp(double *permuted_ttests,int *B,double *permuted,double
- // *Imatrix,int *nc,int *nr,int *g,double *Tinitial,double *ps);
- //void permute_matrix(double *Imatrix,int *nc,int *nr,double
- // *permuted,int *g,double *trial_ts,double *Tinitial,double
- // *counter);
- //void permute_array(int *array, int n);
- //void calc_twosample_ts(double *Pmatrix,int *g,int *nc,int *nr,double
- // *Ts,double *Tinitial,double *counter1);
- //void meanvar(double *pmatrix,int *g,int *nr,int *nc,double *storage);
- //void start(double *Imatrix,int *g,int *nr,int *nc,double *testing,
- // double storage[][9]);
-
- //int metastat_main (char*, int, int, double, int, double**, int);
-
-
#endif