changes while testing

[mothur.git] / mothurmetastats.h

diff --git a/mothurmetastats.h b/mothurmetastats.h
index 37d616670973b6a55063b5df29c0411d4e1ea0dd..4d6cf9166816f9f775e97eedc8a3231ec6daecd8 100644 (file)
--- a/mothurmetastats.h
+++ b/mothurmetastats.h
@@ -23,35 +23,27 @@ class MothurMetastats {
        
        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