X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurmetastats.h;h=4d6cf9166816f9f775e97eedc8a3231ec6daecd8;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=37d616670973b6a55063b5df29c0411d4e1ea0dd;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/mothurmetastats.h b/mothurmetastats.h
index 37d6166..4d6cf91 100644
--- 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