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[mothur.git] / mothurmetastats.h

diff --git a/mothurmetastats.h b/mothurmetastats.h
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+#ifndef MOTHUR_METASTATS
+#define MOTHUR_METASTATS
+
+/*
+ *  mothurmetastats.h
+ *  Mothur
+ *
+ *  Created by westcott on 7/6/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "mothurout.h"
+
+class MothurMetastats {
+       
+       public:
+               MothurMetastats(double, int); //threshold, numPermutations
+               ~MothurMetastats();
+       
+               int runMetastats(string, vector< vector<double> >&, int); //outputFileName, data, secondGroupingStart
+       
+       private:
+               MothurOut* m;
+               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
+