rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / mothurmetastats.h

diff --git a/mothurmetastats.h b/mothurmetastats.h
new file mode 100644 (file)
index 0000000..37d6166
--- /dev/null
+++ b/mothurmetastats.h
@@ -0,0 +1,57 @@
+#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;
+               double threshold;
+       
+               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>&);
+
+
+
+       
+};
+       
+       //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
+