added cooccurence command

[mothur.git] / trialswap2.h

diff --git a/trialswap2.h b/trialswap2.h
new file mode 100644 (file)
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--- /dev/null
+++ b/trialswap2.h
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+#ifndef TRIALSWAP2
+#define TRIALSWAP2
+
+/*
+ *  trialswap2.h
+ *  Mothur
+ *
+ *  Created by Kathryn Iverson on June 27, 2011.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothurout.h"
+
+
+class TrialSwap2 {
+    
+public:
+       TrialSwap2(){  m = MothurOut::getInstance(); };
+    ~TrialSwap2(){};
+    
+    double calc_pvalue_lessthan (vector<double>, double);
+    double calc_pvalue_greaterthan (vector<double>, double);
+    int swap_checkerboards (vector<vector<int> > &);
+    int calc_combo (vector<vector<int> > &);
+    double calc_vratio (vector<int>, vector<int>);
+    int calc_checker (vector<vector<int> > &,vector<int>);
+    double calc_c_score (vector<vector<int> > &,vector<int>);
+    int sho(vector<int>,vector<int>,int k);
+    int havel_hakimi(vector<int>,vector<int>,vector<vector<int> > &);
+    int intrand(int);
+    
+    int sim1 (vector<vector<int> > &);
+    void sim2(vector<vector<int> >&);
+    int sim2plus(vector<int>, vector<vector<int> > &);
+    void sim3(vector<vector<int> > &);
+    int sim4(vector<int>, vector<int>, vector<vector<int> > &);
+    int sim5(vector<int>, vector<int>, vector<vector<int> > &);
+    int sim6(vector<int>, vector<vector<int> > &);
+    int sim7(vector<int>, vector<vector<int> > &);
+    int sim8(vector<int>, vector<int>, vector<vector<int> > &);
+    int transpose_matrix (vector<vector<int> > &, vector<vector<int> > &);
+    int update_row_col_totals(vector<vector<int> > &, vector<int>&, vector<int>&);
+
+    
+private:
+    MothurOut* m;
+    
+    double t_test (double, int, double, vector<double>);
+    int print_matrix(vector<vector<int> > &, int, int);
+    
+    
+
+};
+
+#endif
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