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added kruskal.wallis command. added worked on make.lefse. working of lefse command...
[mothur.git] / kruskalwalliscommand.h
1 /* 
2  * File:   kruskalwalliscommand.h
3  * Author: kiverson
4  *
5  * Created on June 26, 2012, 11:07 AM
6  */
7
8 #ifndef KRUSKALWALLISCOMMAND_H
9 #define KRUSKALWALLISCOMMAND_H
10
11 #include "command.hpp"
12 #include "inputdata.h"
13 #include "designmap.h"
14
15 class KruskalWallisCommand : public Command {
16    
17 public:
18             
19         KruskalWallisCommand(string);   
20         KruskalWallisCommand();
21         ~KruskalWallisCommand(){}
22         
23         vector<string> setParameters();
24         string getCommandName()                 { return "kruskal.wallis";                      }
25         string getCommandCategory()             { return "Hypothesis Testing";  }
26     string getOutputPattern(string);    
27         string getHelpString(); 
28         string getCitation() { return "http://www.mothur.org/wiki/Kruskal.wallis"; }
29         string getDescription()         { return "Non-parametric method for testing whether samples originate from the same distribution."; }
30     
31     struct groupRank {
32         string group;
33         double value;
34         double rank;        
35     };
36     
37     int execute(); 
38         void help() { m->mothurOut(getHelpString()); }
39     void assignRank(vector<groupRank>&);
40     void assignValue(vector<groupRank>&);
41     
42     
43 private:
44     bool abort, allLines;
45     string outputDir, sharedfile, designfile, mclass, classes;
46     vector<string> outputNames;
47     set<string> labels;
48     
49     int process(vector<SharedRAbundVector*>&, DesignMap&);    
50 };
51
52 #endif  /* KRUSKALWALLISCOMMAND_H */
53