added kruskal.wallis command. added worked on make.lefse. working of lefse command...

[mothur.git] / kruskalwalliscommand.h

diff --git a/kruskalwalliscommand.h b/kruskalwalliscommand.h
index feefebd58fdb5650f41e9642a63e6dc68d011a24..a82d208cf15ea424413fdae4eee7c666868f4b35 100644 (file)
--- a/kruskalwalliscommand.h
+++ b/kruskalwalliscommand.h
@@ -10,8 +10,7 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "sharedrabundvector.h"
-
+#include "designmap.h"
 
 class KruskalWallisCommand : public Command {
    
@@ -22,11 +21,11 @@ public:
        ~KruskalWallisCommand(){}
        
        vector<string> setParameters();
-       string getCommandName()                 { return "kruskalwallis";                       }
+       string getCommandName()                 { return "kruskal.wallis";                      }
        string getCommandCategory()             { return "Hypothesis Testing";  }
     string getOutputPattern(string);   
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/kruskalwallis"; }
+       string getCitation() { return "http://www.mothur.org/wiki/Kruskal.wallis"; }
        string getDescription()         { return "Non-parametric method for testing whether samples originate from the same distribution."; }
     
     struct groupRank {
@@ -42,22 +41,12 @@ public:
     
     
 private:
-    string outputDir, sharedfile, groups;
-    bool abort;
+    bool abort, allLines;
+    string outputDir, sharedfile, designfile, mclass, classes;
+    vector<string> outputNames;
     set<string> labels;
-    vector<string> outputNames, Groups;
-    vector<int> counts;
-    vector<double> rankSums;
-    vector<double> rankMeans;
-    
-  
-        
-    static bool comparevalue(const groupRank &a, const groupRank &b) { return a.value < b.value; }
-    static bool equalvalue(const groupRank &a, const groupRank &b) { return a.value == b.value; }
-    static bool comparerank(const groupRank &a, const groupRank &b) { return a.rank < b.rank; }
-    static bool equalrank(const groupRank &a, const groupRank &b) { return a.rank == b.rank; }
-    static bool equalgroup(const groupRank &a, const groupRank &b) { return a.group == b.group; }
     
+    int process(vector<SharedRAbundVector*>&, DesignMap&);    
 };
 
 #endif /* KRUSKALWALLISCOMMAND_H */