X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=kruskalwalliscommand.h;h=a82d208cf15ea424413fdae4eee7c666868f4b35;hp=3b5fdcea8975ecc774116fc4f8a824d0db8e64aa;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=847bb54463913763210bd5974bc1b7830012e3ea

diff --git a/kruskalwalliscommand.h b/kruskalwalliscommand.h
index 3b5fdce..a82d208 100644
--- a/kruskalwalliscommand.h
+++ b/kruskalwalliscommand.h
@@ -9,8 +9,8 @@
 #define	KRUSKALWALLISCOMMAND_H
 
 #include "command.hpp"
-
-
+#include "inputdata.h"
+#include "designmap.h"
 
 class KruskalWallisCommand : public Command {
    
@@ -21,37 +21,32 @@ public:
 	~KruskalWallisCommand(){}
 	
 	vector<string> setParameters();
-	string getCommandName()			{ return "kruskalwallis";			}
+	string getCommandName()			{ return "kruskal.wallis";			}
 	string getCommandCategory()		{ return "Hypothesis Testing";	}
-	string getOutputFileNameTag(string, string);
+    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 {
-        sstring group;
+        string group;
         double value;
         double rank;        
     };
     
     int execute(); 
 	void help() { m->mothurOut(getHelpString()); }
-    void assignRank(vector<groupRank>);
+    void assignRank(vector<groupRank>&);
+    void assignValue(vector<groupRank>&);
     
-private:
-    string outputDir;
-    vector<int> counts;
-    vector<double> rankSums;
-    vector<double> rankMeans;
     
-  
-        
-    bool comparevalue(const groupRank &a, const groupRank &b) { return a.value < b.value; }
-    bool equalvalue(const groupRank &a, const groupRank &b) { return a.value == b.value; }
-    bool comparerank(const groupRank &a, const groupRank &b) { return a.rank < b.rank; }
-    bool equalrank(const groupRank &a, const groupRank &b) { return a.rank == b.rank; }
-    bool equalgroup(const groupRank &a, const groupRank &b) { return a.group == b.group; }
+private:
+    bool abort, allLines;
+    string outputDir, sharedfile, designfile, mclass, classes;
+    vector<string> outputNames;
+    set<string> labels;
     
+    int process(vector<SharedRAbundVector*>&, DesignMap&);    
 };
 
 #endif	/* KRUSKALWALLISCOMMAND_H */