From b07e5c455cbf6907186dd821f7f33462706bd225 Mon Sep 17 00:00:00 2001
From: Kathryn Iverson <kd.iverson@gmail.com>
Date: Thu, 28 Jun 2012 16:17:15 -0400
Subject: [PATCH] updated kruskalwallis struct

---
 kruskalwalliscommand.cpp | 8 ++++----
 kruskalwalliscommand.h   | 7 ++++---
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
index f67fef8..946701b 100644
--- a/kruskalwalliscommand.cpp
+++ b/kruskalwalliscommand.cpp
@@ -7,7 +7,7 @@
 #include "kruskalwalliscommand.h"
 
 //**********************************************************************************************************************
-vector<string> KruskalWallisCommand::setParameters(){	
+/*vector<string> KruskalWallisCommand::setParameters(){	
 	try {
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
@@ -117,7 +117,7 @@ KruskalWallisCommand::KruskalWallisCommand(string option) {
 		m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
 		exit(1);
 	}
-}
+}**/
 //**********************************************************************************************************************
 int KruskalWallisCommand::execute(){
 	try {
@@ -176,7 +176,7 @@ int KruskalWallisCommand::execute(){
 void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
     try {
         double rank = 1;
-        double numRanks, avgRank;
+        double numRanks, avgRank, j;
         vector<groupRank>::iterator it, oldit;
 
         sort (vec.begin(), vec.end(), comparevalue);
@@ -186,7 +186,7 @@ void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
         while ( it != vec.end() ) {
             j = rank;
             oldit = it;
-            if (!equalvalue(*it, *it+1)) { *it->rank = rank; rank++; it++; }
+            if (!equalvalue(*it, *it+1)) { *it->rank = rank; rank=rank+1; it++; }
             else {
                 while(equalrank(*it, *it+1)) {
                     j = j + (j+1.0);
diff --git a/kruskalwalliscommand.h b/kruskalwalliscommand.h
index 3b5fdce..1aadb16 100644
--- a/kruskalwalliscommand.h
+++ b/kruskalwalliscommand.h
@@ -11,7 +11,6 @@
 #include "command.hpp"
 
 
-
 class KruskalWallisCommand : public Command {
    
 public:
@@ -29,17 +28,19 @@ public:
 	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>&);
+    
     
 private:
     string outputDir;
+    bool abort;
     vector<int> counts;
     vector<double> rankSums;
     vector<double> rankMeans;
-- 
2.39.2