X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kruskalwalliscommand.cpp;h=dd5eb09cbd3b54fb439d277cbd166f01dc726f84;hb=d70a1c2d70c5a516e74880709e3b48cfc1ce0321;hp=76aebe05e36b441e29c8632d585d5ba21a4f92a6;hpb=8e67e9de1b200106bea5a468ac02125954656499;p=mothur.git

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
index 76aebe0..dd5eb09 100644
--- a/kruskalwalliscommand.cpp
+++ b/kruskalwalliscommand.cpp
@@ -124,17 +124,36 @@ int KruskalWallisCommand::execute(){
 	try {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
         
+        InputData* input = new InputData(sharedfile, "sharedfile");
+        vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
+		string lastLabel = lookup[0]->getLabel();
+		
+		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+		set<string> processedLabels;
+		set<string> userLabels = labels;
+
+        ofstream out;
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
+        m->openOutputFile(outputFileName, out);
+        outputNames.push_back(outputFileName);  outputTypes["summary"].push_back(outputFileName);
+        out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+        out << "H\tpvalue\n";
+        
         //math goes here
         
-        int N; //= thisLookUp.size();
+        int N = m->getNumGroups();
         double H;
         double tmp = 0.0;
         vector<groupRank> vec;
+        vector<string> groups = m->getGroups();
         string group;
         int count;
         double sum;
                 
         //merge all groups into a vector
+        
+        
+        
         //rank function here
         assignRank(vec);
         
@@ -142,7 +161,7 @@ int KruskalWallisCommand::execute(){
         for (int i=0;i<N;i++) {
             count = 0;
             sum = 0;
-            //group = next group
+            group = groups[i];
             for(int j;j<vec.size();j++) {
                 if (vec[j].group == group) {
                     count++;
@@ -216,7 +235,9 @@ void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
     
 }
 //**********************************************************************************************************************
-
+void KruskalWallisCommand::assignValue(vector<groupRank> &vec) {
+    
+}
 //**********************************************************************************************************************
 //**********************************************************************************************************************
 //**********************************************************************************************************************
\ No newline at end of file