fixed io

[mothur.git] / kruskalwalliscommand.cpp

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
index 263b1c55c1517171f02b70a6d5232277d4ee9861..39afca8c8acb0228a60d18b8df4da9a23eb6adef 100644 (file)
--- a/kruskalwalliscommand.cpp
+++ b/kruskalwalliscommand.cpp
@@ -4,15 +4,9 @@
  *
  * Created on June 26, 2012, 11:06 AM
  */
+
 #include "kruskalwalliscommand.h"
 
-//**********************************************************************************************************************
-class groupRank {
-public:
-    string group;
-    double value;
-    double rank;
-};
 //**********************************************************************************************************************
 vector<string> KruskalWallisCommand::setParameters(){  
        try {
@@ -130,14 +124,49 @@ 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;
-        double ss, H;
+        int N = lookup.size();
+        double H;
         double tmp = 0.0;
+        vector<groupRank> vec;
+        string group;
+        int count;
+        double sum;
                 
         //merge all groups into a vector
         //rank function here
+        assignRank(vec);
+        
+        //populate counts and ranSums vectors
+        for (int i=0;i<N;i++) {
+            count = 0;
+            sum = 0;
+            //group = next group
+            for(int j;j<vec.size();j++) {
+                if (vec[j].group == group) {
+                    count++;
+                    sum = sum + vec[j].rank;
+                }
+            }
+            counts[i] = count;
+            rankSums[i] = sum;
+        }
         
         //test statistic
         for (int i=0;i<N;i++) { tmp = tmp + (pow(rankSums[i],2) / counts[i]); }
@@ -152,8 +181,6 @@ int KruskalWallisCommand::execute(){
         
         //p-value calculation
         
-        
-        
                return 0;
        }
        catch(exception& e) {
@@ -162,22 +189,40 @@ int KruskalWallisCommand::execute(){
        }
 }
 //**********************************************************************************************************************
-multimap<double,double> KruskalWallisCommand::getRank(vector<groupRank> vec) {
+void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
     try {
-        multimap<double,double> rankMap;
         double rank = 1;
-        double previous;
-        double tie = 0.0;
-        int tiecount = 0;
+        double numRanks, avgRank, j;
+        vector<groupRank>::iterator it, oldit;
+
+        sort (vec.begin(), vec.end(), comparevalue);
 
-        sort (vec.begin(), vec.end());
+        it = vec.begin();
+
+        while ( it != vec.end() ) {
+            j = rank;
+            oldit = it;
+            if (!equalvalue(*it, *(it+1))) {
+                (*it).rank = rank; 
+                rank = rank+1; 
+                it++; }
+            else {
+                while(equalrank(*it, *(it+1))) {
+                    j = j + (j+1);
+                    rank++;
+                    it++;
+                }
+                numRanks = double (distance(oldit, it));
+                avgRank = j / numRanks;
+                while(oldit != it) {
+                    (*oldit).rank = avgRank;
+                    oldit++;
+                }
+            }
 
-        for (int i=0;i<vec.size();i++) {
-            if (vec[i] != previous) { rankMap[rank] = vec[i]; }
-            else {tie = tie + rank; tiecount++;}
-            rank++;
-            previous = vec[i];
         }
+        
+
     }
     catch(exception& e) {
                m->errorOut(e, "KruskalWallisCommand", "getRank");