Merge branch 'master' of https://github.com/mothur/mothur.git into development

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
new file mode 100644 (file)
index 0000000..dd5eb09
--- /dev/null
+++ b/kruskalwalliscommand.cpp
@@ -0,0 +1,243 @@
+/* 
+ * File:   kruskalwalliscommand.cpp
+ * Author: kiverson
+ *
+ * Created on June 26, 2012, 11:06 AM
+ */
+
+#include "kruskalwalliscommand.h"
+
+//**********************************************************************************************************************
+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);
+               
+               vector<string> myArray;
+               for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "KruskalWallisCommand", "setParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+string KruskalWallisCommand::getHelpString(){  
+       try {
+               string helpString = "";
+               helpString += "The kruskalwallis command parameter options are \n";
+        helpString += "Kruskal–Wallis one-way analysis of variance is a non-parametric method for testing whether samples originate from the same distribution.";
+               return helpString;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "KruskalWallisCommand", "getHelpString");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+string KruskalWallisCommand::getOutputFileNameTag(string type, string inputName=""){   
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "summary") {  outputFileName =  "cooccurence.summary"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "KruskalWallisCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+KruskalWallisCommand::KruskalWallisCommand(){  
+       try {
+               abort = true; calledHelp = true; 
+               setParameters();
+        vector<string> tempOutNames;
+               outputTypes["summary"] = tempOutNames;
+
+       }
+       catch(exception& e) {
+               m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+KruskalWallisCommand::KruskalWallisCommand(string option) {
+       try {
+               abort = false; calledHelp = false;   
+                               
+               //allow user to run help
+               if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+               
+               else {
+                       vector<string> myArray = setParameters();
+                       
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       map<string,string>::iterator it;
+                       
+                       ValidParameters validParameter;
+                       
+                       //check to make sure all parameters are valid for command
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+
+                       
+                       //if the user changes the input directory command factory will send this info to us in the output parameter 
+                       string inputDir = validParameter.validFile(parameters, "inputdir", false);              
+                       if (inputDir == "not found"){   inputDir = "";          }
+                       else {
+                               string path;
+                               it = parameters.find("shared");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["shared"] = inputDir + it->second;           }
+                               }
+                       }
+               
+            vector<string> tempOutNames;
+            outputTypes["summary"] = tempOutNames;
+
+
+               }
+
+       }
+       catch(exception& e) {
+               m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+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 = 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);
+        
+        //populate counts and ranSums vectors
+        for (int i=0;i<N;i++) {
+            count = 0;
+            sum = 0;
+            group = groups[i];
+            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]); }
+        
+        H = (12 / (N*(N+1))) * tmp - (3*(N+1));
+        
+        //ss = tmp - pow(accumulate(rankSums.begin(), rankSums.end(), 0), 2);
+        
+        //H = ss / ( (N * (N + 1))/12 );
+        
+        //correction for ties?
+        
+        //p-value calculation
+        
+               return 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "KruskalWallisCommand", "execute");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
+    try {
+        double rank = 1;
+        double numRanks, avgRank, j;
+        vector<groupRank>::iterator it, oldit;
+
+        sort (vec.begin(), vec.end(), comparevalue);
+
+        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++;
+                }
+            }
+
+        }
+        
+
+    }
+    catch(exception& e) {
+               m->errorOut(e, "KruskalWallisCommand", "getRank");
+               exit(1);
+       }
+    
+}
+//**********************************************************************************************************************
+void KruskalWallisCommand::assignValue(vector<groupRank> &vec) {
+    
+}
+//**********************************************************************************************************************
+//**********************************************************************************************************************
+//**********************************************************************************************************************
\ No newline at end of file

diff --git a/kruskalwalliscommand.h b/kruskalwalliscommand.h
new file mode 100644 (file)
index 0000000..4a1e189
--- /dev/null
+++ b/kruskalwalliscommand.h
@@ -0,0 +1,64 @@
+/* 
+ * File:   kruskalwalliscommand.h
+ * Author: kiverson
+ *
+ * Created on June 26, 2012, 11:07 AM
+ */
+
+#ifndef KRUSKALWALLISCOMMAND_H
+#define        KRUSKALWALLISCOMMAND_H
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedrabundvector.h"
+
+
+class KruskalWallisCommand : public Command {
+   
+public:
+           
+       KruskalWallisCommand(string);   
+       KruskalWallisCommand();
+       ~KruskalWallisCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "kruskalwallis";                       }
+       string getCommandCategory()             { return "Hypothesis Testing";  }
+       string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/kruskalwallis"; }
+       string getDescription()         { return "Non-parametric method for testing whether samples originate from the same distribution."; }
+    
+    struct groupRank {
+        string group;
+        double value;
+        double rank;        
+    };
+    
+    int execute(); 
+       void help() { m->mothurOut(getHelpString()); }
+    void assignRank(vector<groupRank>&);
+    void assignValue(vector<groupRank>&);
+    
+    
+private:
+    string outputDir, sharedfile;
+    bool abort;
+    set<string> labels;
+    vector<string> outputNames;
+    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; }
+    
+};
+
+#endif /* KRUSKALWALLISCOMMAND_H */
+