X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=kruskalwalliscommand.cpp;h=bf4fafa950f2f180227f61ab41e1377008927c82;hp=76aebe05e36b441e29c8632d585d5ba21a4f92a6;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=8e67e9de1b200106bea5a468ac02125954656499

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
index 76aebe0..bf4fafa 100644
--- a/kruskalwalliscommand.cpp
+++ b/kruskalwalliscommand.cpp
@@ -10,8 +10,10 @@
 //**********************************************************************************************************************
 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);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+        CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups);
+        CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);	
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -36,24 +38,19 @@ string KruskalWallisCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
-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);
-	}
+string KruskalWallisCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "summary") {  pattern = "[filename],cooccurence.summary"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "KruskalWallisCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 KruskalWallisCommand::KruskalWallisCommand(){	
@@ -91,8 +88,27 @@ KruskalWallisCommand::KruskalWallisCommand(string option) {
 			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
-
-			
+            
+            //get shared file
+			sharedfile = validParameter.validFile(parameters, "shared", true);
+			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
+			else if (sharedfile == "not found") { 
+				//if there is a current shared file, use it
+				sharedfile = m->getSharedFile(); 
+				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+			}else { m->setSharedFile(sharedfile); }
+            
+            //if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(sharedfile);		}
+                    
+            groups = validParameter.validFile(parameters, "groups", false);   
+            if (groups == "not found") { groups = "";   }
+            else { 
+            m->splitAtDash(groups, Groups); 
+            }   
+            m->setGroups(Groups);
+				
 			//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 = "";		}
@@ -124,17 +140,39 @@ 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;
+        map<string,string> variables;
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+		string outputFileName = getOutputFileName("summary",variables);
+        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 +180,7 @@ 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 +254,10 @@ void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
     
 }
 //**********************************************************************************************************************
-
+void KruskalWallisCommand::assignValue(vector<groupRank> &vec) {
+    
+}
+//**********************************************************************************************************************
 //**********************************************************************************************************************
 //**********************************************************************************************************************
-//**********************************************************************************************************************
\ No newline at end of file
+