added modify names parameter to set.dir

[mothur.git] / kruskalwalliscommand.cpp

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
index dd5eb09cbd3b54fb439d277cbd166f01dc726f84..bf4fafa950f2f180227f61ab41e1377008927c82 100644 (file)
--- 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 = "";          }
@@ -127,13 +143,16 @@ int KruskalWallisCommand::execute(){
         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");
+        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);
@@ -240,4 +259,5 @@ void KruskalWallisCommand::assignValue(vector<groupRank> &vec) {
 }
 //**********************************************************************************************************************
 //**********************************************************************************************************************
-//**********************************************************************************************************************
\ No newline at end of file
+//**********************************************************************************************************************
+