fixes while testing 1.33.0

[mothur.git] / getrelabundcommand.cpp

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 7c623fbfd8ced3cd88bff70b3579e893d6e6cfa0..791f5631a680fe17968eeec63762388c288ba162 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -12,12 +12,12 @@
 //**********************************************************************************************************************
 vector<string> GetRelAbundCommand::setParameters(){    
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "",false,false); parameters.push_back(pscale);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","relabund",false,true, true); parameters.push_back(pshared);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "","",false,false); parameters.push_back(pscale);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               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);          }
@@ -49,24 +49,19 @@ string GetRelAbundCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string GetRelAbundCommand::getOutputFileNameTag(string type, string inputName=""){     
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string GetRelAbundCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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 == "relabund")         {   outputFileName = "relabund" ;  }
-            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, "GetRelAbundCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "relabund")      {   pattern = "[filename],relabund";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetRelAbundCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 GetRelAbundCommand::GetRelAbundCommand(){      
@@ -174,7 +169,9 @@ int GetRelAbundCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("relabund");
+        map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+               string outputFileName = getOutputFileName("relabund", variables);
                ofstream out;
                m->openOutputFile(outputFileName, out);
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
@@ -195,7 +192,7 @@ int GetRelAbundCommand::execute(){
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
 
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
+                               if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); }
                                getRelAbundance(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -208,7 +205,7 @@ int GetRelAbundCommand::execute(){
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  
                                lookup = input->getSharedRAbundVectors(lastLabel);
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
+                               if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); }
                                getRelAbundance(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -249,7 +246,7 @@ int GetRelAbundCommand::execute(){
                        lookup = input->getSharedRAbundVectors(lastLabel);
                        
                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
+                       if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); }
                        getRelAbundance(lookup, out);
                        
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }