cleaned up code2

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index f886c2369a87d757532b68456af89753f72bb9c6..5f33f3a1fbab70aad5764b20f4e1d8633c8a865b 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -47,7 +47,26 @@ string GetRAbundCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string GetRAbundCommand::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 == "rabund")            {   outputFileName = "rabund";  }
+            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, "GetRAbundCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 GetRAbundCommand::GetRAbundCommand(){  
        try {
@@ -116,12 +135,12 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { listfile = ""; abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else {  format = "list"; inputfile = listfile; }
+                       else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
                        else if (sabundfile == "not found") { sabundfile = ""; }
-                       else {  format = "sabund"; inputfile = sabundfile; }
+                       else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
                        
                        
                        //check for optional parameter and set defaults
@@ -173,7 +192,7 @@ int GetRAbundCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "rabund";
+               filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("rabund");
                m->openOutputFile(filename, out);
                
                input = new InputData(inputfile, format);
@@ -184,14 +203,14 @@ int GetRAbundCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) {  outputTypes.clear();  out.close(); remove(filename.c_str()); delete rabund; delete input; return 0; }
+               if (m->control_pressed) {  outputTypes.clear();  out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; }
                
                while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
                        if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
                                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
                                        
                                        if(sorted)      {   rabund->print(out);                         }
                                        else            {       rabund->nonSortedPrint(out);    }
@@ -208,7 +227,7 @@ int GetRAbundCommand::execute(){
                                        
                                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
                                        
                                        if(sorted)      {   rabund->print(out);                         }
                                        else            {       rabund->nonSortedPrint(out);    }
@@ -246,7 +265,7 @@ int GetRAbundCommand::execute(){
                        
                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                       if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0; }
                        
                        if(sorted)      {   rabund->print(out);                         }
                        else            {       rabund->nonSortedPrint(out);    }