X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=5f33f3a1fbab70aad5764b20f4e1d8633c8a865b;hb=c7e8c2d15bd7cedcfdf18675cb0ea1a0dcd0e3c0;hp=2f49a3b37181603f88065629ddc73f5194be49d9;hpb=10c8178dc5e3f96ef8e92a986f1eddd13e622173;p=mothur.git

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 2f49a3b..5f33f3a 100644
--- 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 {
@@ -69,6 +88,7 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
 		
 		//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();
@@ -115,12 +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
@@ -172,7 +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);
@@ -183,14 +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);	}
@@ -207,7 +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);	}
@@ -245,7 +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);	}