X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.cpp;h=b7c4f1790b152371a6e302f3d56ae79fc60badf1;hb=16f9c4ab6f39769856b13e048eae2c8eaa413c02;hp=57afd85943e956b6bf4364d0b7c0b8bf27657cc3;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 57afd85..b7c4f17 100644
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -49,6 +49,26 @@ string GetListCountCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string GetListCountCommand::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 == "otu") {  outputFileName =  "otu"; }
+            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, "GetListCountCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 GetListCountCommand::GetListCountCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -149,7 +169,7 @@ int GetListCountCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+		if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 		
 		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
@@ -157,7 +177,7 @@ int GetListCountCommand::execute(){
 			
 				process(list);
 				
-				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 							
 				processedLabels.insert(list->getLabel());
 				userLabels.erase(list->getLabel());
@@ -171,7 +191,7 @@ int GetListCountCommand::execute(){
 				
 				process(list);
 				
-				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 
 													
 				processedLabels.insert(list->getLabel());
@@ -208,7 +228,7 @@ int GetListCountCommand::execute(){
 				
 			process(list);	
 			
-			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 			
 			delete list;  
 		}
@@ -234,7 +254,7 @@ void GetListCountCommand::process(ListVector* list) {
 	try {
 		string binnames;
 		if (outputDir == "") { outputDir += m->hasPath(listfile); }
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + "." +getOutputFileNameTag("otu");
 		m->openOutputFile(outputFileName, out);
 		outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);