X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=4e61a58d9e5cb4bc640c544797c87a363580575e;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=9459294fa49945a00b270c1d98529de0a93c008d;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 9459294..4e61a58 100644
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -45,6 +45,27 @@ string ParseListCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string ParseListCommand::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 == "list") {  outputFileName =  "list"; }
+            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, "ParseListCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 ParseListCommand::ParseListCommand(){	
 	try {
@@ -175,11 +196,12 @@ int ParseListCommand::execute(){
 		//fill filehandles with neccessary ofstreams
 		int i;
 		ofstream* temp;
-		for (i=0; i<groupMap->namesOfGroups.size(); i++) {
+		vector<string> gGroups = groupMap->getNamesOfGroups();
+		for (i=0; i<gGroups.size(); i++) {
 			temp = new ofstream;
-			filehandles[groupMap->namesOfGroups[i]] = temp;
+			filehandles[gGroups[i]] = temp;
 			
-			string filename = fileroot +  groupMap->namesOfGroups[i] + ".list";
+			string filename = fileroot +  gGroups[i] + "." + getOutputFileNameTag("list");
 			outputNames.push_back(filename); outputTypes["list"].push_back(filename);
 			m->openOutputFile(filename, *temp);
 		}
@@ -194,7 +216,8 @@ int ParseListCommand::execute(){
 		
 		if (m->control_pressed) { 
 			delete input; delete list; delete groupMap;
-			for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
+			vector<string> gGroups = groupMap->getNamesOfGroups();
+			for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
 			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 			return 0;
 		}
@@ -203,7 +226,7 @@ int ParseListCommand::execute(){
 		
 			if (m->control_pressed) { 
 				delete input; delete list; delete groupMap;
-				for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
+				for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
 				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 				return 0;
 			}
@@ -241,10 +264,10 @@ int ParseListCommand::execute(){
 		}
 		
 		if (m->control_pressed) { 
-				delete input; delete groupMap;
-				for (i=0; i<groupMap->namesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
-				return 0;
+			delete input; delete groupMap;
+			for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+			return 0;
 		}
 		
 		//output error messages about any remaining user labels
@@ -262,10 +285,10 @@ int ParseListCommand::execute(){
 		}
 		
 		if (m->control_pressed) { 
-				delete input; delete groupMap;
-				for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
-				return 0;
+			delete input; delete groupMap;
+			for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+			return 0;
 		}
 		
 		//run last label if you need to