X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=9459294fa49945a00b270c1d98529de0a93c008d;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=c79eb63c31b576359f8b6bf270bea83ba25028d2;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index c79eb63..9459294 100644
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -66,6 +66,7 @@ ParseListCommand::ParseListCommand(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();
@@ -122,7 +123,7 @@ ParseListCommand::ParseListCommand(string option)  {
 					abort = true;
 						
 				}
-			}	
+			}else { m->setListFile(listfile); }	
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }	
@@ -136,6 +137,7 @@ ParseListCommand::ParseListCommand(string option)  {
 					if (error == 1) { abort = true; }
 				}else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();  abort = true; } 
 			}else {  
+				m->setGroupFile(groupfile);
 				groupMap = new GroupMap(groupfile);
 				
 				int error = groupMap->readMap();
@@ -193,7 +195,7 @@ 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 (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 			return 0;
 		}
 		
@@ -202,7 +204,7 @@ 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 (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 				return 0;
 			}
 			
@@ -241,7 +243,7 @@ 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++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 				return 0;
 		}
 		
@@ -262,7 +264,7 @@ 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++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 				return 0;
 		}
 		
@@ -287,7 +289,7 @@ int ParseListCommand::execute(){
 		delete input;
 		
 		if (m->control_pressed) { 
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 			return 0;
 		}