X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=4ae2eaa004f9df9cc75c12b63626ffa7fad71ea7;hb=46626aa16c99fcdf2e3c76a61b80a5d4b0c3b898;hp=820868416b7bfc9bebcc27c8f73c24c6ddb7bbb4;hpb=10c8178dc5e3f96ef8e92a986f1eddd13e622173;p=mothur.git

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 8208684..4ae2eaa 100644
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -67,6 +67,7 @@ GetSAbundCommand::GetSAbundCommand(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();
@@ -113,12 +114,12 @@ GetSAbundCommand::GetSAbundCommand(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); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
 			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
 			else if (rabundfile == "not found") { rabundfile = ""; }
-			else {  format = "rabund"; inputfile = rabundfile; }
+			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 			
 		
 						//check for optional parameter and set defaults
@@ -177,7 +178,7 @@ int GetSAbundCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input; return 0; }
+		if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input; return 0; }
 
 		
 		while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -187,7 +188,7 @@ int GetSAbundCommand::execute(){
 					
 					sabund->print(out);
 					
-				if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
+				if (m->control_pressed) { outputTypes.clear();  out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 
 					processedLabels.insert(sabund->getLabel());
 					userLabels.erase(sabund->getLabel());
@@ -202,7 +203,7 @@ int GetSAbundCommand::execute(){
 					m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 					sabund->print(out);
 					
-					if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
+					if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 
 					processedLabels.insert(sabund->getLabel());
 					userLabels.erase(sabund->getLabel());
@@ -240,7 +241,7 @@ int GetSAbundCommand::execute(){
 			sabund->print(out);
 			delete sabund;
 			
-			if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; return 0; }
 			
 		}