X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeotuscommand.cpp;h=25ed99eacbbd3c6dcbcad18daf5fef44ec13b746;hb=791f42d21a85f794529fd4c912dcc27d873c25e8;hp=6c8cf6a76561c151eead8d4ac151c286ba0283ad;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 6c8cf6a..25ed99e 100644
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -75,6 +75,7 @@ RemoveOtusCommand::RemoveOtusCommand(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();
@@ -133,7 +134,8 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
 			//check for required parameters
 			accnosfile = validParameter.validFile(parameters, "accnos", true);
 			if (accnosfile == "not open") { abort = true; }
-			else if (accnosfile == "not found") {  accnosfile = ""; }	
+			else if (accnosfile == "not found") {  accnosfile = ""; }
+			else { m->setAccnosFile(accnosfile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
@@ -141,7 +143,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
 				groupfile = m->getGroupFile(); 
 				if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setGroupFile(groupfile); }	
 			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
@@ -149,7 +151,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
 				listfile = m->getListFile(); 
 				if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setListFile(listfile); }	
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
@@ -185,7 +187,8 @@ int RemoveOtusCommand::execute(){
 		//make sure groups are valid
 		//takes care of user setting groupNames that are invalid or setting groups=all
 		SharedUtil* util = new SharedUtil();
-		util->setGroups(Groups, groupMap->namesOfGroups);
+		vector<string> allGroups = groupMap->getNamesOfGroups();
+		util->setGroups(Groups, allGroups);
 		delete util;
 		
 		if (m->control_pressed) { delete groupMap; return 0; }
@@ -193,7 +196,7 @@ int RemoveOtusCommand::execute(){
 		//read through the list file keeping any otus that contain any sequence from the groups selected
 		readListGroup();
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 		
 		if (outputNames.size() != 0) {
 			m->mothurOutEndLine();
@@ -256,7 +259,7 @@ int RemoveOtusCommand::readListGroup(){
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((list != NULL) && (userLabels.size() != 0)) {
 			
-			if (m->control_pressed) {  delete list; delete input; out.close();  outGroup.close(); remove(outputFileName.c_str());  remove(outputGroupFileName.c_str());return 0;  }
+			if (m->control_pressed) {  delete list; delete input; out.close();  outGroup.close(); m->mothurRemove(outputFileName);  m->mothurRemove(outputGroupFileName);return 0;  }
 			
 			if(labels.count(list->getLabel()) == 1){
 				processList(list, groupMap, out, outGroup, wroteSomething);
@@ -290,7 +293,7 @@ int RemoveOtusCommand::readListGroup(){
 		}
 		
 		
-		if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); remove(outputFileName.c_str());  remove(outputGroupFileName.c_str()); return 0;  }
+		if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName);  m->mothurRemove(outputGroupFileName); return 0;  }
 		
 		//output error messages about any remaining user labels
 		set<string>::iterator it;