X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getotuscommand.cpp;h=4e8d3198c9b6c560d57ff579b26eb9985e452b35;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=d29773ca340cf1119f04c312f897a0e5f2d7d4e8;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index d29773c..4e8d319 100644
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -187,7 +187,9 @@ int GetOtusCommand::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> gNamesOfGroups = groupMap->getNamesOfGroups();
+		util->setGroups(Groups, gNamesOfGroups);
+		groupMap->setNamesOfGroups(gNamesOfGroups);
 		delete util;
 		
 		if (m->control_pressed) { delete groupMap; return 0; }
@@ -195,7 +197,7 @@ int GetOtusCommand::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();
@@ -258,7 +260,7 @@ int GetOtusCommand::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);
@@ -292,7 +294,7 @@ int GetOtusCommand::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;