X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removerarecommand.cpp;h=24b616560de3bed794d423f4cb7a3544f0d48f5f;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=c320fa4d8854f003486bc71c8e6b0806ec7ae0e3;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index c320fa4..24b6165 100644
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -220,7 +220,7 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
 			
 			string temp = validParameter.validFile(parameters, "nseqs", false);	 
 			if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
-			else { convert(temp, nseqs); }
+			else { m->mothurConvert(temp, nseqs); }
 			
 			temp = validParameter.validFile(parameters, "bygroup", false);	 if (temp == "not found") { temp = "f"; }
 			byGroup = m->isTrue(temp);
@@ -251,7 +251,7 @@ int RemoveRareCommand::execute(){
 		if (listfile != "")			{		processList();		}
 		if (sharedfile != "")		{		processShared();	}
 		
-		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();
@@ -353,7 +353,8 @@ int RemoveRareCommand::processList(){
 		if (groupfile != "") { 
 			groupMap = new GroupMap(groupfile); groupMap->readMap(); 
 			SharedUtil util;
-			util.setGroups(Groups, groupMap->namesOfGroups);
+			vector<string> namesGroups = groupMap->getNamesOfGroups();
+			util.setGroups(Groups, namesGroups);
 			m->openOutputFile(outputGroupFileName, outGroup);
 		}
 		
@@ -365,7 +366,7 @@ int RemoveRareCommand::processList(){
 			
 			//for each bin
 			for (int i = 0; i < list->getNumBins(); i++) {
-				if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); remove(outputGroupFileName.c_str()); } out.close();  remove(outputFileName.c_str());  return 0; }
+				if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close();  m->mothurRemove(outputFileName);  return 0; }
 				
 				//parse out names that are in accnos file
 				string binnames = list->get(i);
@@ -624,7 +625,7 @@ int RemoveRareCommand::processRabund(){
 //**********************************************************************************************************************
 int RemoveRareCommand::processShared(){
 	try {
-		m->Groups = Groups;
+		m->setGroups(Groups);
 		
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }