X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitabundcommand.cpp;h=8131fa9195f6b8d939b27891605dd862d618964b;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=aa47940a030f968e02686b915d26e84c29584b8d;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index aa47940..8131fa9 100644
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -181,7 +181,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 			groups = validParameter.validFile(parameters, "groups", false);		
 			if (groups == "not found") { groups = ""; }
 			else if (groups == "all") { 
-				if (groupfile != "") {  Groups = groupMap->namesOfGroups;  } 
+				if (groupfile != "") {  Groups = groupMap->getNamesOfGroups();  } 
 				else {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";   }
 			}else { 
 				m->splitAtDash(groups, Groups);
@@ -213,10 +213,9 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 			accnos = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);				if (temp == "not found") { temp = "0"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 
 			if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
-
 		}
 
 	}
@@ -250,11 +249,11 @@ int SplitAbundCommand::execute(){
 			if (namefile != "") {  readNamesFile();		}
 			else				{ createNameMap(list);	}
 			
-			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 			
 			while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
-				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 				
 				if(allLines == 1 || labels.count(list->getLabel()) == 1){
 						
@@ -288,7 +287,7 @@ int SplitAbundCommand::execute(){
 				list = input->getListVector(); //get new list vector to process
 			}
 			
-			if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+			if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 			
 			//output error messages about any remaining user labels
 			set<string>::iterator it;
@@ -304,7 +303,7 @@ int SplitAbundCommand::execute(){
 
 			}
 			
-			if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+			if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 			
 			//run last label if you need to
 			if (needToRun == true)  {
@@ -319,7 +318,7 @@ int SplitAbundCommand::execute(){
 			
 			delete input;
 			
-			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;	}
 									
 		}else { //you are using the namefile to determine abundance
 			if (outputDir == "") { outputDir = m->hasPath(namefile); }