X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=64bdbb4ceebd18f5abeff63b26fbb4d4ac3dc924;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=717fec2fea1fc1ba23564fc683149e38d177496e;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 717fec2..64bdbb4 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -158,14 +158,14 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
 			else { 
 				m->splitAtDash(groups, Groups);
 			}
-			m->Groups = Groups;
+			m->setGroups(Groups);
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, freq); 
+			m->mothurConvert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, nIters); 
+			m->mothurConvert(temp, nIters); 
 			
 			temp = validParameter.validFile(parameters, "jumble", false);			if (temp == "not found") { temp = "T"; }
 			if (m->isTrue(temp)) { jumble = true; }
@@ -211,10 +211,10 @@ int RareFactSharedCommand::execute(){
 		string lastLabel = lookup[0]->getLabel();
 		
 		if (m->control_pressed) { 
-			m->Groups.clear(); 
+			m->clearGroups(); 
 			delete input;
 			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
 			return 0;
 		}
@@ -233,10 +233,10 @@ int RareFactSharedCommand::execute(){
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			if (m->control_pressed) { 
-				m->Groups.clear(); 
+				m->clearGroups(); 
 				delete input;
 				for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
 				for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
 				return 0;
 			}
@@ -278,10 +278,10 @@ int RareFactSharedCommand::execute(){
 		}
 		
 		if (m->control_pressed) { 
-			m->Groups.clear(); 
+			m->clearGroups(); 
 			delete input;
 			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
 			return 0;
 		}
 		
@@ -299,10 +299,10 @@ int RareFactSharedCommand::execute(){
 		}
 		
 		if (m->control_pressed) { 
-			m->Groups.clear(); 
+			m->clearGroups(); 
 			delete input; 
 			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
 			return 0;
 		}
 		
@@ -319,10 +319,10 @@ int RareFactSharedCommand::execute(){
 		}
 		
 		for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}	
-		m->Groups.clear(); 
+		m->clearGroups(); 
 		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; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();