X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.cpp;h=47136938a19e6c5d4b8dd2b8110849249ac50b06;hb=e98d56be8369a799e61a411bc13d3bd1fa3451e5;hp=ec4d35ceef2d37172d21d4d40a2ca6cfb9737404;hpb=013bc4d9503742c7e8661373b3a65621a5ad2212;p=mothur.git

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index ec4d35c..4713693 100644
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -182,14 +182,14 @@ HClusterCommand::HClusterCommand(string option)  {
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
 			hard = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0)); 
 			
 			method = validParameter.validFile(parameters, "method", false);
@@ -260,7 +260,7 @@ int HClusterCommand::execute(){
 				sabundFile.close();
 				rabundFile.close();
 				listFile.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 				return 0;  
 			}
 			
@@ -276,7 +276,7 @@ int HClusterCommand::execute(){
 			sabundFile.close();
 			rabundFile.close();
 			listFile.close();
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 			return 0;  
 		}
 
@@ -306,7 +306,7 @@ int HClusterCommand::execute(){
 				sabundFile.close();
 				rabundFile.close();
 				listFile.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 				return 0;  
 		}
 
@@ -326,7 +326,7 @@ int HClusterCommand::execute(){
 				sabundFile.close();
 				rabundFile.close();
 				listFile.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 				return 0;  
 			}
 
@@ -340,7 +340,7 @@ int HClusterCommand::execute(){
 						sabundFile.close();
 						rabundFile.close();
 						listFile.close();
-						for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+						for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 						return 0;  
 					}
 
@@ -373,7 +373,7 @@ int HClusterCommand::execute(){
 			sabundFile.close();
 			rabundFile.close();
 			listFile.close();
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 			return 0;  
 		}
 					
@@ -390,7 +390,7 @@ int HClusterCommand::execute(){
 		delete cluster;
 		
 		if (m->control_pressed) {  
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 			return 0;  
 		}