X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=e0d62dd5ddd7acd106d18af31de013f6fce9c462;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=5bd9fd75c474aeafdf632d8800b9c184916ccc83;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 5bd9fd7..e0d62dd 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -280,13 +280,13 @@ CollectCommand::CollectCommand(string option)  {
 
 			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, "abund", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, abund); 
+			m->mothurConvert(temp, abund); 
 			
 			temp = validParameter.validFile(parameters, "size", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, size); 
+			m->mothurConvert(temp, size); 
 		}
 		
 	}
@@ -307,7 +307,7 @@ int CollectCommand::execute(){
 	
 		for (int p = 0; p < inputFileNames.size(); p++) {
 			
-			if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}  m->Groups.clear();  return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}  m->clearGroups();  return 0; }
 			
 			if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
 			string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
@@ -413,10 +413,10 @@ int CollectCommand::execute(){
 			
 			if (m->control_pressed) {  
 				for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-				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(); 
 				delete input;  
 				delete order; 
-				m->Groups.clear();
+				m->clearGroups();
 				return 0;
 			}
 
@@ -425,10 +425,10 @@ int CollectCommand::execute(){
 			
 				if (m->control_pressed) { 
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					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(); 
 					delete input;  
 					delete order; 
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 				}
 
@@ -474,9 +474,9 @@ int CollectCommand::execute(){
 			
 			if (m->control_pressed) { 
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					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(); 
 					delete input;  
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 			}
 				
@@ -506,10 +506,10 @@ int CollectCommand::execute(){
 				
 				if (m->control_pressed) { 
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					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(); 
 					delete input;  
 					delete order;
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 				}
 				delete order;
@@ -520,7 +520,7 @@ int CollectCommand::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; }
 				
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -551,7 +551,7 @@ vector<string> CollectCommand::parseSharedFile(string filename) {
 		
 		//clears file before we start to write to it below
 		for (int i=0; i<lookup.size(); i++) {
-			remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+			m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 			filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 		}