X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.cpp;h=2117daff4f2558e26bcf0008666f87bee0180f4d;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=8e8ec2bc51362d8b8876d6e3cbb10ef9ff5e167e;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 8e8ec2b..2117daf 100644
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -167,7 +167,7 @@ BinSeqCommand::BinSeqCommand(string option) {
 			}
 			
 			namesfile = validParameter.validFile(parameters, "name", true);
-			if (namesfile == "not open") { abort = true; }	
+			if (namesfile == "not open") { namesfile = ""; abort = true; }	
 			else if (namesfile == "not found") { namesfile = ""; }
 			else {  m->setNameFile(namesfile); }
 
@@ -176,6 +176,11 @@ BinSeqCommand::BinSeqCommand(string option) {
 			else if (groupfile == "not found") { groupfile = ""; }
 			else { m->setGroupFile(groupfile); }
 			
+			if (namesfile == ""){
+				vector<string> files; files.push_back(fastafile); 
+				parser.getNameFile(files);
+			}
+			
 		}
 	}
 	catch(exception& e) {
@@ -221,12 +226,12 @@ int BinSeqCommand::execute(){
 				
 		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
-			if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
+			if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
 			
 			if(allLines == 1 || labels.count(list->getLabel()) == 1){
 				
 				error = process(list);	
-				if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
+				if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
 							
 				processedLabels.insert(list->getLabel());
 				userLabels.erase(list->getLabel());
@@ -239,7 +244,7 @@ int BinSeqCommand::execute(){
 				list = input->getListVector(lastLabel);
 				
 				error = process(list);	
-				if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
+				if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 													
 				processedLabels.insert(list->getLabel());
 				userLabels.erase(list->getLabel());
@@ -254,7 +259,7 @@ int BinSeqCommand::execute(){
 			list = input->getListVector();
 		}
 		
-		if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
+		if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
 
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
@@ -275,7 +280,7 @@ int BinSeqCommand::execute(){
 			list = input->getListVector(lastLabel);
 				
 			error = process(list);	
-			if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
+			if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 			
 			delete list;  
 		}
@@ -284,7 +289,7 @@ int BinSeqCommand::execute(){
 		delete fasta; 
 		if (groupfile != "") {  delete groupMap;   } 
 		
-		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();