X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.cpp;h=2117daff4f2558e26bcf0008666f87bee0180f4d;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=3f9378fbdb4650078cf27091326c0dc5e87c993a;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 3f9378f..2117daf 100644
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -71,6 +71,7 @@ BinSeqCommand::BinSeqCommand(string option) {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -137,6 +138,7 @@ BinSeqCommand::BinSeqCommand(string option) {
 				else { 	m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (fastafile == "not open") { abort = true; }	
+			else { m->setFastaFile(fastafile); }
 			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not found") { 			
@@ -145,6 +147,7 @@ BinSeqCommand::BinSeqCommand(string option) {
 				else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (listfile == "not open") { listfile = ""; abort = true; }	
+			else { m->setListFile(listfile); }
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -164,12 +167,19 @@ 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); }
 
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
 			else if (groupfile == "not found") { groupfile = ""; }
+			else { m->setGroupFile(groupfile); }
+			
+			if (namesfile == ""){
+				vector<string> files; files.push_back(fastafile); 
+				parser.getNameFile(files);
+			}
 			
 		}
 	}
@@ -216,12 +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());
@@ -234,7 +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());
@@ -249,7 +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;
@@ -270,7 +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;  
 		}
@@ -279,11 +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; }	
-		
-		delete input;  
-		delete fasta; 
-		if (groupfile != "") {  delete groupMap;   } 
+		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();