X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listseqscommand.cpp;h=a8a9d2b5a6cff6da2ab8e86e22af19782f5ce0bf;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=1488cdadac766b243252e87053a0132975961884;hpb=4ad32478c7b1bbb464c839a6e133f5b517a3efec;p=mothur.git

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 1488cda..a8a9d2b 100644
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -26,8 +26,7 @@ vector<string> ListSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ListSeqsCommand::ListSeqsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["accnos"] = tempOutNames;
 	}
@@ -63,10 +62,10 @@ vector<string> ListSeqsCommand::getRequiredFiles(){
 
 ListSeqsCommand::ListSeqsCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -206,7 +205,7 @@ void ListSeqsCommand::help(){
 int ListSeqsCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//read functions fill names vector
 		if (fastafile != "")		{	inputFileName = fastafile;	readFasta();	}
@@ -227,6 +226,7 @@ int ListSeqsCommand::execute(){
 
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
+		outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
 		
 		//output to .accnos file
 		for (int i = 0; i < names.size(); i++) {
@@ -238,12 +238,21 @@ int ListSeqsCommand::execute(){
 		out.close();
 		
 		if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0; }
-
+		
+		m->setAccnosFile(outputFileName);
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(outputFileName); m->mothurOutEndLine();	outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
+		m->mothurOut(outputFileName); m->mothurOutEndLine();	
 		m->mothurOutEndLine();
 		
+		//set accnos file as new current accnosfile
+		string current = "";
+		itTypes = outputTypes.find("accnos");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+		}
+		
 		return 0;		
 	}
 
@@ -260,7 +269,7 @@ int ListSeqsCommand::readFasta(){
 		ifstream in;
 		m->openInputFile(fastafile, in);
 		string name;
-	
+		
 		while(!in.eof()){
 			
 			if (m->control_pressed) { in.close(); return 0; }
@@ -445,6 +454,7 @@ int ListSeqsCommand::readTax(){
 			names.push_back(firstCol);
 			
 			m->gobble(in);
+			
 		}
 		in.close();