//**********************************************************************************************************************
ListSeqsCommand::ListSeqsCommand(){
try {
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["accnos"] = tempOutNames;
}
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
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(); }
if (m->control_pressed) { in.close(); return 0; }
- in >> name; //read from first column
+ in >> name; m->gobble(in); //read from first column
in >> group; //read from second column
names.push_back(name);