//**********************************************************************************************************************
AlignCheckCommand::AlignCheckCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["aligncheck"] = tempOutNames;
}
AlignCheckCommand::AlignCheckCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
haderror = 0;
//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 AlignCheckCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get secondary structure info.
readMap();