//**********************************************************************************************************************
ConcensusCommand::ConcensusCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
outputTypes["nodepairs"] = tempOutNames;
ConcensusCommand::ConcensusCommand(string fileroot) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//initialize outputTypes
vector<string> tempOutNames;
int ConcensusCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
else {
numNodes = t[0]->getNumNodes();
numLeaves = t[0]->getNumLeaves();
outputFile = filename + ".cons.tre"; outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
m->openOutputFile(outputFile, out);
- consensusTree->printForBoot(out);
+ consensusTree->print(out, "boot");
out.close(); out2.close();