if(option == "help") { help(); abort = true; }
else {
- if (option != "") { cout << "There are no valid parameters for the get.group command." << endl; abort = true; }
+ if (option != "") { mothurOut("There are no valid parameters for the get.group command."); mothurOutEndLine(); abort = true; }
- if ((globaldata->getSharedFile() == "")) { cout << "You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command." << endl; abort = true; }
+ if ((globaldata->getSharedFile() == "")) { mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); mothurOutEndLine(); abort = true; }
if (abort == false) {
//open shared file
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetgroupCommand class Function GetgroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "GetgroupCommand", "GetgroupCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetgroupCommand class function GetgroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
//**********************************************************************************************************************
void GetgroupCommand::help(){
try {
- cout << "The get.group command can only be executed after a successful read.otu command." << "\n";
- //cout << "The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the concensus command." << "\n";
- cout << "You may not use any parameters with the get.group command." << "\n";
- cout << "The get.group command should be in the following format: " << "\n";
- cout << "get.group()" << "\n";
- cout << "Example get.group()." << "\n";
+ mothurOut("The get.group command can only be executed after a successful read.otu command.\n");
+ //mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the concensus command.\n");
+ mothurOut("You may not use any parameters with the get.group command.\n");
+ mothurOut("The get.group command should be in the following format: \n");
+ mothurOut("get.group()\n");
+ mothurOut("Example get.group().\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetgroupCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "GetgroupCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetgroupCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
holdLabel = label;
//output first group
- cout << groupN << endl;
+ mothurOut(groupN); mothurOutEndLine();
out << groupN << '\t' << groupN << endl;
//get rest of line
count++;
//output next group
- cout << groupN << endl;
+ mothurOut(groupN); mothurOutEndLine();
out << groupN << '\t' << groupN << endl;
//fill vector.
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetgroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "GetgroupCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetgroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}