added logfile feature

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 7dd35fd673a7bc62e109a0095efe847d5b097588..db11f8c0dc890dff846787dee0fc48ea8930384a 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -159,14 +159,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                return command;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "CommandFactory", "getCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the CommandFactory class function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
 }
 
 /***********************************************************************/
@@ -177,21 +172,17 @@ bool CommandFactory::isValidCommand(string command) {
                if ((commands.find(command)) != (commands.end())) {
                        return true;
                }else{
-                       cout << command << " is not a valid command in Mothur.  Valid commands are ";
+                       mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
                        for (it = commands.begin(); it != commands.end(); it++) {
-                               cout << it->first << ", ";
+                               mothurOut(it->first + ", ");
                        }
-                       cout << endl;
+                       mothurOutEndLine();
                        return false;
                }
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the CommandFactory class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "CommandFactory", "isValidCommand");
                exit(1);
        }
 }
@@ -206,11 +197,7 @@ void CommandFactory::printCommands(ostream& out) {
                out << endl;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the CommandFactory class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "CommandFactory", "printCommands");
                exit(1);
        }
 }