added logfile feature

[mothur.git] / commandoptionparser.cpp

diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
index e4db11d1993f3ee257b36b010fb22944abc3b1cd..f013a25361366bfecbecdccf0dd1d00c7805d16e 100644 (file)
--- a/commandoptionparser.cpp
+++ b/commandoptionparser.cpp
@@ -25,21 +25,16 @@ CommandOptionParser::CommandOptionParser(string input){
                        commandString = input.substr(0, openParen);   //commandString contains everything before "("
                        optionString = input.substr((openParen+1), (closeParen-openParen-1)); //optionString contains everything between "(" and ")".
                }
-               else if (openParen == -1) { cout << "You are missing (" << endl; }
-               else if (closeParen == -1) { cout << "You are missing )" << endl; }
+               else if (openParen == -1) { mothurOut("You are missing ("); mothurOutEndLine(); }
+               else if (closeParen == -1) { mothurOut("You are missing )"); mothurOutEndLine(); }
                                        
                //GlobalData* globaldata = GlobalData::getInstance();
                //globaldata->parseGlobalData(commandString, optionString);                     //parser to separate and check options
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the CommandOptionParser class Function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "CommandOptionParser", "CommandOptionParser");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the CommandOptionParser class function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
 }
 
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