added logfile feature

[mothur.git] / helpcommand.cpp

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 93def59137b8ecadb3e45b26ff3fac35bc976405..47fb72ad6e561f35b74e210c3a715561dc78a398 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -14,7 +14,7 @@
 HelpCommand::HelpCommand(string option){
 
        
-       if (option != "") { cout << "There are no valid parameters for the help() command." << endl;  }
+       if (option != "") { mothurOut("There are no valid parameters for the help() command."); mothurOutEndLine();  }
        
        validCommands = new CommandFactory();
 }
@@ -28,11 +28,11 @@ HelpCommand::~HelpCommand(){}
 int HelpCommand::execute(){
 
        validCommands->printCommands(cout);
-       cout << "For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'" << endl;
+       mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); mothurOutEndLine();
        
        delete validCommands;
        
-       cout << endl << "For further assistance please refer to the Mothur manual on our wiki at http://schloss.micro.umass.edu/mothur/, or contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+       mothurOutEndLine(); mothurOut("For further assistance please refer to the Mothur manual on our wiki at http://schloss.micro.umass.edu/mothur/, or contact Pat Schloss at pschloss@microbio.umass.edu.\n");
        return 0;
 }