created mothurOut class to handle logfiles

[mothur.git] / helpcommand.cpp

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 948c31760a6ace11e2eba806c46d44e9f89f6719..608ff3e275a1c7240975b506961d3a7ecf78fa79 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -11,7 +11,7 @@
 
 //**********************************************************************************************************************
 
-HelpCommand::HelpCommand(string option){
+HelpCommand::HelpCommand(string option)  {
        
        validCommands = CommandFactory::getInstance();
 }
@@ -25,9 +25,9 @@ HelpCommand::~HelpCommand(){}
 int HelpCommand::execute(){
 
        validCommands->printCommands(cout);
-       mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); mothurOutEndLine();
+       m->mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); m->mothurOutEndLine();
        
-       mothurOutEndLine(); mothurOut("For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.\n");
+       m->mothurOutEndLine(); m->mothurOut("For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.\n");
        return 0;
 }