added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / helpcommand.cpp

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 0acce707e01e6567f9111bd58f83910aa90eba92..948c31760a6ace11e2eba806c46d44e9f89f6719 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -12,12 +12,9 @@
 //**********************************************************************************************************************
 
 HelpCommand::HelpCommand(string option){
-       globaldata = GlobalData::getInstance();
        
-       if (option != "") { cout << "There are no valid parameters for the help() command." << endl;  }
-       
-       validCommands = new ValidCommands();
-       }
+       validCommands = CommandFactory::getInstance();
+}
 
 //**********************************************************************************************************************
 
@@ -28,11 +25,9 @@ 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;
-       
-       delete validCommands;
+       mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); mothurOutEndLine();
        
-       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://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.\n");
        return 0;
 }