X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=helpcommand.cpp;h=ba4f53d942b899d4dc02d65c8acc68a63fdd45f7;hb=952a85d59a12e664f5efa6d01681be189e4fff9c;hp=0acce707e01e6567f9111bd58f83910aa90eba92;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 0acce70..ba4f53d 100644
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -12,12 +12,12 @@
 //**********************************************************************************************************************
 
 HelpCommand::HelpCommand(string option){
-	globaldata = GlobalData::getInstance();
+
 	
-	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 ValidCommands();
-	}
+	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://www.mothur.org/wiki, or contact Pat Schloss at pschloss@umich.edu.\n");
 	return 0;
 }