fixed clearcut version bug, added group count output to get.groups and remove.groups

[mothur.git] / helpcommand.cpp

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 4a97342c27f801ea7bb959f0c411ace6f33393dc..3c799b0903afdc58c20a244356b3ecd8f51cf972 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -9,12 +9,46 @@
 
 #include "helpcommand.h"
 
+//**********************************************************************************************************************
+vector<string> HelpCommand::getValidParameters(){      
+       try {
+               
+               vector<string> myArray; 
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HelpCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> HelpCommand::getRequiredParameters(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HelpCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> HelpCommand::getRequiredFiles(){        
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HelpCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
-HelpCommand::HelpCommand(string option){
+HelpCommand::HelpCommand(string option)  {
+       
+       validCommands = CommandFactory::getInstance();
        
-       if (option != "") { cout << "There are no valid parameters for the help() command." << endl;  } 
-       validCommands = new ValidCommands();
 }
 
 //**********************************************************************************************************************
@@ -24,14 +58,18 @@ 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;
+       try {
+               validCommands->printCommands(cout);
+               m->mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); m->mothurOutEndLine();
        
-       delete validCommands;
+               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");
        
-       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";
-       return 0;
+               return 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HelpCommand", "execute");
+               exit(1);
+       }
 }
 
 //**********************************************************************************************************************/