added read.shared, broke up globaldata a bit

[mothur.git] / validcommands.cpp

diff --git a/validcommands.cpp b/validcommands.cpp
index 53ee7431b49fecc06002e5b9330259371bd35729..79b09d38dbad7325c8bbbff8e352a17d0ddaeaba 100644 (file)
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -17,6 +17,7 @@ ValidCommands::ValidCommands() {
                commands["read.dist"]                   = "read.dist"; 
                commands["read.otu"]                    = "read.otu";
                commands["read.tree"]                   = "read.tree"; 
+               commands["read.shared"]                 = "read.shared";
                commands["cluster"]                             = "cluster"; 
                commands["deconvolute"]                 = "deconvolute"; 
                commands["parsimony"]                   = "parsimony";
@@ -55,7 +56,11 @@ bool ValidCommands::isValidCommand(string command) {
                if ((commands.find(command)) != (commands.end())) {
                        return true;
                }else{
-                       cout << command << " is not a valid command in Mothur.  Valid commands are read.dist(), read.otu(), read.tree(), cluster(), deconvolute(), collect.single(), collect.shared(), rarefaction.single(), rarefaction.shared(), summary.single(), summary.shared(), parsimony(), unifrac.weighted(), unifrac.unweighted(), quit(), help()." << endl;
+                       cout << command << " is not a valid command in Mothur.  Valid commands are ";
+                       for (it = commands.begin(); it != commands.end(); it++) {
+                               cout << it->first << ", ";
+                       }
+                       cout << endl;
                        return false;
                }
                
@@ -71,3 +76,24 @@ bool ValidCommands::isValidCommand(string command) {
 }
 
 /***********************************************************************/
+void ValidCommands::printCommands(ostream& out) {
+       try {   
+               out << "Valid commands are ";
+               for (it = commands.begin(); it != commands.end(); it++) {
+                       out << it->first << ", ";
+               }
+               out << endl;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ValidCommands class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+
+
+