added topdown parameter to pre.cluster. added more debugging output to bayesian...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index a691509ab0ae00e5f19ae52a8bffe6801fc26a31..c8421d29c513f65bfe8684fe10a09e8c439d7915 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -892,6 +892,41 @@ void CommandFactory::printCommands(ostream& out) {
        }
 }
 /***********************************************************************/
+void CommandFactory::printCommandsCategories(ostream& out) {
+    try {
+        map<string, string> commands = getListCommands();
+        map<string, string>::iterator it;
+
+        map<string, string> categories;
+        map<string, string>::iterator itCat;
+        //loop through each command outputting info
+        for (it = commands.begin(); it != commands.end(); it++) {
+    
+            Command* thisCommand = getCommand(it->first);
+    
+            //don't add hidden commands
+            if (thisCommand->getCommandCategory() != "Hidden") {
+                itCat = categories.find(thisCommand->getCommandCategory());
+                if (itCat == categories.end()) {
+                    categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
+                }else {
+                    categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
+                }
+            }
+        }
+        
+        for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
+            out << itCat->first << " commmands include: " << itCat->second << endl;
+        }
+
+    }
+       catch(exception& e) {
+               m->errorOut(e, "CommandFactory", "printCommandsCategories");
+               exit(1);
+       }
+}      
+
+/***********************************************************************/