added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 9adf6791505060d7379fbfc387e1ce6f5d9f5afd..5f07abb59e03e161bd46bc60065eb15e37107a06 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -57,6 +57,7 @@
 #include "secondarystructurecommand.h"
 #include "getsharedotucommand.h"
 #include "getlistcountcommand.h"
+#include "hclustercommand.h"
 
 /***********************************************************/
 
@@ -113,6 +114,8 @@ CommandFactory::CommandFactory(){
        commands["get.sharedotu"]               = "get.sharedotu";
        commands["get.listcount"]               = "get.listcount";
        commands["quit"]                                = "quit"; 
+       
+       commands["hcluster"]                    = "hcluster"; 
 
 }
 /***********************************************************/
@@ -177,6 +180,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                  }
                else if(commandName == "get.sharedotu")                 {       command = new GetSharedOTUCommand(optionString);                }
                else if(commandName == "get.listcount")                 {       command = new GetListCountCommand(optionString);                }
+               
+               else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                    }
                else                                                                                    {       command = new NoCommand(optionString);                                  }
 
                return command;