added phylo.diversity command. added hard parameter to cluster, hcluster and read...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 32d42113d60a997b2404053bf0de39c68a28c71a..30b76f813f6710ff9c2cda0819305ca8837f7bf5 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -72,6 +72,7 @@
 #include "chimerapintailcommand.h"
 #include "chimerabellerophoncommand.h"
 #include "setlogfilecommand.h"
+#include "phylodiversitycommand.h"
 
 /*******************************************************/
 
@@ -151,6 +152,7 @@ CommandFactory::CommandFactory(){
        commands["parse.list"]                  = "parse.list";
        commands["parse.sff"]                   = "parse.sff";
        commands["set.logfile"]                 = "set.logfile";
+       commands["phylo.diversity"]             = "phylo.diversity";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -267,6 +269,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
                else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
                else if(commandName == "parse.sff")                             {       command = new ParseSFFCommand(optionString);                            }
+               else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;