added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5eb4ff5df0eaf4999808925e658e61c1eedccf31..964847478ae6e9e42f7ebb7c8ef35b5f452ff3f5 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -134,9 +134,10 @@ CommandFactory::CommandFactory(){
        commands["phylotype"]                   = "phylotype";
        commands["mgcluster"]                   = "mgcluster";
        commands["pre.cluster"]                 = "pre.cluster";
-       commands["pca"]                                 = "pca";
+       commands["pcoa"]                                = "pcoa";
        commands["otu.hierarchy"]               = "otu.hierarchy";
        commands["set.dir"]                             = "set.dir";
+       commands["merge.files"]                 = "merge.files";
 }
 /***********************************************************/
 
@@ -217,7 +218,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                   }
                else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                   }
                else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                  }
-               else if(commandName == "pca")                                   {       command = new PCACommand(optionString);                                 }
+               else if(commandName == "pcoa")                                  {       command = new PCACommand(optionString);                                 }
                else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                }
                else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);        }
                else                                                                                    {       command = new NoCommand(optionString);                                  }