changed random forest output filename

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 407b67473566d880e951e87dabb35982ec367885..6ceabbfc6eee41a10f70ef8391fc3a12e202696f 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -146,6 +146,8 @@
 #include "makelookupcommand.h"
 #include "renameseqscommand.h"
 #include "makelefsecommand.h"
+#include "lefsecommand.h"
+#include "kruskalwalliscommand.h"
 
 /*******************************************************/
 
@@ -310,11 +312,13 @@ CommandFactory::CommandFactory(){
     commands["get.dists"]           = "get.dists";
     commands["remove.dists"]        = "remove.dists";
     commands["merge.taxsummary"]    = "merge.taxsummary";
-    commands["get.metacommunity"]   = "get.metacommunity";
+    commands["get.communitytype"]   = "get.communitytype";
     commands["sparcc"]              = "sparcc";
     commands["make.lookup"]         = "make.lookup";
     commands["rename.seqs"]         = "rename.seqs";
     commands["make.lefse"]          = "make.lefse";
+    commands["lefse"]               = "lefse";
+    commands["kruskal.wallis"]      = "kruskal.wallis";
     
 
 }
@@ -535,11 +539,13 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "get.dists")             {      command = new GetDistsCommand(optionString);                }
         else if(commandName == "remove.dists")          {      command = new RemoveDistsCommand(optionString);             }
         else if(commandName == "merge.taxsummary")      {      command = new MergeTaxSummaryCommand(optionString);         }
-        else if(commandName == "get.metacommunity")     {      command = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "get.communitytype")     {      command = new GetMetaCommunityCommand(optionString);        }
         else if(commandName == "sparcc")                {      command = new SparccCommand(optionString);                  }
         else if(commandName == "make.lookup")                  {       command = new MakeLookupCommand(optionString);                          }
         else if(commandName == "rename.seqs")                  {       command = new RenameSeqsCommand(optionString);                          }
         else if(commandName == "make.lefse")                   {       command = new MakeLefseCommand(optionString);                           }
+        else if(commandName == "lefse")                 {      command = new LefseCommand(optionString);                   }
+        else if(commandName == "kruskal.wallis")        {      command = new KruskalWallisCommand(optionString);           }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -701,11 +707,13 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "get.dists")             {      pipecommand = new GetDistsCommand(optionString);                }
         else if(commandName == "remove.dists")          {      pipecommand = new RemoveDistsCommand(optionString);             }
         else if(commandName == "merge.taxsummary")      {      pipecommand = new MergeTaxSummaryCommand(optionString);         }
-        else if(commandName == "get.metacommunity")     {      pipecommand = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "get.communitytype")     {      pipecommand = new GetMetaCommunityCommand(optionString);        }
         else if(commandName == "sparcc")                {      pipecommand = new SparccCommand(optionString);                  }
         else if(commandName == "make.lookup")                  {       pipecommand = new MakeLookupCommand(optionString);                              }
         else if(commandName == "rename.seqs")                  {       pipecommand = new RenameSeqsCommand(optionString);                              }
         else if(commandName == "make.lefse")                   {       pipecommand = new MakeLefseCommand(optionString);                               }
+        else if(commandName == "lefse")                 {      pipecommand = new LefseCommand(optionString);                   }
+        else if(commandName == "kruskal.wallis")        {      pipecommand = new KruskalWallisCommand(optionString);           }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -853,11 +861,13 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "get.dists")             {      shellcommand = new GetDistsCommand();               }
         else if(commandName == "remove.dists")          {      shellcommand = new RemoveDistsCommand();            }
         else if(commandName == "merge.taxsummary")      {      shellcommand = new MergeTaxSummaryCommand();        }
-        else if(commandName == "get.metacommunity")     {      shellcommand = new GetMetaCommunityCommand();       }
+        else if(commandName == "get.communitytype")     {      shellcommand = new GetMetaCommunityCommand();       }
         else if(commandName == "sparcc")                {      shellcommand = new SparccCommand();                 }
         else if(commandName == "make.lookup")                  {       shellcommand = new MakeLookupCommand();                         }
         else if(commandName == "rename.seqs")                  {       shellcommand = new RenameSeqsCommand();                         }
         else if(commandName == "make.lefse")                   {       shellcommand = new MakeLefseCommand();                          }
+        else if(commandName == "lefse")                 {      shellcommand = new LefseCommand();                  }
+        else if(commandName == "kruskal.wallis")        {      shellcommand = new KruskalWallisCommand();          }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;