added modify names parameter to set.dir

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 193c53c4d610111cf369084f1a153400bfbe38e5..387ee10833323300a66a0e6d1161a64bff6fb9ee 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -141,6 +141,9 @@
 #include "getdistscommand.h"
 #include "removedistscommand.h"
 #include "mergetaxsummarycommand.h"
+#include "getmetacommunitycommand.h"
+#include "sparcccommand.h"
+#include "makelookupcommand.h"
 
 /*******************************************************/
 
@@ -305,6 +308,9 @@ CommandFactory::CommandFactory(){
     commands["get.dists"]           = "get.dists";
     commands["remove.dists"]        = "remove.dists";
     commands["merge.taxsummary"]    = "merge.taxsummary";
+    commands["get.metacommunity"]   = "get.metacommunity";
+    commands["sparcc"]              = "sparcc";
+    commands["make.lookup"]         = "make.lookup";
     
 
 }
@@ -525,6 +531,9 @@ 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 == "sparcc")                {      command = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")                  {       command = new MakeLookupCommand(optionString);                          }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -686,6 +695,9 @@ 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 == "sparcc")                {      pipecommand = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")                  {       pipecommand = new MakeLookupCommand(optionString);                              }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -833,6 +845,9 @@ 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 == "sparcc")                {      shellcommand = new SparccCommand();                 }
+        else if(commandName == "make.lookup")                  {       shellcommand = new MakeLookupCommand();                         }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;