rarefaction.shared() fixed bug

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 224a4cc7761fe145da05c48297f36a46d29fe09c..ed6aebe7cadcf302c180a553ca5f586486371874 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -8,15 +8,11 @@
  */
 
 #include "command.hpp"
-#include "readdistphylipfilecommand.h"
-#include "readdistcolumnfilecommand.h"
-#include "readlistfilecommand.h"
-#include "readrabundfilecommand.h"
-#include "readsabundfilecommand.h"
-#include "readsharedfilecommand.h"
+#include "readdistcommand.h"
+#include "readtreecommand.h"
+#include "readotucommand.h"
 #include "clustercommand.h"
 #include "parselistcommand.h"
-#include "sharedcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
 #include "rarefactcommand.h"
@@ -27,6 +23,7 @@
 #include "quitcommand.h"
 #include "helpcommand.h"
 #include "commandfactory.hpp"
+#include "deconvolutecommand.h"
 #include <exception>
 
 
@@ -52,23 +49,19 @@ Command* CommandFactory::getCommand(string commandName){
        try {
                delete command;   //delete the old command
 
-                        if(commandName == "read.phylip")                       {       command = new ReadDistPhylipFileCommand();      }
-               else if(commandName == "read.column")                   {       command = new ReadDistColumnFileCommand();      }
-               else if(commandName == "read.list")                             {       command = new ReadListFileCommand();    }
-               else if(commandName == "read.rabund")                   {       command = new ReadRAbundFileCommand();  }
-               else if(commandName == "read.sabund")                   {       command = new ReadSAbundFileCommand();  }
-               else if(commandName == "read.shared")                   {       command = new ReadSharedFileCommand();  }
+                        if(commandName == "read.dist")                         {       command = new ReadDistCommand();                }
+               else if(commandName == "read.otu")                              {       command = new ReadOtuCommand();                 }
+               //else if(commandName == "read.tree")                           {       command = new ReadTreeCommand();                }
                else if(commandName == "cluster")                               {       command = new ClusterCommand();                 }
+               else if(commandName == "deconvolute")                   {       command = new DeconvoluteCommand();             }
                else if(commandName == "help")                                  {       command = new HelpCommand();                    }
                else if(commandName == "quit")                                  {       command = new QuitCommand();                    }
                else if(commandName == "collect.single")                {       command = new CollectCommand();                 }
-               else if(commandName == "shared")                                {       command = new SharedCommand();                  }
                else if(commandName == "collect.shared")                {       command = new CollectSharedCommand();   }
                else if(commandName == "rarefaction.single")    {       command = new RareFactCommand();                }
                else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand();  }
                else if(commandName == "summary.single")                {       command = new SummaryCommand();                 }
                else if(commandName == "summary.shared")                {       command = new SummarySharedCommand();   }
-               else if(commandName == "parselist")                             {       command = new ParseListCommand();               }
                else                                                                                    {       command = new NoCommand();                              }
 
                return command;