added read.shared, broke up globaldata a bit

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 49d197c40b9fe215f8067fa8d8a8f6ddb262f45c..0c1b3e075ee8ade15e0ea619463df962e9eac846 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -9,8 +9,9 @@
 
 #include "command.hpp"
 #include "readdistcommand.h"
+#include "readtreecommand.h"
+#include "readsharedcommand.h"
 #include "readotucommand.h"
-#include "readlistcommand.h"
 #include "clustercommand.h"
 #include "parselistcommand.h"
 #include "collectcommand.h"
@@ -24,6 +25,9 @@
 #include "helpcommand.h"
 #include "commandfactory.hpp"
 #include "deconvolutecommand.h"
+#include "parsimonycommand.h"
+#include "unifracunweightedcommand.h"
+#include "unifracweightedcommand.h"
 #include <exception>
 
 
@@ -49,21 +53,25 @@ Command* CommandFactory::getCommand(string commandName){
        try {
                delete command;   //delete the old command
 
-                        if(commandName == "read.dist")                         {       command = new ReadDistCommand();                }
-               else if(commandName == "read.otu")                              {       command = new ReadOtuCommand();                 }
-               else if(commandName == "read.list")                             {       command = new ReadListFileCommand();    }
-               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 == "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                                                                                    {       command = new NoCommand();                              }
-
+                        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 == "read.shared")                   {       command = new ReadSharedCommand();                      }
+               else if(commandName == "cluster")                               {       command = new ClusterCommand();                         }
+               else if(commandName == "deconvolute")                   {       command = new DeconvoluteCommand();                     }
+               else if(commandName == "parsimony")                             {       command = new ParsimonyCommand();                       }
+               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 == "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 == "unifrac.weighted")              {       command = new UnifracWeightedCommand();         }
+               else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand();       }
+               else                                                                                    {       command = new NoCommand();                                      }
+                       
                return command;
        }
        catch(exception& e) {
@@ -78,4 +86,3 @@ Command* CommandFactory::getCommand(string commandName){
 }
 /***********************************************************/
 
-/***********************************************************/
\ No newline at end of file