deleted read.shared command and added its functionality to read.otu.

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0c1b3e075ee8ade15e0ea619463df962e9eac846..a5ec5f12c48059089496af3a39d26b0fedb12f52 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -10,12 +10,14 @@
 #include "command.hpp"
 #include "readdistcommand.h"
 #include "readtreecommand.h"
-#include "readsharedcommand.h"
 #include "readotucommand.h"
 #include "clustercommand.h"
 #include "parselistcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
+#include "getgroupcommand.h"
+#include "getlabelcommand.h"
+#include "getlinecommand.h"
 #include "rarefactcommand.h"
 #include "summarycommand.h"
 #include "summarysharedcommand.h"
@@ -28,7 +30,7 @@
 #include "parsimonycommand.h"
 #include "unifracunweightedcommand.h"
 #include "unifracweightedcommand.h"
-#include <exception>
+#include "mothur.h"
 
 
 /***********************************************************/
@@ -56,7 +58,6 @@ Command* CommandFactory::getCommand(string commandName){
                         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();                       }
@@ -70,8 +71,11 @@ Command* CommandFactory::getCommand(string commandName){
                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 if(commandName == "get.group")             {   command = new GetgroupCommand();        }
+               else if(commandName == "get.label")             {   command = new GetlabelCommand();        }
+               else if(commandName == "get.line")              {   command = new GetlineCommand();         }
                else                                                                                    {       command = new NoCommand();                                      }
-                       
+
                return command;
        }
        catch(exception& e) {