X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=7670d412df334d2d656000cf07349aa404ffd21b;hb=66f474db0824eebab0cebd53992728a0e5c789ca;hp=e05f8dffa1cb5d1c13716152773793fc509ad96c;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index e05f8df..7670d41 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -10,7 +10,6 @@
 #include "command.hpp"
 #include "readdistcommand.h"
 #include "readtreecommand.h"
-#include "readsharedcommand.h"
 #include "readotucommand.h"
 #include "clustercommand.h"
 #include "parselistcommand.h"
@@ -23,7 +22,6 @@
 #include "summarycommand.h"
 #include "summarysharedcommand.h"
 #include "rarefactsharedcommand.h"
-#include "nocommand.h"
 #include "quitcommand.h"
 #include "helpcommand.h"
 #include "commandfactory.hpp"
@@ -31,7 +29,9 @@
 #include "parsimonycommand.h"
 #include "unifracunweightedcommand.h"
 #include "unifracweightedcommand.h"
+#include "libshuffcommand.h"
 #include "mothur.h"
+#include "nocommands.h"
 
 
 /***********************************************************/
@@ -40,7 +40,6 @@
 CommandFactory::CommandFactory(){
 	command = new NoCommand();
 }
-
 /***********************************************************/
 
 /***********************************************************/
@@ -59,7 +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();			}
@@ -73,9 +71,10 @@ 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 if(commandName == "get.group")             {   command = new GetgroupCommand();			}
+		else if(commandName == "get.label")             {   command = new GetlabelCommand();			}
+		else if(commandName == "get.line")              {   command = new GetlineCommand();				}
+		else if(commandName == "libshuff")              {   command = new LibShuffCommand();			}
 		else											{	command = new NoCommand();					}
 
 		return command;