made sorting optional but sort by default, in case the user wants to see the heatmap...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 840eaaccc82c392de096729a5db32d7c72cdf08a..56fd56b348bdb497cdb04b01d01f4c3a87901a61 100644 (file)
--- 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 +29,10 @@
 #include "parsimonycommand.h"
 #include "unifracunweightedcommand.h"
 #include "unifracweightedcommand.h"
-#include <exception>
+#include "libshuffcommand.h"
+#include "heatmapcommand.h"
+#include "mothur.h"
+#include "nocommands.h"
 
 
 /***********************************************************/
@@ -40,7 +41,6 @@
 CommandFactory::CommandFactory(){
        command = new NoCommand();
 }
-
 /***********************************************************/
 
 /***********************************************************/
@@ -59,7 +59,6 @@ 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 +72,11 @@ 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 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 if(commandName == "heatmap")                               {   command = new HeatMapCommand();                             }
                else                                                                                    {       command = new NoCommand();                                      }
 
                return command;