X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=a691509ab0ae00e5f19ae52a8bffe6801fc26a31;hb=601d30778afd12a8dcdd0e2825d54754a3980cf4;hp=02af6767b00b724459c054839b789798f4b295f7;hpb=d70a1c2d70c5a516e74880709e3b48cfc1ce0321;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 02af676..a691509 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -134,6 +134,9 @@
 #include "removeotulabelscommand.h"
 #include "makecontigscommand.h"
 #include "loadlogfilecommand.h"
+#include "sffmultiplecommand.h"
+#include "classifysharedcommand.h"
+#include "filtersharedcommand.h"
 
 /*******************************************************/
 
@@ -290,7 +293,11 @@ CommandFactory::CommandFactory(){
     commands["make.contigs"]        = "make.contigs";
     commands["load.logfile"]        = "load.logfile";
     commands["make.table"]          = "make.table";
+    commands["sff.multiple"]        = "sff.multiple";
 	commands["quit"]				= "MPIEnabled"; 
+    commands["classify.shared"]		= "classify.shared"; 
+    commands["filter.shared"]		= "filter.shared"; 
+    
 
 }
 /***********************************************************/
@@ -503,6 +510,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "remove.otulabels")      {	command = new RemoveOtuLabelsCommand(optionString);         }
         else if(commandName == "make.contigs")          {	command = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {	command = new LoadLogfileCommand(optionString);             }
+        else if(commandName == "sff.multiple")          {	command = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.shared")       {	command = new ClassifySharedCommand(optionString);          }
+        else if(commandName == "filter.shared")         {	command = new FilterSharedCommand(optionString);            }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -657,6 +667,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "remove.otulabels")      {	pipecommand = new RemoveOtuLabelsCommand(optionString);         }
         else if(commandName == "make.contigs")          {	pipecommand = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {	pipecommand = new LoadLogfileCommand(optionString);             }
+        else if(commandName == "sff.multiple")          {	pipecommand = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.shared")       {	pipecommand = new ClassifySharedCommand(optionString);          }
+        else if(commandName == "filter.shared")         {	pipecommand = new FilterSharedCommand(optionString);            }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -797,6 +810,9 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "remove.otulabels")      {	shellcommand = new RemoveOtuLabelsCommand();        }
         else if(commandName == "make.contigs")          {	shellcommand = new MakeContigsCommand();            }
         else if(commandName == "load.logfile")          {	shellcommand = new LoadLogfileCommand();            }
+        else if(commandName == "sff.multiple")          {	shellcommand = new SffMultipleCommand();            }
+        else if(commandName == "classify.shared")       {	shellcommand = new ClassifySharedCommand();         }
+        else if(commandName == "filter.shared")         {	shellcommand = new FilterSharedCommand();           }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;