added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs parameters to sffinfo to allow...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 02af6767b00b724459c054839b789798f4b295f7..8653643a0e5f89058f95842bfdb134b711ab4de5 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -134,6 +134,7 @@
 #include "removeotulabelscommand.h"
 #include "makecontigscommand.h"
 #include "loadlogfilecommand.h"
+#include "sffmultiplecommand.h"
 
 /*******************************************************/
 
@@ -290,6 +291,7 @@ 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"; 
 
 }
@@ -503,6 +505,7 @@ 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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -657,6 +660,7 @@ 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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -797,6 +801,7 @@ 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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;