added make.lefse command. fixed bug in make.contigs with trimming reverse barcodes...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index a0796a34fc243916081632e54a54233bef679a5f..407b67473566d880e951e87dabb35982ec367885 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -145,6 +145,7 @@
 #include "sparcccommand.h"
 #include "makelookupcommand.h"
 #include "renameseqscommand.h"
+#include "makelefsecommand.h"
 
 /*******************************************************/
 
@@ -313,6 +314,7 @@ CommandFactory::CommandFactory(){
     commands["sparcc"]              = "sparcc";
     commands["make.lookup"]         = "make.lookup";
     commands["rename.seqs"]         = "rename.seqs";
+    commands["make.lefse"]          = "make.lefse";
     
 
 }
@@ -537,6 +539,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "sparcc")                {      command = new SparccCommand(optionString);                  }
         else if(commandName == "make.lookup")                  {       command = new MakeLookupCommand(optionString);                          }
         else if(commandName == "rename.seqs")                  {       command = new RenameSeqsCommand(optionString);                          }
+        else if(commandName == "make.lefse")                   {       command = new MakeLefseCommand(optionString);                           }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -702,6 +705,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "sparcc")                {      pipecommand = new SparccCommand(optionString);                  }
         else if(commandName == "make.lookup")                  {       pipecommand = new MakeLookupCommand(optionString);                              }
         else if(commandName == "rename.seqs")                  {       pipecommand = new RenameSeqsCommand(optionString);                              }
+        else if(commandName == "make.lefse")                   {       pipecommand = new MakeLefseCommand(optionString);                               }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -853,6 +857,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "sparcc")                {      shellcommand = new SparccCommand();                 }
         else if(commandName == "make.lookup")                  {       shellcommand = new MakeLookupCommand();                         }
         else if(commandName == "rename.seqs")                  {       shellcommand = new RenameSeqsCommand();                         }
+        else if(commandName == "make.lefse")                   {       shellcommand = new MakeLefseCommand();                          }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;