fixed bug with trim.flows that was adding flow files names to the .flow.files file...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 69bb568e761f590e2419ee61079783679c914efa..364c5ed2eae3f9cb90dc4db6d3edced157c2168d 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -124,6 +124,7 @@
 #include "clearmemorycommand.h"
 #include "summarytaxcommand.h"
 #include "chimeraperseuscommand.h"
+#include "shhhseqscommand.h"
 
 /*******************************************************/
 
@@ -268,7 +269,8 @@ CommandFactory::CommandFactory(){
        commands["shhh.flows"]                  = "MPIEnabled";
        commands["sens.spec"]                   = "sens.spec";
        commands["seq.error"]                   = "seq.error";
-       commands["seq.error"]                   = "summary.tax";
+       commands["summary.tax"]                 = "summary.tax";
+       commands["shhh.seqs"]                   = "shhh.seqs";
        
        commands["quit"]                                = "MPIEnabled"; 
 
@@ -428,6 +430,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
                else if(commandName == "summary.tax")                   {       command = new SummaryTaxCommand(optionString);                          }
                else if(commandName == "chimera.perseus")               {       command = new ChimeraPerseusCommand(optionString);                      }
+               else if(commandName == "shhh.seqs")                             {       command = new ShhhSeqsCommand(optionString);                            }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -570,6 +573,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
                else if(commandName == "summary.tax")                   {       pipecommand = new SummaryTaxCommand(optionString);                              }
                else if(commandName == "chimera.perseus")               {       pipecommand = new ChimeraPerseusCommand(optionString);                  }
+               else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhhSeqsCommand(optionString);                                }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -700,6 +704,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
                else if(commandName == "summary.tax")                   {       shellcommand = new SummaryTaxCommand();                         }
                else if(commandName == "chimera.perseus")               {       shellcommand = new ChimeraPerseusCommand();                     }
+               else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhhSeqsCommand();                           }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;