added shhh.seqs command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5d9679a498f70eea896664bad38c057710fd01bd..7d47491f7e32a3dc2adf518aa5d97cc2265f7121 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -105,6 +105,7 @@
 #include "consensusseqscommand.h"
 #include "trimflowscommand.h"
 #include "corraxescommand.h"
+#include "shhhercommand.h"
 
 /*******************************************************/
 
@@ -229,6 +230,7 @@ CommandFactory::CommandFactory(){
        commands["screen.seqs"]                 = "MPIEnabled";
        commands["summary.seqs"]                = "MPIEnabled";
        commands["cluster.split"]               = "MPIEnabled";
+       commands["shhh.seqs"]                   = "MPIEnabled";
        commands["sens.spec"]                   = "sens.spec";
        commands["seq.error"]                   = "seq.error";
        commands["quit"]                                = "MPIEnabled"; 
@@ -313,6 +315,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
                else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
                else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
+               else if(commandName == "shhh.seqs")                             {       command = new ShhherCommand(optionString);                                      }
                else if(commandName == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(optionString);                         }
                else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
                else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
@@ -437,6 +440,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "reverse.seqs")                  {       pipecommand = new ReverseSeqsCommand(optionString);                             }
                else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
                else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
+               else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhherCommand(optionString);                                  }
                else if(commandName == "chimera.seqs")                  {       pipecommand = new ChimeraSeqsCommand(optionString);                             }
                else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
                else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
@@ -548,6 +552,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "reverse.seqs")                  {       shellcommand = new ReverseSeqsCommand();                        }
                else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
                else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
+               else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhherCommand();                                     }
                else if(commandName == "chimera.seqs")                  {       shellcommand = new ChimeraSeqsCommand();                        }
                else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
                else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }