addition of trim.flows

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index f1a710508b537aa35085c5af3d04c31ee3d9bdcd..5d9679a498f70eea896664bad38c057710fd01bd 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -103,6 +103,7 @@
 #include "removeotuscommand.h"
 #include "indicatorcommand.h"
 #include "consensusseqscommand.h"
+#include "trimflowscommand.h"
 #include "corraxescommand.h"
 
 /*******************************************************/
@@ -167,6 +168,7 @@ CommandFactory::CommandFactory(){
        commands["help"]                                = "help";
        commands["reverse.seqs"]                = "reverse.seqs";
        commands["trim.seqs"]                   = "trim.seqs";
+       commands["trim.flows"]                  = "trim.flows";
        commands["list.seqs"]                   = "list.seqs";
        commands["get.seqs"]                    = "get.seqs";
        commands["remove.seqs"]                 = "get.seqs";
@@ -310,6 +312,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(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 == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(optionString);                         }
                else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
                else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
@@ -433,6 +436,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "screen.seqs")                   {       pipecommand = new ScreenSeqsCommand(optionString);                              }
                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 == "chimera.seqs")                  {       pipecommand = new ChimeraSeqsCommand(optionString);                             }
                else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
                else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
@@ -543,6 +547,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "screen.seqs")                   {       shellcommand = new ScreenSeqsCommand();                         }
                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 == "chimera.seqs")                  {       shellcommand = new ChimeraSeqsCommand();                        }
                else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
                else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }