removed parse.sff command and made its functionality part of sffinfo command. fixed...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 7d47491f7e32a3dc2adf518aa5d97cc2265f7121..5a7b23712c3c3503c44e31e2276123fb7b5c3c56 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -65,7 +65,6 @@
 #include "otuhierarchycommand.h"
 #include "setdircommand.h"
 #include "parselistscommand.h"
-#include "parsesffcommand.h"
 #include "chimeraccodecommand.h"
 #include "chimeracheckcommand.h"
 #include "chimeraslayercommand.h"
@@ -186,7 +185,6 @@ CommandFactory::CommandFactory(){
        commands["set.dir"]                             = "set.dir";
        commands["merge.files"]                 = "merge.files";
        commands["parse.list"]                  = "parse.list";
-       commands["parse.sff"]                   = "parse.sff";
        commands["set.logfile"]                 = "set.logfile";
        commands["phylo.diversity"]             = "phylo.diversity";
        commands["make.group"]                  = "make.group";
@@ -340,7 +338,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
                else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
                else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
-               else if(commandName == "parse.sff")                             {       command = new ParseSFFCommand(optionString);                            }
                else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
                else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
                else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
@@ -465,7 +462,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "set.dir")                               {       pipecommand = new SetDirectoryCommand(optionString);                    }
                else if(commandName == "set.logfile")                   {       pipecommand = new SetLogFileCommand(optionString);                              }
                else if(commandName == "parse.list")                    {       pipecommand = new ParseListCommand(optionString);                               }
-               else if(commandName == "parse.sff")                             {       pipecommand = new ParseSFFCommand(optionString);                                }
                else if(commandName == "phylo.diversity")               {       pipecommand = new PhyloDiversityCommand(optionString);                  }
                else if(commandName == "make.group")                    {       pipecommand = new MakeGroupCommand(optionString);                               }
                else if(commandName == "chop.seqs")                             {       pipecommand = new ChopSeqsCommand(optionString);                                }
@@ -577,7 +573,6 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
                else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }
                else if(commandName == "parse.list")                    {       shellcommand = new ParseListCommand();                          }
-               else if(commandName == "parse.sff")                             {       shellcommand = new ParseSFFCommand();                           }
                else if(commandName == "phylo.diversity")               {       shellcommand = new PhyloDiversityCommand();                     }
                else if(commandName == "make.group")                    {       shellcommand = new MakeGroupCommand();                          }
                else if(commandName == "chop.seqs")                             {       shellcommand = new ChopSeqsCommand();                           }