changed dups parameter to dereplicate in chimera.uchime.

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 54ff4a12d120ddcc482d84876ac53a04f6e3a04a..6d87a68c49c6d9154572adcbc51ebc3b4555a35f 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -134,6 +134,8 @@
 #include "removeotulabelscommand.h"
 #include "makecontigscommand.h"
 #include "loadlogfilecommand.h"
+#include "sffmultiplecommand.h"
+#include "classifysharedcommand.h"
 
 /*******************************************************/
 
@@ -289,7 +291,11 @@ CommandFactory::CommandFactory(){
     commands["remove.otulabels"]    = "remove.otulabels";
     commands["make.contigs"]        = "make.contigs";
     commands["load.logfile"]        = "load.logfile";
+    commands["make.table"]          = "make.table";
+    commands["sff.multiple"]        = "sff.multiple";
        commands["quit"]                                = "MPIEnabled"; 
+    commands["classify.shared"]                = "classify.shared"; 
+    
 
 }
 /***********************************************************/
@@ -482,7 +488,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "make.shared")                   {       command = new SharedCommand(optionString);                                      }
                else if(commandName == "get.commandinfo")               {       command = new GetCommandInfoCommand(optionString);                      }
                else if(commandName == "deunique.tree")                 {       command = new DeuniqueTreeCommand(optionString);                        }
-               else if(commandName == "count.seqs")                    {       command = new CountSeqsCommand(optionString);                           }
+               else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       command = new CountSeqsCommand(optionString);                           }
                else if(commandName == "count.groups")                  {       command = new CountGroupsCommand(optionString);                         }
                else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
                else if(commandName == "summary.tax")                   {       command = new SummaryTaxCommand(optionString);                          }
@@ -502,6 +508,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "remove.otulabels")      {      command = new RemoveOtuLabelsCommand(optionString);         }
         else if(commandName == "make.contigs")          {      command = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {      command = new LoadLogfileCommand(optionString);             }
+        else if(commandName == "sff.multiple")          {      command = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.shared")       {      command = new ClassifySharedCommand(optionString);          }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -636,7 +644,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "make.shared")                   {       pipecommand = new SharedCommand(optionString);                                  }
                else if(commandName == "get.commandinfo")               {       pipecommand = new GetCommandInfoCommand(optionString);                  }
                else if(commandName == "deunique.tree")                 {       pipecommand = new DeuniqueTreeCommand(optionString);                    }
-               else if(commandName == "count.seqs")                    {       pipecommand = new CountSeqsCommand(optionString);                               }
+               else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       pipecommand = new CountSeqsCommand(optionString);                               }
                else if(commandName == "count.groups")                  {       pipecommand = new CountGroupsCommand(optionString);                             }
                else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
                else if(commandName == "summary.tax")                   {       pipecommand = new SummaryTaxCommand(optionString);                              }
@@ -656,6 +664,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "remove.otulabels")      {      pipecommand = new RemoveOtuLabelsCommand(optionString);         }
         else if(commandName == "make.contigs")          {      pipecommand = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {      pipecommand = new LoadLogfileCommand(optionString);             }
+        else if(commandName == "sff.multiple")          {      pipecommand = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.shared")       {      pipecommand = new ClassifySharedCommand(optionString);          }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -776,7 +786,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "make.shared")                   {       shellcommand = new SharedCommand();                                     }
                else if(commandName == "get.commandinfo")               {       shellcommand = new GetCommandInfoCommand();                     }
                else if(commandName == "deunique.tree")                 {       shellcommand = new DeuniqueTreeCommand();                       }
-               else if(commandName == "count.seqs")                    {       shellcommand = new CountSeqsCommand();                          }
+               else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       shellcommand = new CountSeqsCommand();                          }
                else if(commandName == "count.groups")                  {       shellcommand = new CountGroupsCommand();                        }
                else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
                else if(commandName == "summary.tax")                   {       shellcommand = new SummaryTaxCommand();                         }
@@ -796,6 +806,8 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "remove.otulabels")      {      shellcommand = new RemoveOtuLabelsCommand();        }
         else if(commandName == "make.contigs")          {      shellcommand = new MakeContigsCommand();            }
         else if(commandName == "load.logfile")          {      shellcommand = new LoadLogfileCommand();            }
+        else if(commandName == "sff.multiple")          {      shellcommand = new SffMultipleCommand();            }
+        else if(commandName == "classify.shared")       {      shellcommand = new ClassifySharedCommand();         }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;