added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 620536d8628931d8b9f9a5db1132ab04e28f456f..5aaa7b7b120ffdd5b0258b16643ce4bad89be93e 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -120,6 +120,7 @@
 #include "getcommandinfocommand.h"
 #include "deuniquetreecommand.h"
 #include "countseqscommand.h"
+#include "clearmemorycommand.h"
 
 /*******************************************************/
 
@@ -243,6 +244,7 @@ CommandFactory::CommandFactory(){
        commands["get.commandinfo"]             = "get.commandinfo";
        commands["deunique.tree"]               = "deunique.tree";
        commands["count.seqs"]                  = "count.seqs";
+       commands["clear.memory"]                = "clear.memory";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -415,6 +417,7 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -553,6 +556,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                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 == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -679,6 +683,7 @@ Command* CommandFactory::getCommand(string commandName){
                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 == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;