added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 71558a9292280dcc9f28acb29b2944fb62a05eb6..620536d8628931d8b9f9a5db1132ab04e28f456f 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -119,6 +119,7 @@
 #include "sharedcommand.h"
 #include "getcommandinfocommand.h"
 #include "deuniquetreecommand.h"
+#include "countseqscommand.h"
 
 /*******************************************************/
 
@@ -241,6 +242,7 @@ CommandFactory::CommandFactory(){
        commands["set.current"]                 = "set.current";
        commands["get.commandinfo"]             = "get.commandinfo";
        commands["deunique.tree"]               = "deunique.tree";
+       commands["count.seqs"]                  = "count.seqs";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -412,6 +414,7 @@ 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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -549,6 +552,7 @@ 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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -674,6 +678,7 @@ 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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;