added create.database command. fixed help in get.sharedseqs. added new constructor...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 49dcd2cb6f42edfc7208738966a119147192b415..b61c2d2dc820c7cf05b7f82d3983017f2d6d4c55 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -131,6 +131,7 @@
 #include "classifytreecommand.h"
 #include "cooccurrencecommand.h"
 #include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
 
 /*******************************************************/
 
@@ -283,6 +284,7 @@ CommandFactory::CommandFactory(){
     commands["classify.tree"]       = "classify.tree";
     commands["cooccurrence"]        = "cooccurrence";
     commands["pcr.seqs"]            = "pcr.seqs";
+    commands["create.database"]     = "create.database";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -449,6 +451,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "classify.tree")         {      command = new ClassifyTreeCommand(optionString);            }
         else if(commandName == "cooccurrence")          {      command = new CooccurrenceCommand(optionString);            }
         else if(commandName == "pcr.seqs")              {      command = new PcrSeqsCommand(optionString);                 }
+        else if(commandName == "create.database")       {      command = new CreateDatabaseCommand(optionString);          }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -598,6 +601,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "classify.tree")         {      pipecommand = new ClassifyTreeCommand(optionString);            }
         else if(commandName == "cooccurrence")          {      pipecommand = new CooccurrenceCommand(optionString);            }
         else if(commandName == "pcr.seqs")              {      pipecommand = new PcrSeqsCommand(optionString);                 }
+        else if(commandName == "create.database")       {      pipecommand = new CreateDatabaseCommand(optionString);          }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -735,6 +739,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "classify.tree")         {      shellcommand = new ClassifyTreeCommand();           }
         else if(commandName == "cooccurrence")          {      shellcommand = new CooccurrenceCommand();           }
         else if(commandName == "pcr.seqs")              {      shellcommand = new PcrSeqsCommand();                }
+        else if(commandName == "create.database")       {      shellcommand = new CreateDatabaseCommand();         }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;