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[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index e18e6ac1956e3f21f990d6c5b1c45be42dafebf9..63e0690f40cebb2b1ac0bf1b481a6848261c71bd 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -48,7 +48,6 @@
 #include "reversecommand.h"
 #include "trimseqscommand.h"
 #include "mergefilecommand.h"
-#include "chimeraseqscommand.h"
 #include "listseqscommand.h"
 #include "getseqscommand.h"
 #include "removeseqscommand.h"
@@ -116,6 +115,8 @@
 #include "anosimcommand.h"
 #include "getcurrentcommand.h"
 #include "setcurrentcommand.h"
+#include "sharedcommand.h"
+#include "getcommandinfocommand.h"
 
 /*******************************************************/
 
@@ -151,6 +152,7 @@ CommandFactory::CommandFactory(){
        commands["read.dist"]                   = "read.dist"; 
        commands["read.otu"]                    = "read.otu";
        commands["read.tree"]                   = "read.tree"; 
+       commands["make.shared"]                 = "make.shared"; 
        commands["bin.seqs"]                    = "bin.seqs"; 
        commands["get.oturep"]                  = "get.oturep";
        commands["cluster"]                             = "cluster"; 
@@ -182,7 +184,7 @@ CommandFactory::CommandFactory(){
        commands["trim.flows"]                  = "trim.flows";
        commands["list.seqs"]                   = "list.seqs";
        commands["get.seqs"]                    = "get.seqs";
-       commands["remove.seqs"]                 = "get.seqs";
+       commands["remove.seqs"]                 = "remove.seqs";
        commands["system"]                              = "system";
        commands["align.check"]                 = "align.check";
        commands["get.sharedseqs"]              = "get.sharedseqs";
@@ -235,13 +237,13 @@ CommandFactory::CommandFactory(){
        commands["merge.groups"]                = "merge.groups";
        commands["get.current"]                 = "get.current";
        commands["set.current"]                 = "set.current";
+       commands["get.commandinfo"]             = "get.commandinfo";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
        commands["align.seqs"]                  = "MPIEnabled";
-       commands["chimera.seqs"]                = "chimera.seqs";
        commands["chimera.ccode"]               = "MPIEnabled";
        commands["chimera.check"]               = "MPIEnabled";
        commands["chimera.slayer"]              = "MPIEnabled";
@@ -336,7 +338,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
                else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
                else if(commandName == "shhh.seqs")                             {       command = new ShhherCommand(optionString);                                      }
-               else if(commandName == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(optionString);                         }
                else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
                else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
                else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
@@ -403,6 +404,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "get.current")                   {       command = new GetCurrentCommand(optionString);                          }
                else if(commandName == "set.current")                   {       command = new SetCurrentCommand(optionString);                          }
                else if(commandName == "anosim")                                {       command = new AnosimCommand(optionString);                                      }
+               else if(commandName == "make.shared")                   {       command = new SharedCommand(optionString);                                      }
+               else if(commandName == "get.commandinfo")               {       command = new GetCommandInfoCommand(optionString);                      }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -471,7 +474,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
                else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
                else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhherCommand(optionString);                                  }
-               else if(commandName == "chimera.seqs")                  {       pipecommand = new ChimeraSeqsCommand(optionString);                             }
                else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
                else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
                else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
@@ -537,6 +539,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "make.fastq")                    {       pipecommand = new MakeFastQCommand(optionString);                               }
                else if(commandName == "get.current")                   {       pipecommand = new GetCurrentCommand(optionString);                              }
                else if(commandName == "set.current")                   {       pipecommand = new SetCurrentCommand(optionString);                              }
+               else if(commandName == "make.shared")                   {       pipecommand = new SharedCommand(optionString);                                  }
+               else if(commandName == "get.commandinfo")               {       pipecommand = new GetCommandInfoCommand(optionString);                  }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -593,7 +597,6 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
                else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
                else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhherCommand();                                     }
-               else if(commandName == "chimera.seqs")                  {       shellcommand = new ChimeraSeqsCommand();                        }
                else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
                else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
                else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }
@@ -659,6 +662,8 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "make.fastq")                    {       shellcommand = new MakeFastQCommand();                          }
                else if(commandName == "get.current")                   {       shellcommand = new GetCurrentCommand();                         }
                else if(commandName == "set.current")                   {       shellcommand = new SetCurrentCommand();                         }
+               else if(commandName == "make.shared")                   {       shellcommand = new SharedCommand();                                     }
+               else if(commandName == "get.commandinfo")               {       shellcommand = new GetCommandInfoCommand();                     }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;