added subsample, tiers and processors to tree.shared command. removed bootstrap.share...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index b61c2d2dc820c7cf05b7f82d3983017f2d6d4c55..0c9504d09a109a39168af9b9d582ef20732e6647 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -36,8 +36,6 @@
 #include "binsequencecommand.h"
 #include "getoturepcommand.h"
 #include "treegroupscommand.h"
-#include "bootstrapsharedcommand.h"
-//#include "consensuscommand.h"
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "matrixoutputcommand.h"
@@ -191,8 +189,6 @@ CommandFactory::CommandFactory(){
        commands["get.label"]           = "get.label";
        commands["get.sabund"]          = "get.sabund";
        commands["get.rabund"]          = "get.rabund";
-       commands["bootstrap.shared"]    = "bootstrap.shared";
-       //commands["consensus"]                 = "consensus";
        commands["help"]                                = "help";
        commands["reverse.seqs"]                = "reverse.seqs";
        commands["trim.seqs"]                   = "trim.seqs";
@@ -359,8 +355,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                               }
                else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                               }
                else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);                    }
-               else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                              }
-               else if(commandName == "consensus")                             {   command = new ConcensusCommand(optionString);                               }
                else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                                }
                else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                                   }
                else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                          }
@@ -510,8 +504,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "get.oturep")                    {   pipecommand = new GetOTURepCommand(optionString);                           }
                else if(commandName == "tree.shared")                   {   pipecommand = new TreeGroupCommand(optionString);                           }
                else if(commandName == "dist.shared")                   {   pipecommand = new MatrixOutputCommand(optionString);                        }
-               else if(commandName == "bootstrap.shared")              {   pipecommand = new BootSharedCommand(optionString);                          }
-               else if(commandName == "consensus")                             {   pipecommand = new ConcensusCommand(optionString);                           }
                else if(commandName == "dist.seqs")                             {   pipecommand = new DistanceCommand(optionString);                            }
                else if(commandName == "align.seqs")                    {   pipecommand = new AlignCommand(optionString);                                       }
                else if(commandName == "summary.seqs")                  {       pipecommand = new SeqSummaryCommand(optionString);                              }
@@ -648,8 +640,6 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "get.oturep")                    {   shellcommand = new GetOTURepCommand();                              }
                else if(commandName == "tree.shared")                   {   shellcommand = new TreeGroupCommand();                              }
                else if(commandName == "dist.shared")                   {   shellcommand = new MatrixOutputCommand();                   }
-               else if(commandName == "bootstrap.shared")              {   shellcommand = new BootSharedCommand();                             }
-               else if(commandName == "consensus")                             {   shellcommand = new ConcensusCommand();                              }
                else if(commandName == "dist.seqs")                             {   shellcommand = new DistanceCommand();                               }
                else if(commandName == "align.seqs")                    {   shellcommand = new AlignCommand();                                  }
                else if(commandName == "summary.seqs")                  {       shellcommand = new SeqSummaryCommand();                         }