fixed bug in bootstrap command that was caused by globaldata's breakup, and made...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index db11f8c0dc890dff846787dee0fc48ea8930384a..3ad7425071a938025921cc3f143ccb69781a24ce 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -12,7 +12,6 @@
 #include "readtreecommand.h"
 #include "readotucommand.h"
 #include "clustercommand.h"
-#include "parselistcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
 #include "getgroupcommand.h"
@@ -39,7 +38,7 @@
 #include "getoturepcommand.h"
 #include "treegroupscommand.h"
 #include "bootstrapsharedcommand.h"
-#include "concensuscommand.h"
+//#include "concensuscommand.h"
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "matrixoutputcommand.h"
@@ -89,7 +88,7 @@ CommandFactory::CommandFactory(){
        commands["get.sabund"]          = "get.sabund";
        commands["get.rabund"]          = "get.rabund";
        commands["bootstrap.shared"]    = "bootstrap.shared";
-       commands["concensus"]                   = "concensus";
+       //commands["concensus"]                 = "concensus";
        commands["help"]                                = "help"; 
        commands["filter.seqs"]                 = "filter.seqs";
        commands["align.seqs"]                  = "align.seqs";
@@ -146,7 +145,7 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "concensus")                             {   command = new ConcensusCommand(optionString);                       }
+               //else if(commandName == "concensus")                           {   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);                  }