consensus.seqs can now find a consensus on a whole fasta file without needing a listfile

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 8d038e0c08e6010d21188808b3ff3ad40087a7f7..b7b49922e48b28ef2f3ae9503dc4b4feb2f62d8a 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -101,6 +101,8 @@
 #include "getgroupscommand.h"
 #include "getotuscommand.h"
 #include "removeotuscommand.h"
+#include "indicatorcommand.h"
+#include "consensusseqscommand.h"
 
 /*******************************************************/
 
@@ -206,6 +208,8 @@ CommandFactory::CommandFactory(){
        commands["get.groups"]                  = "get.groups";
        commands["get.otus"]                    = "get.otus";
        commands["remove.otus"]                 = "remove.otus";
+       commands["indicator"]                   = "indicator";
+       commands["consensus.seqs"]              = "consensus.seqs";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -358,6 +362,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "pairwise.seqs")                 {       command = new PairwiseSeqsCommand(optionString);                        }
                else if(commandName == "cluster.classic")               {       command = new ClusterDoturCommand(optionString);                        }
                else if(commandName == "sub.sample")                    {       command = new SubSampleCommand(optionString);                           }
+               else if(commandName == "indicator")                             {       command = new IndicatorCommand(optionString);                           }
+               else if(commandName == "consensus.seqs")                {       command = new ConsensusSeqsCommand(optionString);                       }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -477,6 +483,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "pairwise.seqs")                 {       pipecommand = new PairwiseSeqsCommand(optionString);                    }
                else if(commandName == "cluster.classic")               {       pipecommand = new ClusterDoturCommand(optionString);                    }
                else if(commandName == "sub.sample")                    {       pipecommand = new SubSampleCommand(optionString);                               }
+               else if(commandName == "indicator")                             {       pipecommand = new IndicatorCommand(optionString);                               }
+               else if(commandName == "consensus.seqs")                {       pipecommand = new ConsensusSeqsCommand(optionString);                   }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -584,6 +592,8 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "pairwise.seqs")                 {       shellcommand = new PairwiseSeqsCommand();                       }
                else if(commandName == "cluster.classic")               {       shellcommand = new ClusterDoturCommand();                       }
                else if(commandName == "sub.sample")                    {       shellcommand = new SubSampleCommand();                          }
+               else if(commandName == "indicator")                             {       shellcommand = new IndicatorCommand();                          }
+               else if(commandName == "consensus.seqs")                {       shellcommand = new ConsensusSeqsCommand();                      }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;