added calcs to tree.shared. working on remove.rare command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ae59a8dcef9c43927b08759108c65f4c63d6a0cb..26b8c8620e96b545fbeed8a47be96130ebe1e615 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -107,6 +107,7 @@
 #include "shhhercommand.h"
 #include "pcacommand.h"
 #include "nmdscommand.h"
+#include "removerarecommand.h"
 
 /*******************************************************/
 
@@ -217,6 +218,7 @@ CommandFactory::CommandFactory(){
        commands["corr.axes"]                   = "corr.axes";
        commands["pca"]                                 = "pca";
        commands["nmds"]                                = "nmds";
+       commands["remove.rare"]                 = "remove.rare";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -376,6 +378,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "indicator")                             {       command = new IndicatorCommand(optionString);                           }
                else if(commandName == "consensus.seqs")                {       command = new ConsensusSeqsCommand(optionString);                       }
                else if(commandName == "corr.axes")                             {       command = new CorrAxesCommand(optionString);                            }
+               else if(commandName == "remove.rare")                   {       command = new RemoveRareCommand(optionString);                          }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -501,6 +504,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "indicator")                             {       pipecommand = new IndicatorCommand(optionString);                               }
                else if(commandName == "consensus.seqs")                {       pipecommand = new ConsensusSeqsCommand(optionString);                   }
                else if(commandName == "corr.axes")                             {       pipecommand = new CorrAxesCommand(optionString);                                }
+               else if(commandName == "remove.rare")                   {       pipecommand = new RemoveRareCommand(optionString);                              }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -614,6 +618,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "indicator")                             {       shellcommand = new IndicatorCommand();                          }
                else if(commandName == "consensus.seqs")                {       shellcommand = new ConsensusSeqsCommand();                      }
                else if(commandName == "corr.axes")                             {       shellcommand = new CorrAxesCommand();                           }
+               else if(commandName == "remove.rare")                   {       shellcommand = new RemoveRareCommand();                         }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;