fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index f581b6db86bb7e8727c76ba28abc57dfe98c06f5..ae59a8dcef9c43927b08759108c65f4c63d6a0cb 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -106,6 +106,7 @@
 #include "corraxescommand.h"
 #include "shhhercommand.h"
 #include "pcacommand.h"
+#include "nmdscommand.h"
 
 /*******************************************************/
 
@@ -215,6 +216,7 @@ CommandFactory::CommandFactory(){
        commands["consensus.seqs"]              = "consensus.seqs";
        commands["corr.axes"]                   = "corr.axes";
        commands["pca"]                                 = "pca";
+       commands["nmds"]                                = "nmds";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -337,6 +339,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                          }
                else if(commandName == "pcoa")                                  {       command = new PCOACommand(optionString);                                        }
                else if(commandName == "pca")                                   {       command = new PCACommand(optionString);                                         }
+               else if(commandName == "nmds")                                  {       command = new NMDSCommand(optionString);                                        }
                else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
                else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
                else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
@@ -462,6 +465,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "pre.cluster")                   {       pipecommand = new PreClusterCommand(optionString);                              }
                else if(commandName == "pcoa")                                  {       pipecommand = new PCOACommand(optionString);                                    }
                else if(commandName == "pca")                                   {       pipecommand = new PCACommand(optionString);                                             }
+               else if(commandName == "nmds")                                  {       pipecommand = new NMDSCommand(optionString);                                    }
                else if(commandName == "otu.hierarchy")                 {       pipecommand = new OtuHierarchyCommand(optionString);                    }
                else if(commandName == "set.dir")                               {       pipecommand = new SetDirectoryCommand(optionString);                    }
                else if(commandName == "set.logfile")                   {       pipecommand = new SetLogFileCommand(optionString);                              }
@@ -574,6 +578,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "pre.cluster")                   {       shellcommand = new PreClusterCommand();                         }
                else if(commandName == "pcoa")                                  {       shellcommand = new PCOACommand();                                       }
                else if(commandName == "pca")                                   {       shellcommand = new PCACommand();                                        }
+               else if(commandName == "nmds")                                  {       shellcommand = new NMDSCommand();                                       }
                else if(commandName == "otu.hierarchy")                 {       shellcommand = new OtuHierarchyCommand();                       }
                else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
                else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }