pat's updates on 7/19/10

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index bd519eebfd6eaa24134dad9ac08f2193004e6386..f86a354fdcb2fd4c5fb0b744f921e70cdb45abbf 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -80,6 +80,11 @@
 #include "splitabundcommand.h"
 #include "clustersplitcommand.h"
 #include "classifyotucommand.h"
+#include "degapseqscommand.h"
+#include "getrelabundcommand.h"
+#include "sensspeccommand.h"
+#include "sffinfocommand.h"
+#include "seqerrorcommand.h"
 
 /*******************************************************/
 
@@ -165,8 +170,10 @@ CommandFactory::CommandFactory(){
        commands["clearcut"]                    = "clearcut";
        commands["catchall"]                    = "catchall";
        commands["split.abund"]                 = "split.abund";
-       commands["cluster.split"]               = "cluster.split";
        commands["classify.otu"]                = "classify.otu";
+       commands["degap.seqs"]                  = "degap.seqs";
+       commands["get.relabund"]                = "get.relabund";
+       commands["sffinfo"]                             = "sffinfo";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -179,6 +186,9 @@ CommandFactory::CommandFactory(){
        commands["chimera.bellerophon"] = "MPIEnabled";
        commands["screen.seqs"]                 = "MPIEnabled";
        commands["summary.seqs"]                = "MPIEnabled";
+       commands["cluster.split"]               = "MPIEnabled";
+       commands["sens.spec"]                   = "sens.spec";
+       commands["seq.error"]                   = "seq.error";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -291,6 +301,11 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
                else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
                else if(commandName == "classify.otu")                  {       command = new ClassifyOtuCommand(optionString);                         }
+               else if(commandName == "degap.seqs")                    {       command = new DegapSeqsCommand(optionString);                           }
+               else if(commandName == "get.relabund")                  {       command = new GetRelAbundCommand(optionString);                         }
+               else if(commandName == "sens.spec")                             {       command = new SensSpecCommand(optionString);                            }
+               else if(commandName == "seq.error")                             {       command = new SeqErrorCommand(optionString);                            }
+               else if(commandName == "sffinfo")                               {       command = new SffInfoCommand(optionString);                                     }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;