pat's updates on 7/19/10

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0612c6c51977327cbbd8f100f7c1b13d6b18c7da..f86a354fdcb2fd4c5fb0b744f921e70cdb45abbf 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -81,6 +81,10 @@
 #include "clustersplitcommand.h"
 #include "classifyotucommand.h"
 #include "degapseqscommand.h"
+#include "getrelabundcommand.h"
+#include "sensspeccommand.h"
+#include "sffinfocommand.h"
+#include "seqerrorcommand.h"
 
 /*******************************************************/
 
@@ -168,6 +172,8 @@ CommandFactory::CommandFactory(){
        commands["split.abund"]                 = "split.abund";
        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";
@@ -181,6 +187,8 @@ CommandFactory::CommandFactory(){
        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"; 
 
 }
@@ -294,6 +302,10 @@ Command* CommandFactory::getCommand(string commandName, string 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;