added parse.fastaq command, added permute option to venn command, fixed bug with...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index fc20ee5abbcda080d7965c133199e9a86e4a74cb..5fbdfa891db7e57957df05538b5f2f4325684fe4 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -84,6 +84,14 @@
 #include "getrelabundcommand.h"
 #include "sensspeccommand.h"
 #include "sffinfocommand.h"
+#include "seqerrorcommand.h"
+#include "normalizesharedcommand.h"
+#include "metastatscommand.h"
+#include "splitgroupscommand.h"
+#include "clusterfragmentscommand.h"
+#include "getlineagecommand.h"
+#include "removelineagecommand.h"
+#include "parsefastaqcommand.h"
 
 /*******************************************************/
 
@@ -173,6 +181,13 @@ CommandFactory::CommandFactory(){
        commands["degap.seqs"]                  = "degap.seqs";
        commands["get.relabund"]                = "get.relabund";
        commands["sffinfo"]                             = "sffinfo";
+       commands["normalize.shared"]    = "normalize.shared";
+       commands["metastats"]                   = "metastats";
+       commands["split.groups"]                = "split.groups";
+       commands["cluster.fragments"]   = "cluster.fragments";
+       commands["get.lineage"]                 = "get.lineage";
+       commands["remove.lineage"]              = "remove.lineage";
+       commands["parse.fastaq"]                = "parse.fastaq";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -187,6 +202,7 @@ CommandFactory::CommandFactory(){
        commands["summary.seqs"]                = "MPIEnabled";
        commands["cluster.split"]               = "MPIEnabled";
        commands["sens.spec"]                   = "sens.spec";
+       commands["seq.error"]                   = "seq.error";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -302,7 +318,15 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
+               else if(commandName == "metastats")                             {       command = new MetaStatsCommand(optionString);                           }
+               else if(commandName == "split.groups")                  {       command = new SplitGroupCommand(optionString);                          }
+               else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
+               else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
+               else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
+               else if(commandName == "parse.fastaq")                  {       command = new ParseFastaQCommand(optionString);                         }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;