working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 2fc6875c6430bd769e3e8b56e484b5da1561a30c..69bb568e761f590e2419ee61079783679c914efa 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -123,6 +123,7 @@
 #include "countgroupscommand.h"
 #include "clearmemorycommand.h"
 #include "summarytaxcommand.h"
+#include "chimeraperseuscommand.h"
 
 /*******************************************************/
 
@@ -258,6 +259,7 @@ CommandFactory::CommandFactory(){
        commands["chimera.check"]               = "MPIEnabled";
        commands["chimera.slayer"]              = "MPIEnabled";
        commands["chimera.uchime"]              = "chimera.uchime";
+       commands["chimera.perseus"]             = "chimera.perseus";
        commands["chimera.pintail"]             = "MPIEnabled";
        commands["chimera.bellerophon"] = "MPIEnabled";
        commands["screen.seqs"]                 = "MPIEnabled";
@@ -267,6 +269,7 @@ CommandFactory::CommandFactory(){
        commands["sens.spec"]                   = "sens.spec";
        commands["seq.error"]                   = "seq.error";
        commands["seq.error"]                   = "summary.tax";
+       
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -424,6 +427,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "count.groups")                  {       command = new CountGroupsCommand(optionString);                         }
                else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
                else if(commandName == "summary.tax")                   {       command = new SummaryTaxCommand(optionString);                          }
+               else if(commandName == "chimera.perseus")               {       command = new ChimeraPerseusCommand(optionString);                      }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -565,6 +569,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "count.groups")                  {       pipecommand = new CountGroupsCommand(optionString);                             }
                else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
                else if(commandName == "summary.tax")                   {       pipecommand = new SummaryTaxCommand(optionString);                              }
+               else if(commandName == "chimera.perseus")               {       pipecommand = new ChimeraPerseusCommand(optionString);                  }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -694,6 +699,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "count.groups")                  {       shellcommand = new CountGroupsCommand();                        }
                else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
                else if(commandName == "summary.tax")                   {       shellcommand = new SummaryTaxCommand();                         }
+               else if(commandName == "chimera.perseus")               {       shellcommand = new ChimeraPerseusCommand();                     }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;