fixed bug with trim.flows that was adding flow files names to the .flow.files file...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 8e61e6e7ecef2bf38ea19ddb9171312bae3ade7b..364c5ed2eae3f9cb90dc4db6d3edced157c2168d 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -122,6 +122,9 @@
 #include "countseqscommand.h"
 #include "countgroupscommand.h"
 #include "clearmemorycommand.h"
+#include "summarytaxcommand.h"
+#include "chimeraperseuscommand.h"
+#include "shhhseqscommand.h"
 
 /*******************************************************/
 
@@ -257,14 +260,18 @@ 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";
        commands["summary.seqs"]                = "MPIEnabled";
        commands["cluster.split"]               = "MPIEnabled";
-       commands["shhh.seqs"]                   = "MPIEnabled";
+       commands["shhh.flows"]                  = "MPIEnabled";
        commands["sens.spec"]                   = "sens.spec";
        commands["seq.error"]                   = "seq.error";
+       commands["summary.tax"]                 = "summary.tax";
+       commands["shhh.seqs"]                   = "shhh.seqs";
+       
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -347,7 +354,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
                else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
                else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
-               else if(commandName == "shhh.seqs")                             {       command = new ShhherCommand(optionString);                                      }
+               else if(commandName == "shhh.flows")                    {       command = new ShhherCommand(optionString);                                      }
                else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
                else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
                else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
@@ -421,6 +428,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "count.seqs")                    {       command = new CountSeqsCommand(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 if(commandName == "shhh.seqs")                             {       command = new ShhhSeqsCommand(optionString);                            }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -488,7 +498,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "reverse.seqs")                  {       pipecommand = new ReverseSeqsCommand(optionString);                             }
                else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
                else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
-               else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhherCommand(optionString);                                  }
+               else if(commandName == "shhh.flows")                    {       pipecommand = new ShhherCommand(optionString);                                  }
                else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
                else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
                else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
@@ -561,6 +571,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "count.seqs")                    {       pipecommand = new CountSeqsCommand(optionString);                               }
                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 if(commandName == "shhh.seqs")                             {       pipecommand = new ShhhSeqsCommand(optionString);                                }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -616,7 +629,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "reverse.seqs")                  {       shellcommand = new ReverseSeqsCommand();                        }
                else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
                else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
-               else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhherCommand();                                     }
+               else if(commandName == "shhh.flows")                    {       shellcommand = new ShhherCommand();                                     }
                else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
                else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
                else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }
@@ -689,6 +702,9 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "count.seqs")                    {       shellcommand = new CountSeqsCommand();                          }
                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 if(commandName == "shhh.seqs")                             {       shellcommand = new ShhhSeqsCommand();                           }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;