added summary.tax command and fixed bug with root level totals in tax.summary file

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 8e61e6e7ecef2bf38ea19ddb9171312bae3ade7b..b8261670c44d35b4bcc04a01db993d12fd653823 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -122,6 +122,7 @@
 #include "countseqscommand.h"
 #include "countgroupscommand.h"
 #include "clearmemorycommand.h"
+#include "summarytaxcommand.h"
 
 /*******************************************************/
 
@@ -265,6 +266,7 @@ CommandFactory::CommandFactory(){
        commands["shhh.seqs"]                   = "MPIEnabled";
        commands["sens.spec"]                   = "sens.spec";
        commands["seq.error"]                   = "seq.error";
+       commands["seq.error"]                   = "summary.tax";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -421,6 +423,7 @@ 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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -561,6 +564,7 @@ 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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -689,6 +693,7 @@ 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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;