added set.logfile command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index aaeec67f1b4eec4e2194fc014e87064c1d5c2b5c..cad0442747f2ff7a5ada7b24d4ba18ad9138643c 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -71,6 +71,7 @@
 #include "chimeraslayercommand.h"
 #include "chimerapintailcommand.h"
 #include "chimerabellerophoncommand.h"
+#include "setlogfilecommand.h"
 
 /*******************************************************/
 
@@ -97,6 +98,8 @@ CommandFactory::CommandFactory(){
        command = new NoCommand(s);
        
        outputDir = ""; inputDir = "";
+       logFileName = "";
+       append = false;
        
        //initialize list of valid commands
        commands["read.dist"]                   = "read.dist"; 
@@ -149,6 +152,7 @@ CommandFactory::CommandFactory(){
        commands["merge.files"]                 = "merge.files";
        commands["parse.list"]                  = "parse.list";
        commands["parse.sff"]                   = "parse.sff";
+       commands["set.logfile"]                 = "set.logfile";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -260,6 +264,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "pcoa")                                  {       command = new PCACommand(optionString);                                         }
                else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
                else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
+               else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
                else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
                else if(commandName == "parse.sff")                             {       command = new ParseSFFCommand(optionString);                            }
                else                                                                                    {       command = new NoCommand(optionString);                                          }