X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=c247f908ca190087e4a30bb05ea31d88a0e7fd6b;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=6ceabbfc6eee41a10f70ef8391fc3a12e202696f;hpb=875ab4b2eec77b920e9fa0042f9a2aae2faff2b0;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 6ceabbf..c247f90 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -135,7 +135,7 @@
 #include "makecontigscommand.h"
 #include "loadlogfilecommand.h"
 #include "sffmultiplecommand.h"
-#include "classifysharedcommand.h"
+#include "classifyrfsharedcommand.h"
 #include "filtersharedcommand.h"
 #include "primerdesigncommand.h"
 #include "getdistscommand.h"
@@ -306,7 +306,7 @@ CommandFactory::CommandFactory(){
     commands["make.table"]          = "make.table";
     commands["sff.multiple"]        = "sff.multiple";
 	commands["quit"]				= "MPIEnabled"; 
-    commands["classify.shared"]		= "classify.shared"; 
+    commands["classify.rf"]         = "classify.rf"; 
     commands["filter.shared"]		= "filter.shared"; 
     commands["primer.design"]		= "primer.design";
     commands["get.dists"]           = "get.dists";
@@ -408,7 +408,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 			else { optionString += "inputdir=" + inputDir; }
 		}
 		
-		if(commandName == "cluster")				{	command = new ClusterCommand(optionString);					}
+		if(commandName == "cluster")                    {	command = new ClusterCommand(optionString);					}
 		else if(commandName == "unique.seqs")			{	command = new DeconvoluteCommand(optionString);				}
 		else if(commandName == "parsimony")				{	command = new ParsimonyCommand(optionString);				}
 		else if(commandName == "help")					{	command = new HelpCommand(optionString);					}
@@ -533,7 +533,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "make.contigs")          {	command = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {	command = new LoadLogfileCommand(optionString);             }
         else if(commandName == "sff.multiple")          {	command = new SffMultipleCommand(optionString);             }
-        else if(commandName == "classify.shared")       {	command = new ClassifySharedCommand(optionString);          }
+        else if(commandName == "classify.rf")           {	command = new ClassifyRFSharedCommand(optionString);          }
         else if(commandName == "filter.shared")         {	command = new FilterSharedCommand(optionString);            }
         else if(commandName == "primer.design")         {	command = new PrimerDesignCommand(optionString);            }
         else if(commandName == "get.dists")             {	command = new GetDistsCommand(optionString);                }
@@ -701,7 +701,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "make.contigs")          {	pipecommand = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {	pipecommand = new LoadLogfileCommand(optionString);             }
         else if(commandName == "sff.multiple")          {	pipecommand = new SffMultipleCommand(optionString);             }
-        else if(commandName == "classify.shared")       {	pipecommand = new ClassifySharedCommand(optionString);          }
+        else if(commandName == "classify.rf")           {	pipecommand = new ClassifyRFSharedCommand(optionString);        }
         else if(commandName == "filter.shared")         {	pipecommand = new FilterSharedCommand(optionString);            }
         else if(commandName == "primer.design")         {	pipecommand = new PrimerDesignCommand(optionString);            }
         else if(commandName == "get.dists")             {	pipecommand = new GetDistsCommand(optionString);                }
@@ -855,7 +855,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "make.contigs")          {	shellcommand = new MakeContigsCommand();            }
         else if(commandName == "load.logfile")          {	shellcommand = new LoadLogfileCommand();            }
         else if(commandName == "sff.multiple")          {	shellcommand = new SffMultipleCommand();            }
-        else if(commandName == "classify.shared")       {	shellcommand = new ClassifySharedCommand();         }
+        else if(commandName == "classify.rf")           {	shellcommand = new ClassifyRFSharedCommand();       }
         else if(commandName == "filter.shared")         {	shellcommand = new FilterSharedCommand();           }
         else if(commandName == "primer.design")         {	shellcommand = new PrimerDesignCommand();           }
         else if(commandName == "get.dists")             {	shellcommand = new GetDistsCommand();               }