X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=6d87a68c49c6d9154572adcbc51ebc3b4555a35f;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=54ff4a12d120ddcc482d84876ac53a04f6e3a04a;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 54ff4a1..6d87a68 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -134,6 +134,8 @@
 #include "removeotulabelscommand.h"
 #include "makecontigscommand.h"
 #include "loadlogfilecommand.h"
+#include "sffmultiplecommand.h"
+#include "classifysharedcommand.h"
 
 /*******************************************************/
 
@@ -289,7 +291,11 @@ CommandFactory::CommandFactory(){
     commands["remove.otulabels"]    = "remove.otulabels";
     commands["make.contigs"]        = "make.contigs";
     commands["load.logfile"]        = "load.logfile";
+    commands["make.table"]          = "make.table";
+    commands["sff.multiple"]        = "sff.multiple";
 	commands["quit"]				= "MPIEnabled"; 
+    commands["classify.shared"]		= "classify.shared"; 
+    
 
 }
 /***********************************************************/
@@ -482,7 +488,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "make.shared")			{	command = new SharedCommand(optionString);					}
 		else if(commandName == "get.commandinfo")		{	command = new GetCommandInfoCommand(optionString);			}
 		else if(commandName == "deunique.tree")			{	command = new DeuniqueTreeCommand(optionString);			}
-		else if(commandName == "count.seqs")			{	command = new CountSeqsCommand(optionString);				}
+		else if((commandName == "count.seqs") || (commandName == "make.table"))			{	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);				}
@@ -502,6 +508,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "remove.otulabels")      {	command = new RemoveOtuLabelsCommand(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											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -636,7 +644,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "make.shared")			{	pipecommand = new SharedCommand(optionString);					}
 		else if(commandName == "get.commandinfo")		{	pipecommand = new GetCommandInfoCommand(optionString);			}
 		else if(commandName == "deunique.tree")			{	pipecommand = new DeuniqueTreeCommand(optionString);			}
-		else if(commandName == "count.seqs")			{	pipecommand = new CountSeqsCommand(optionString);				}
+		else if((commandName == "count.seqs") || (commandName == "make.table"))			{	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);				}
@@ -656,6 +664,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "remove.otulabels")      {	pipecommand = new RemoveOtuLabelsCommand(optionString);         }
         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											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -776,7 +786,7 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "make.shared")			{	shellcommand = new SharedCommand();					}
 		else if(commandName == "get.commandinfo")		{	shellcommand = new GetCommandInfoCommand();			}
 		else if(commandName == "deunique.tree")			{	shellcommand = new DeuniqueTreeCommand();			}
-		else if(commandName == "count.seqs")			{	shellcommand = new CountSeqsCommand();				}
+		else if((commandName == "count.seqs") || (commandName == "make.table"))			{	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();				}
@@ -796,6 +806,8 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "remove.otulabels")      {	shellcommand = new RemoveOtuLabelsCommand();        }
         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											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;