X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=407b67473566d880e951e87dabb35982ec367885;hb=ad4f75fd7c938090d3b1ce4cfefcc21edf1869eb;hp=193c53c4d610111cf369084f1a153400bfbe38e5;hpb=4e3080b15a3d0c02f7ef2fd779ead433ffdece31;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 193c53c..407b674 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -141,6 +141,11 @@
 #include "getdistscommand.h"
 #include "removedistscommand.h"
 #include "mergetaxsummarycommand.h"
+#include "getmetacommunitycommand.h"
+#include "sparcccommand.h"
+#include "makelookupcommand.h"
+#include "renameseqscommand.h"
+#include "makelefsecommand.h"
 
 /*******************************************************/
 
@@ -305,6 +310,11 @@ CommandFactory::CommandFactory(){
     commands["get.dists"]           = "get.dists";
     commands["remove.dists"]        = "remove.dists";
     commands["merge.taxsummary"]    = "merge.taxsummary";
+    commands["get.metacommunity"]   = "get.metacommunity";
+    commands["sparcc"]              = "sparcc";
+    commands["make.lookup"]         = "make.lookup";
+    commands["rename.seqs"]         = "rename.seqs";
+    commands["make.lefse"]          = "make.lefse";
     
 
 }
@@ -525,6 +535,11 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "get.dists")             {	command = new GetDistsCommand(optionString);                }
         else if(commandName == "remove.dists")          {	command = new RemoveDistsCommand(optionString);             }
         else if(commandName == "merge.taxsummary")      {	command = new MergeTaxSummaryCommand(optionString);         }
+        else if(commandName == "get.metacommunity")     {	command = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "sparcc")                {	command = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")			{	command = new MakeLookupCommand(optionString);				}
+        else if(commandName == "rename.seqs")			{	command = new RenameSeqsCommand(optionString);				}
+        else if(commandName == "make.lefse")			{	command = new MakeLefseCommand(optionString);				}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -686,6 +701,11 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "get.dists")             {	pipecommand = new GetDistsCommand(optionString);                }
         else if(commandName == "remove.dists")          {	pipecommand = new RemoveDistsCommand(optionString);             }
         else if(commandName == "merge.taxsummary")      {	pipecommand = new MergeTaxSummaryCommand(optionString);         }
+        else if(commandName == "get.metacommunity")     {	pipecommand = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "sparcc")                {	pipecommand = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")			{	pipecommand = new MakeLookupCommand(optionString);				}
+        else if(commandName == "rename.seqs")			{	pipecommand = new RenameSeqsCommand(optionString);				}
+        else if(commandName == "make.lefse")			{	pipecommand = new MakeLefseCommand(optionString);				}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -833,6 +853,11 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "get.dists")             {	shellcommand = new GetDistsCommand();               }
         else if(commandName == "remove.dists")          {	shellcommand = new RemoveDistsCommand();            }
         else if(commandName == "merge.taxsummary")      {	shellcommand = new MergeTaxSummaryCommand();        }
+        else if(commandName == "get.metacommunity")     {	shellcommand = new GetMetaCommunityCommand();       }
+        else if(commandName == "sparcc")                {	shellcommand = new SparccCommand();                 }
+        else if(commandName == "make.lookup")			{	shellcommand = new MakeLookupCommand();				}
+        else if(commandName == "rename.seqs")			{	shellcommand = new RenameSeqsCommand();				}
+        else if(commandName == "make.lefse")			{	shellcommand = new MakeLefseCommand();				}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;