X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.cpp;h=6ceabbfc6eee41a10f70ef8391fc3a12e202696f;hp=6c6bc17bb3dfd47f31b68facd01d6e0724cf3d8d;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=4a760c2d164aa955dee7d3d38da323822763d906

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 6c6bc17..6ceabbf 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -142,6 +142,12 @@
 #include "removedistscommand.h"
 #include "mergetaxsummarycommand.h"
 #include "getmetacommunitycommand.h"
+#include "sparcccommand.h"
+#include "makelookupcommand.h"
+#include "renameseqscommand.h"
+#include "makelefsecommand.h"
+#include "lefsecommand.h"
+#include "kruskalwalliscommand.h"
 
 /*******************************************************/
 
@@ -306,7 +312,13 @@ CommandFactory::CommandFactory(){
     commands["get.dists"]           = "get.dists";
     commands["remove.dists"]        = "remove.dists";
     commands["merge.taxsummary"]    = "merge.taxsummary";
-    commands["get.metacommunity"]   = "get.metacommunity";
+    commands["get.communitytype"]   = "get.communitytype";
+    commands["sparcc"]              = "sparcc";
+    commands["make.lookup"]         = "make.lookup";
+    commands["rename.seqs"]         = "rename.seqs";
+    commands["make.lefse"]          = "make.lefse";
+    commands["lefse"]               = "lefse";
+    commands["kruskal.wallis"]      = "kruskal.wallis";
     
 
 }
@@ -527,7 +539,13 @@ 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 == "get.communitytype")     {	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 if(commandName == "lefse")                 {	command = new LefseCommand(optionString);                   }
+        else if(commandName == "kruskal.wallis")        {	command = new KruskalWallisCommand(optionString);           }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -689,7 +707,13 @@ 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 == "get.communitytype")     {	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 if(commandName == "lefse")                 {	pipecommand = new LefseCommand(optionString);                   }
+        else if(commandName == "kruskal.wallis")        {	pipecommand = new KruskalWallisCommand(optionString);           }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -837,7 +861,13 @@ 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 == "get.communitytype")     {	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 if(commandName == "lefse")                 {	shellcommand = new LefseCommand();                  }
+        else if(commandName == "kruskal.wallis")        {	shellcommand = new KruskalWallisCommand();          }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;