X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=41a67297c4199ab819ef7f0498dfd27e6debd515;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=407b67473566d880e951e87dabb35982ec367885;hpb=ad4f75fd7c938090d3b1ce4cfefcc21edf1869eb;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 407b674..41a6729 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -146,6 +146,8 @@
 #include "makelookupcommand.h"
 #include "renameseqscommand.h"
 #include "makelefsecommand.h"
+#include "lefsecommand.h"
+#include "kruskalwalliscommand.h"
 
 /*******************************************************/
 
@@ -315,6 +317,8 @@ CommandFactory::CommandFactory(){
     commands["make.lookup"]         = "make.lookup";
     commands["rename.seqs"]         = "rename.seqs";
     commands["make.lefse"]          = "make.lefse";
+    commands["lefse"]               = "lefse";
+    commands["kruskal.wallis"]      = "kruskal.wallis";
     
 
 }
@@ -540,6 +544,8 @@ Command* CommandFactory::getCommand(string commandName, string 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;
@@ -706,6 +712,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         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;
@@ -858,6 +866,8 @@ Command* CommandFactory::getCommand(string commandName){
         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;