X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=525d81b2aaf360853aca14c8f3ec796c79fd0249;hb=5553e33be3a45eee6bed2ac9a5c4ca0aa0e8d5e4;hp=26b8c8620e96b545fbeed8a47be96130ebe1e615;hpb=259b6adf51ef0639cafd88cf862e4ffd5e0c7576;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 26b8c86..525d81b 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -108,6 +108,10 @@
 #include "pcacommand.h"
 #include "nmdscommand.h"
 #include "removerarecommand.h"
+#include "mergegroupscommand.h"
+#include "amovacommand.h"
+#include "homovacommand.h"
+#include "mantelcommand.h"
 
 /*******************************************************/
 
@@ -219,6 +223,10 @@ CommandFactory::CommandFactory(){
 	commands["pca"]					= "pca";
 	commands["nmds"]				= "nmds";
 	commands["remove.rare"]			= "remove.rare";
+	commands["amova"]				= "amova";
+	commands["homova"]				= "homova";
+	commands["mantel"]				= "mantel";
+	commands["merge.groups"]		= "merge.groups";
 	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
@@ -379,6 +387,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "consensus.seqs")		{	command = new ConsensusSeqsCommand(optionString);			}
 		else if(commandName == "corr.axes")				{	command = new CorrAxesCommand(optionString);				}
 		else if(commandName == "remove.rare")			{	command = new RemoveRareCommand(optionString);				}
+		else if(commandName == "merge.groups")			{	command = new MergeGroupsCommand(optionString);				}
+		else if(commandName == "amova")					{	command = new AmovaCommand(optionString);					}
+		else if(commandName == "homova")				{	command = new HomovaCommand(optionString);					}
+		else if(commandName == "mantel")				{	command = new MantelCommand(optionString);					}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -505,6 +517,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "consensus.seqs")		{	pipecommand = new ConsensusSeqsCommand(optionString);			}
 		else if(commandName == "corr.axes")				{	pipecommand = new CorrAxesCommand(optionString);				}
 		else if(commandName == "remove.rare")			{	pipecommand = new RemoveRareCommand(optionString);				}
+		else if(commandName == "merge.groups")			{	pipecommand = new MergeGroupsCommand(optionString);				}
+		else if(commandName == "amova")					{	pipecommand = new AmovaCommand(optionString);					}
+		else if(commandName == "homova")				{	pipecommand = new HomovaCommand(optionString);					}
+		else if(commandName == "mantel")				{	pipecommand = new MantelCommand(optionString);					}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -619,6 +635,10 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "consensus.seqs")		{	shellcommand = new ConsensusSeqsCommand();			}
 		else if(commandName == "corr.axes")				{	shellcommand = new CorrAxesCommand();				}
 		else if(commandName == "remove.rare")			{	shellcommand = new RemoveRareCommand();				}
+		else if(commandName == "merge.groups")			{	shellcommand = new MergeGroupsCommand();			}
+		else if(commandName == "amova")					{	shellcommand = new AmovaCommand();					}
+		else if(commandName == "homova")				{	shellcommand = new HomovaCommand();					}
+		else if(commandName == "mantel")				{	shellcommand = new MantelCommand();					}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;