X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=ae59a8dcef9c43927b08759108c65f4c63d6a0cb;hb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;hp=f581b6db86bb7e8727c76ba28abc57dfe98c06f5;hpb=5b3bedc6fbfed63854cc6a7d47454580b2734c08;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index f581b6d..ae59a8d 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -106,6 +106,7 @@
 #include "corraxescommand.h"
 #include "shhhercommand.h"
 #include "pcacommand.h"
+#include "nmdscommand.h"
 
 /*******************************************************/
 
@@ -215,6 +216,7 @@ CommandFactory::CommandFactory(){
 	commands["consensus.seqs"]		= "consensus.seqs";
 	commands["corr.axes"]			= "corr.axes";
 	commands["pca"]					= "pca";
+	commands["nmds"]				= "nmds";
 	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
@@ -337,6 +339,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "pre.cluster")			{	command = new PreClusterCommand(optionString);				}
 		else if(commandName == "pcoa")					{	command = new PCOACommand(optionString);					}
 		else if(commandName == "pca")					{	command = new PCACommand(optionString);						}
+		else if(commandName == "nmds")					{	command = new NMDSCommand(optionString);					}
 		else if(commandName == "otu.hierarchy")			{	command = new OtuHierarchyCommand(optionString);			}
 		else if(commandName == "set.dir")				{	command = new SetDirectoryCommand(optionString);			}
 		else if(commandName == "set.logfile")			{	command = new SetLogFileCommand(optionString);				}
@@ -462,6 +465,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "pre.cluster")			{	pipecommand = new PreClusterCommand(optionString);				}
 		else if(commandName == "pcoa")					{	pipecommand = new PCOACommand(optionString);					}
 		else if(commandName == "pca")					{	pipecommand = new PCACommand(optionString);						}
+		else if(commandName == "nmds")					{	pipecommand = new NMDSCommand(optionString);					}
 		else if(commandName == "otu.hierarchy")			{	pipecommand = new OtuHierarchyCommand(optionString);			}
 		else if(commandName == "set.dir")				{	pipecommand = new SetDirectoryCommand(optionString);			}
 		else if(commandName == "set.logfile")			{	pipecommand = new SetLogFileCommand(optionString);				}
@@ -574,6 +578,7 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "pre.cluster")			{	shellcommand = new PreClusterCommand();				}
 		else if(commandName == "pcoa")					{	shellcommand = new PCOACommand();					}
 		else if(commandName == "pca")					{	shellcommand = new PCACommand();					}
+		else if(commandName == "nmds")					{	shellcommand = new NMDSCommand();					}
 		else if(commandName == "otu.hierarchy")			{	shellcommand = new OtuHierarchyCommand();			}
 		else if(commandName == "set.dir")				{	shellcommand = new SetDirectoryCommand();			}
 		else if(commandName == "set.logfile")			{	shellcommand = new SetLogFileCommand();				}