X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=924e3f78479f449d09a6ce6d9bd3985aa846409c;hb=902e0fcab76e75009ac43d3f4537e08182628d6f;hp=f581b6db86bb7e8727c76ba28abc57dfe98c06f5;hpb=37eac2026d91179acda0494c4dcca22f176551b9;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index f581b6d..924e3f7 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -106,6 +106,11 @@
 #include "corraxescommand.h"
 #include "shhhercommand.h"
 #include "pcacommand.h"
+#include "nmdscommand.h"
+#include "removerarecommand.h"
+#include "mergegroupscommand.h"
+#include "amovacommand.h"
+#include "homovacommand.h"
 
 /*******************************************************/
 
@@ -215,6 +220,11 @@ CommandFactory::CommandFactory(){
 	commands["consensus.seqs"]		= "consensus.seqs";
 	commands["corr.axes"]			= "corr.axes";
 	commands["pca"]					= "pca";
+	commands["nmds"]				= "nmds";
+	commands["remove.rare"]			= "remove.rare";
+	commands["amova"]				= "amova";
+	commands["homova"]				= "homova";
+	commands["merge.groups"]		= "merge.groups";
 	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
@@ -337,6 +347,7 @@ 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);				}
@@ -373,6 +384,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "indicator")				{	command = new IndicatorCommand(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											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -462,6 +477,7 @@ 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);				}
@@ -497,6 +513,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "indicator")				{	pipecommand = new IndicatorCommand(optionString);				}
 		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											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -574,6 +594,7 @@ 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();				}
@@ -609,6 +630,10 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "indicator")				{	shellcommand = new IndicatorCommand();				}
 		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											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;