X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=e18e6ac1956e3f21f990d6c5b1c45be42dafebf9;hb=9bc68cbe7fd7c5cf00b66d73d60624de80fb7933;hp=ae59a8dcef9c43927b08759108c65f4c63d6a0cb;hpb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ae59a8d..e18e6ac 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -107,6 +107,15 @@
 #include "shhhercommand.h"
 #include "pcacommand.h"
 #include "nmdscommand.h"
+#include "removerarecommand.h"
+#include "mergegroupscommand.h"
+#include "amovacommand.h"
+#include "homovacommand.h"
+#include "mantelcommand.h"
+#include "makefastqcommand.h"
+#include "anosimcommand.h"
+#include "getcurrentcommand.h"
+#include "setcurrentcommand.h"
 
 /*******************************************************/
 
@@ -217,6 +226,15 @@ CommandFactory::CommandFactory(){
 	commands["corr.axes"]			= "corr.axes";
 	commands["pca"]					= "pca";
 	commands["nmds"]				= "nmds";
+	commands["remove.rare"]			= "remove.rare";
+	commands["amova"]				= "amova";
+	commands["homova"]				= "homova";
+	commands["mantel"]				= "mantel";
+	commands["anosim"]				= "anosim";
+	commands["make.fastq"]			= "make.fastq";
+	commands["merge.groups"]		= "merge.groups";
+	commands["get.current"]			= "get.current";
+	commands["set.current"]			= "set.current";
 	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
@@ -376,6 +394,15 @@ 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 if(commandName == "mantel")				{	command = new MantelCommand(optionString);					}
+		else if(commandName == "make.fastq")			{	command = new MakeFastQCommand(optionString);				}
+		else if(commandName == "get.current")			{	command = new GetCurrentCommand(optionString);				}
+		else if(commandName == "set.current")			{	command = new SetCurrentCommand(optionString);				}
+		else if(commandName == "anosim")				{	command = new AnosimCommand(optionString);					}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -501,6 +528,15 @@ 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 if(commandName == "mantel")				{	pipecommand = new MantelCommand(optionString);					}
+		else if(commandName == "anosim")				{	pipecommand = new AnosimCommand(optionString);					}
+		else if(commandName == "make.fastq")			{	pipecommand = new MakeFastQCommand(optionString);				}
+		else if(commandName == "get.current")			{	pipecommand = new GetCurrentCommand(optionString);				}
+		else if(commandName == "set.current")			{	pipecommand = new SetCurrentCommand(optionString);				}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -614,6 +650,15 @@ 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 if(commandName == "mantel")				{	shellcommand = new MantelCommand();					}
+		else if(commandName == "anosim")				{	shellcommand = new AnosimCommand();					}
+		else if(commandName == "make.fastq")			{	shellcommand = new MakeFastQCommand();				}
+		else if(commandName == "get.current")			{	shellcommand = new GetCurrentCommand();				}
+		else if(commandName == "set.current")			{	shellcommand = new SetCurrentCommand();				}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;