X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=25d6cfe14e183ce072cb656322676babfdaa094f;hb=8173238f9f94af9baab8471de58bed7c8830948d;hp=1f77b71bfb63b0519527bac53cfbf51511fdbb68;hpb=e3e0858c684c4608d679840024e5095ddc8e2719;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 1f77b71..25d6cfe 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -99,7 +99,9 @@
 #include "subsamplecommand.h"
 #include "removegroupscommand.h"
 #include "getgroupscommand.h"
-
+#include "getotuscommand.h"
+#include "removeotuscommand.h"
+#include "indicatorcommand.h"
 
 /*******************************************************/
 
@@ -203,6 +205,9 @@ CommandFactory::CommandFactory(){
 	commands["sub.sample"]			= "sub.sample";
 	commands["remove.groups"]		= "remove.groups";
 	commands["get.groups"]			= "get.groups";
+	commands["get.otus"]			= "get.otus";
+	commands["remove.otus"]			= "remove.otus";
+	commands["indicator"]			= "indicator";
 	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
@@ -347,12 +352,15 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "remove.lineage")		{	command = new RemoveLineageCommand(optionString);			}
 		else if(commandName == "get.groups")			{	command = new GetGroupsCommand(optionString);				}
 		else if(commandName == "remove.groups")			{	command = new RemoveGroupsCommand(optionString);			}
+		else if(commandName == "get.otus")				{	command = new GetOtusCommand(optionString);					}
+		else if(commandName == "remove.otus")			{	command = new RemoveOtusCommand(optionString);				}
 		else if(commandName == "fastq.info")			{	command = new ParseFastaQCommand(optionString);				}
 		else if(commandName == "pipeline.pds")			{	command = new PipelineCommand(optionString);				}
 		else if(commandName == "deunique.seqs")			{	command = new DeUniqueSeqsCommand(optionString);			}
 		else if(commandName == "pairwise.seqs")			{	command = new PairwiseSeqsCommand(optionString);			}
 		else if(commandName == "cluster.classic")		{	command = new ClusterDoturCommand(optionString);			}
 		else if(commandName == "sub.sample")			{	command = new SubSampleCommand(optionString);				}
+		else if(commandName == "indicator")				{	command = new IndicatorCommand(optionString);				}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -465,11 +473,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "get.groups")			{	pipecommand = new GetGroupsCommand(optionString);				}
 		else if(commandName == "remove.lineage")		{	pipecommand = new RemoveLineageCommand(optionString);			}
 		else if(commandName == "remove.groups")			{	pipecommand = new RemoveGroupsCommand(optionString);			}
+		else if(commandName == "get.otus")				{	pipecommand = new GetOtusCommand(optionString);					}
+		else if(commandName == "remove.otus")			{	pipecommand = new RemoveOtusCommand(optionString);				}
 		else if(commandName == "fastq.info")			{	pipecommand = new ParseFastaQCommand(optionString);				}
 		else if(commandName == "deunique.seqs")			{	pipecommand = new DeUniqueSeqsCommand(optionString);			}
 		else if(commandName == "pairwise.seqs")			{	pipecommand = new PairwiseSeqsCommand(optionString);			}
 		else if(commandName == "cluster.classic")		{	pipecommand = new ClusterDoturCommand(optionString);			}
 		else if(commandName == "sub.sample")			{	pipecommand = new SubSampleCommand(optionString);				}
+		else if(commandName == "indicator")				{	pipecommand = new IndicatorCommand(optionString);				}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -570,11 +581,14 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "remove.lineage")		{	shellcommand = new RemoveLineageCommand();			}
 		else if(commandName == "get.groups")			{	shellcommand = new GetGroupsCommand();				}
 		else if(commandName == "remove.groups")			{	shellcommand = new RemoveGroupsCommand();			}
+		else if(commandName == "get.otus")				{	shellcommand = new GetOtusCommand();				}
+		else if(commandName == "remove.otus")			{	shellcommand = new RemoveOtusCommand();				}
 		else if(commandName == "fastq.info")			{	shellcommand = new ParseFastaQCommand();			}
 		else if(commandName == "deunique.seqs")			{	shellcommand = new DeUniqueSeqsCommand();			}
 		else if(commandName == "pairwise.seqs")			{	shellcommand = new PairwiseSeqsCommand();			}
 		else if(commandName == "cluster.classic")		{	shellcommand = new ClusterDoturCommand();			}
 		else if(commandName == "sub.sample")			{	shellcommand = new SubSampleCommand();				}
+		else if(commandName == "indicator")				{	shellcommand = new IndicatorCommand();				}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;