X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=d813e1b5e22f9184de49151d3183b528c1dfc7cd;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=8c8fe3cb340f0ee56ba8ec7bc9e34ee69c32c021;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 8c8fe3c..d813e1b 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -126,6 +126,7 @@
 #include "chimeraperseuscommand.h"
 #include "shhhseqscommand.h"
 #include "summaryqualcommand.h"
+#include "otuassociationcommand.h"
 
 /*******************************************************/
 
@@ -273,6 +274,7 @@ CommandFactory::CommandFactory(){
 	commands["summary.tax"]			= "summary.tax";
 	commands["summary.qual"]		= "summary.qual";
 	commands["shhh.seqs"]			= "shhh.seqs";
+	commands["otu.association"]		= "otu.association";
 	commands["quit"]				= "MPIEnabled"; 
 
 }
@@ -433,6 +435,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "summary.qual")			{	command = new SummaryQualCommand(optionString);				}
 		else if(commandName == "chimera.perseus")		{	command = new ChimeraPerseusCommand(optionString);			}
 		else if(commandName == "shhh.seqs")				{	command = new ShhhSeqsCommand(optionString);				}
+		else if(commandName == "otu.association")		{	command = new OTUAssociationCommand(optionString);			}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -577,6 +580,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "summary.qual")			{	pipecommand = new SummaryQualCommand(optionString);				}
 		else if(commandName == "chimera.perseus")		{	pipecommand = new ChimeraPerseusCommand(optionString);			}
 		else if(commandName == "shhh.seqs")				{	pipecommand = new ShhhSeqsCommand(optionString);				}
+		else if(commandName == "otu.association")		{	pipecommand = new OTUAssociationCommand(optionString);			}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -709,6 +713,7 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "summary.qual")			{	shellcommand = new SummaryQualCommand();			}
 		else if(commandName == "chimera.perseus")		{	shellcommand = new ChimeraPerseusCommand();			}
 		else if(commandName == "shhh.seqs")				{	shellcommand = new ShhhSeqsCommand();				}
+		else if(commandName == "otu.association")		{	shellcommand = new OTUAssociationCommand();			}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;