X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=d813e1b5e22f9184de49151d3183b528c1dfc7cd;hb=7bc094aa6462a45ed539827b55753d47b4627a37;hp=b49df720cf5a87d9db41126f2c8a148c6f5245ca;hpb=88fbc534a92cb91900e98a3288dfa1f68828b69b;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index b49df72..d813e1b 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -125,6 +125,8 @@
 #include "summarytaxcommand.h"
 #include "chimeraperseuscommand.h"
 #include "shhhseqscommand.h"
+#include "summaryqualcommand.h"
+#include "otuassociationcommand.h"
 
 /*******************************************************/
 
@@ -270,8 +272,9 @@ CommandFactory::CommandFactory(){
 	commands["sens.spec"]			= "sens.spec";
 	commands["seq.error"]			= "seq.error";
 	commands["summary.tax"]			= "summary.tax";
+	commands["summary.qual"]		= "summary.qual";
 	commands["shhh.seqs"]			= "shhh.seqs";
-	
+	commands["otu.association"]		= "otu.association";
 	commands["quit"]				= "MPIEnabled"; 
 
 }
@@ -429,8 +432,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "count.groups")			{	command = new CountGroupsCommand(optionString);				}
 		else if(commandName == "clear.memory")			{	command = new ClearMemoryCommand(optionString);				}
 		else if(commandName == "summary.tax")			{	command = new SummaryTaxCommand(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;
@@ -572,8 +577,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "count.groups")			{	pipecommand = new CountGroupsCommand(optionString);				}
 		else if(commandName == "clear.memory")			{	pipecommand = new ClearMemoryCommand(optionString);				}
 		else if(commandName == "summary.tax")			{	pipecommand = new SummaryTaxCommand(optionString);				}
+		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;
@@ -703,8 +710,10 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "count.groups")			{	shellcommand = new CountGroupsCommand();			}
 		else if(commandName == "clear.memory")			{	shellcommand = new ClearMemoryCommand();			}
 		else if(commandName == "summary.tax")			{	shellcommand = new SummaryTaxCommand();				}
+		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;