X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=94da28fdd112dcd7347768088f58164d3973ca05;hb=ca0785e447ca7aa7e2f0ab8bb1155db126b551ea;hp=fc20ee5abbcda080d7965c133199e9a86e4a74cb;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index fc20ee5..94da28f 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -84,6 +84,13 @@
 #include "getrelabundcommand.h"
 #include "sensspeccommand.h"
 #include "sffinfocommand.h"
+#include "seqerrorcommand.h"
+#include "normalizesharedcommand.h"
+#include "metastatscommand.h"
+#include "splitgroupscommand.h"
+#include "clusterfragmentscommand.h"
+#include "getlineagecommand.h"
+#include "removelineagecommand.h"
 
 /*******************************************************/
 
@@ -173,6 +180,12 @@ CommandFactory::CommandFactory(){
 	commands["degap.seqs"]			= "degap.seqs";
 	commands["get.relabund"]		= "get.relabund";
 	commands["sffinfo"]				= "sffinfo";
+	commands["normalize.shared"]	= "normalize.shared";
+	commands["metastats"]			= "metastats";
+	commands["split.groups"]		= "split.groups";
+	commands["cluster.fragments"]	= "cluster.fragments";
+	commands["get.lineage"]			= "get.lineage";
+	commands["remove.lineage"]		= "remove.lineage";
 	commands["classify.seqs"]		= "MPIEnabled"; 
 	commands["dist.seqs"]			= "MPIEnabled";
 	commands["filter.seqs"]			= "MPIEnabled";
@@ -187,6 +200,7 @@ CommandFactory::CommandFactory(){
 	commands["summary.seqs"]		= "MPIEnabled";
 	commands["cluster.split"]		= "MPIEnabled";
 	commands["sens.spec"]			= "sens.spec";
+	commands["seq.error"]			= "seq.error";
 	commands["quit"]				= "MPIEnabled"; 
 
 }
@@ -302,7 +316,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "degap.seqs")			{	command = new DegapSeqsCommand(optionString);				}
 		else if(commandName == "get.relabund")			{	command = new GetRelAbundCommand(optionString);				}
 		else if(commandName == "sens.spec")				{	command = new SensSpecCommand(optionString);				}
+		else if(commandName == "seq.error")				{	command = new SeqErrorCommand(optionString);				}
 		else if(commandName == "sffinfo")				{	command = new SffInfoCommand(optionString);					}
+		else if(commandName == "normalize.shared")		{	command = new NormalizeSharedCommand(optionString);			}
+		else if(commandName == "metastats")				{	command = new MetaStatsCommand(optionString);				}
+		else if(commandName == "split.groups")			{	command = new SplitGroupCommand(optionString);				}
+		else if(commandName == "cluster.fragments")		{	command = new ClusterFragmentsCommand(optionString);		}
+		else if(commandName == "get.lineage")			{	command = new GetLineageCommand(optionString);				}
+		else if(commandName == "remove.lineage")		{	command = new RemoveLineageCommand(optionString);			}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;