X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=bd519eebfd6eaa24134dad9ac08f2193004e6386;hb=a6c4005cb8b45030d6621404d6082723b3b98003;hp=0bca8c0ee3db3706404b3fc5c4ff42b8c8f99388;hpb=725a3d4ff2442c79bfde0a75ed3e0904edcf03b7;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0bca8c0..bd519ee 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -79,6 +79,7 @@
 #include "catchallcommand.h"
 #include "splitabundcommand.h"
 #include "clustersplitcommand.h"
+#include "classifyotucommand.h"
 
 /*******************************************************/
 
@@ -165,6 +166,7 @@ CommandFactory::CommandFactory(){
 	commands["catchall"]			= "catchall";
 	commands["split.abund"]			= "split.abund";
 	commands["cluster.split"]		= "cluster.split";
+	commands["classify.otu"]		= "classify.otu";
 	commands["classify.seqs"]		= "MPIEnabled"; 
 	commands["dist.seqs"]			= "MPIEnabled";
 	commands["filter.seqs"]			= "MPIEnabled";
@@ -249,7 +251,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "tree.shared")			{   command = new TreeGroupCommand(optionString);				}
 		else if(commandName == "dist.shared")			{   command = new MatrixOutputCommand(optionString);			}
 		else if(commandName == "bootstrap.shared")		{   command = new BootSharedCommand(optionString);				}
-		//else if(commandName == "consensus")			{   command = new ConcensusCommand(optionString);				}
+		else if(commandName == "consensus")				{   command = new ConcensusCommand(optionString);				}
 		else if(commandName == "dist.seqs")				{   command = new DistanceCommand(optionString);				}
 		else if(commandName == "align.seqs")			{   command = new AlignCommand(optionString);					}
 		else if(commandName == "summary.seqs")			{	command = new SeqSummaryCommand(optionString);				}
@@ -288,6 +290,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "catchall")				{	command = new CatchAllCommand(optionString);				}
 		else if(commandName == "split.abund")			{	command = new SplitAbundCommand(optionString);				}
 		else if(commandName == "cluster.split")			{	command = new ClusterSplitCommand(optionString);			}
+		else if(commandName == "classify.otu")			{	command = new ClassifyOtuCommand(optionString);				}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -339,9 +342,9 @@ bool CommandFactory::isValidCommand(string command) {
 /***********************************************************************/
 void CommandFactory::printCommands(ostream& out) {
 	try {	
-		out << "Valid commands are ";
+		out << "Valid commands are: ";
 		for (it = commands.begin(); it != commands.end(); it++) {
-			out << it->first << ", ";
+			out << it->first << ",";
 		}
 		out << endl;
 	}