X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=bbdd61692b7e328937d526e887ef5f0590528f2e;hb=7bf581f8c46b08eb3bb40715dac94695edee4a67;hp=2ac61e33e3252af5581b78b21168a5e2fbe760fb;hpb=21805b1c466a341d64a5a451f156a56d12c75dca;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 2ac61e3..bbdd616 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -75,6 +75,18 @@
 #include "phylodiversitycommand.h"
 #include "makegroupcommand.h"
 #include "chopseqscommand.h"
+#include "clearcutcommand.h"
+#include "catchallcommand.h"
+#include "splitabundcommand.h"
+#include "clustersplitcommand.h"
+#include "classifyotucommand.h"
+#include "degapseqscommand.h"
+#include "getrelabundcommand.h"
+#include "sensspeccommand.h"
+#include "sffinfocommand.h"
+#include "seqerrorcommand.h"
+#include "normalizesharedcommand.h"
+#include "metastatscommand.h"
 
 /*******************************************************/
 
@@ -157,6 +169,15 @@ CommandFactory::CommandFactory(){
 	commands["phylo.diversity"]		= "phylo.diversity";
 	commands["make.group"]			= "make.group";
 	commands["chop.seqs"]			= "chop.seqs";
+	commands["clearcut"]			= "clearcut";
+	commands["catchall"]			= "catchall";
+	commands["split.abund"]			= "split.abund";
+	commands["classify.otu"]		= "classify.otu";
+	commands["degap.seqs"]			= "degap.seqs";
+	commands["get.relabund"]		= "get.relabund";
+	commands["sffinfo"]				= "sffinfo";
+	commands["normalize.shared"]	= "normalize.shared";
+	commands["metastats"]			= "metastats";
 	commands["classify.seqs"]		= "MPIEnabled"; 
 	commands["dist.seqs"]			= "MPIEnabled";
 	commands["filter.seqs"]			= "MPIEnabled";
@@ -169,6 +190,9 @@ CommandFactory::CommandFactory(){
 	commands["chimera.bellerophon"]	= "MPIEnabled";
 	commands["screen.seqs"]			= "MPIEnabled";
 	commands["summary.seqs"]		= "MPIEnabled";
+	commands["cluster.split"]		= "MPIEnabled";
+	commands["sens.spec"]			= "sens.spec";
+	commands["seq.error"]			= "seq.error";
 	commands["quit"]				= "MPIEnabled"; 
 
 }
@@ -241,7 +265,7 @@ 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);				}
@@ -276,6 +300,18 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "phylo.diversity")		{	command = new PhyloDiversityCommand(optionString);			}
 		else if(commandName == "make.group")			{	command = new MakeGroupCommand(optionString);				}
 		else if(commandName == "chop.seqs")				{	command = new ChopSeqsCommand(optionString);				}
+		else if(commandName == "clearcut")				{	command = new ClearcutCommand(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 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											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -327,9 +363,9 @@ 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;
 	}