X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=725ce8cb7d2c4c9685e0f95ae6f67bc5cbb5fc83;hb=bc4c4d63e983a3e91e74b5038bfec6705e1a3a2e;hp=e2d114a3ba25e41474af369a8d41752be7616ccd;hpb=0319c36f068f092c766e1bff34b3554c1858255a;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index e2d114a..725ce8c 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -74,6 +74,15 @@
 #include "setlogfilecommand.h"
 #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"
 
 /*******************************************************/
 
@@ -155,6 +164,13 @@ CommandFactory::CommandFactory(){
 	commands["set.logfile"]			= "set.logfile";
 	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["classify.seqs"]		= "MPIEnabled"; 
 	commands["dist.seqs"]			= "MPIEnabled";
 	commands["filter.seqs"]			= "MPIEnabled";
@@ -167,6 +183,8 @@ CommandFactory::CommandFactory(){
 	commands["chimera.bellerophon"]	= "MPIEnabled";
 	commands["screen.seqs"]			= "MPIEnabled";
 	commands["summary.seqs"]		= "MPIEnabled";
+	commands["cluster.split"]		= "MPIEnabled";
+	commands["sens.spec"]			= "sens.spec";
 	commands["quit"]				= "MPIEnabled"; 
 
 }
@@ -239,7 +257,7 @@ 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);				}
@@ -273,6 +291,15 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "parse.sff")				{	command = new ParseSFFCommand(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											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -324,9 +351,9 @@ 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;
 	}