X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=7de4d06f25ddbb1414aaea8e7f4b8d7f72d25590;hb=af2ce19e213e5191f8c9fac4061e43f6e31a7fbf;hp=cad0442747f2ff7a5ada7b24d4ba18ad9138643c;hpb=84f93a9e670eb7f7e69e0468b9be4c53890c07f2;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index cad0442..7de4d06 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -72,6 +72,15 @@
 #include "chimerapintailcommand.h"
 #include "chimerabellerophoncommand.h"
 #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"
 
 /*******************************************************/
 
@@ -130,9 +139,7 @@ CommandFactory::CommandFactory(){
 	commands["get.rabund"]          = "get.rabund";
 	commands["bootstrap.shared"]	= "bootstrap.shared";
 	//commands["consensus"]			= "consensus";
-	commands["help"]				= "help"; 
-	commands["summary.seqs"]		= "summary.seqs";
-	commands["screen.seqs"]			= "screen.seqs";
+	commands["help"]				= "help";
 	commands["reverse.seqs"]		= "reverse.seqs";
 	commands["trim.seqs"]			= "trim.seqs";
 	commands["list.seqs"]			= "list.seqs";
@@ -153,6 +160,15 @@ CommandFactory::CommandFactory(){
 	commands["parse.list"]			= "parse.list";
 	commands["parse.sff"]			= "parse.sff";
 	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["cluster.split"]		= "cluster.split";
+	commands["classify.otu"]		= "classify.otu";
+	commands["degap.seqs"]			= "degap.seqs";
 	commands["classify.seqs"]		= "MPIEnabled"; 
 	commands["dist.seqs"]			= "MPIEnabled";
 	commands["filter.seqs"]			= "MPIEnabled";
@@ -163,6 +179,8 @@ CommandFactory::CommandFactory(){
 	commands["chimera.slayer"]		= "MPIEnabled";
 	commands["chimera.pintail"]		= "MPIEnabled";
 	commands["chimera.bellerophon"]	= "MPIEnabled";
+	commands["screen.seqs"]			= "MPIEnabled";
+	commands["summary.seqs"]		= "MPIEnabled";
 	commands["quit"]				= "MPIEnabled"; 
 
 }
@@ -235,7 +253,7 @@ 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);				}
@@ -267,6 +285,15 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "set.logfile")			{	command = new SetLogFileCommand(optionString);				}
 		else if(commandName == "parse.list")			{	command = new ParseListCommand(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											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -318,9 +345,9 @@ 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;
 	}