X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=bd519eebfd6eaa24134dad9ac08f2193004e6386;hb=7a8fc1115b3871107c09a4b9b307b1f2ab7d3fcf;hp=aaeec67f1b4eec4e2194fc014e87064c1d5c2b5c;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index aaeec67..bd519ee 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -71,6 +71,15 @@
 #include "chimeraslayercommand.h"
 #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"
 
 /*******************************************************/
 
@@ -97,6 +106,8 @@ CommandFactory::CommandFactory(){
 	command = new NoCommand(s);
 	
 	outputDir = ""; inputDir = "";
+	logFileName = "";
+	append = false;
 	
 	//initialize list of valid commands
 	commands["read.dist"]			= "read.dist"; 
@@ -127,9 +138,7 @@ 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";
@@ -149,6 +158,15 @@ CommandFactory::CommandFactory(){
 	commands["merge.files"]			= "merge.files";
 	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["classify.seqs"]		= "MPIEnabled"; 
 	commands["dist.seqs"]			= "MPIEnabled";
 	commands["filter.seqs"]			= "MPIEnabled";
@@ -159,6 +177,8 @@ 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"; 
 
 }
@@ -231,7 +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);				}
@@ -260,8 +280,17 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "pcoa")					{	command = new PCACommand(optionString);						}
 		else if(commandName == "otu.hierarchy")			{	command = new OtuHierarchyCommand(optionString);			}
 		else if(commandName == "set.dir")				{	command = new SetDirectoryCommand(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											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -313,9 +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;
 	}