X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=4d2b0ae2b93a6e205ae8b8d24a86dea37c2f6606;hb=62568a297aaf939ab753334f17abde82ec8e8531;hp=b4f36549c0c65a22d0b2ad6057b9e07e294a4c65;hpb=17a6a53298a907c005fa93fb82af9e533adcda09;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index b4f3654..4d2b0ae 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -65,6 +65,20 @@
 #include "otuhierarchycommand.h"
 #include "setdircommand.h"
 #include "parselistscommand.h"
+#include "parsesffcommand.h"
+#include "chimeraccodecommand.h"
+#include "chimeracheckcommand.h"
+#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"
 
 /*******************************************************/
 
@@ -78,6 +92,12 @@ CommandFactory* CommandFactory::getInstance() {
 /***********************************************************/
 
 /***********************************************************/
+//note: This class is resposible for knowing which commands are mpiEnabled,
+//If a command is not enabled only process 0 will execute the command. 
+//This avoids redundant outputs on pieces of code we have not paralellized. 
+//If you add mpi code to a existing command you need to modify the list below or the code will hang on MPI blocking commands like FIle_open. 
+//example:  commands["dist.seqs"] = "MPIEnabled";
+
 CommandFactory::CommandFactory(){
 	string s = "";
 	m = MothurOut::getInstance();
@@ -85,6 +105,8 @@ CommandFactory::CommandFactory(){
 	command = new NoCommand(s);
 	
 	outputDir = ""; inputDir = "";
+	logFileName = "";
+	append = false;
 	
 	//initialize list of valid commands
 	commands["read.dist"]			= "read.dist"; 
@@ -94,7 +116,6 @@ CommandFactory::CommandFactory(){
 	commands["get.oturep"]			= "get.oturep";
 	commands["cluster"]				= "cluster"; 
 	commands["unique.seqs"]			= "unique.seqs"; 
-	commands["dist.seqs"]			= "dist.seqs";
 	commands["dist.shared"]			= "dist.shared";
 	commands["collect.single"]		= "collect.single"; 
 	commands["collect.shared"]		= "collect.shared"; 
@@ -116,14 +137,9 @@ CommandFactory::CommandFactory(){
 	commands["get.rabund"]          = "get.rabund";
 	commands["bootstrap.shared"]	= "bootstrap.shared";
 	//commands["consensus"]			= "consensus";
-	commands["help"]				= "help"; 
-	commands["filter.seqs"]			= "MPIEnabled";
-	commands["align.seqs"]			= "align.seqs";
-	commands["summary.seqs"]		= "summary.seqs";
-	commands["screen.seqs"]			= "screen.seqs";
+	commands["help"]				= "help";
 	commands["reverse.seqs"]		= "reverse.seqs";
 	commands["trim.seqs"]			= "trim.seqs";
-	commands["chimera.seqs"]		= "chimera.seqs";
 	commands["list.seqs"]			= "list.seqs";
 	commands["get.seqs"]			= "get.seqs";
 	commands["remove.seqs"]			= "get.seqs";
@@ -131,9 +147,7 @@ CommandFactory::CommandFactory(){
 	commands["align.check"]			= "align.check";
 	commands["get.sharedseqs"]		= "get.sharedseqs";
 	commands["get.otulist"]			= "get.otulist";
-	commands["quit"]				= "MPIEnabled"; 
 	commands["hcluster"]			= "hcluster"; 
-	commands["classify.seqs"]		= "classify.seqs"; 
 	commands["phylotype"]			= "phylotype";
 	commands["mgcluster"]			= "mgcluster";
 	commands["pre.cluster"]			= "pre.cluster";
@@ -142,6 +156,29 @@ CommandFactory::CommandFactory(){
 	commands["set.dir"]				= "set.dir";
 	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.seqs"]		= "MPIEnabled"; 
+	commands["dist.seqs"]			= "MPIEnabled";
+	commands["filter.seqs"]			= "MPIEnabled";
+	commands["align.seqs"]			= "MPIEnabled";
+	commands["chimera.seqs"]		= "chimera.seqs";
+	commands["chimera.ccode"]		= "MPIEnabled";
+	commands["chimera.check"]		= "MPIEnabled";
+	commands["chimera.slayer"]		= "MPIEnabled";
+	commands["chimera.pintail"]		= "MPIEnabled";
+	commands["chimera.bellerophon"]	= "MPIEnabled";
+	commands["screen.seqs"]			= "MPIEnabled";
+	commands["summary.seqs"]		= "MPIEnabled";
+	commands["quit"]				= "MPIEnabled"; 
+
 }
 /***********************************************************/
 
@@ -230,13 +267,27 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "get.otulist")			{	command = new GetListCountCommand(optionString);			}
 		else if(commandName == "hcluster")				{	command = new HClusterCommand(optionString);				}
 		else if(commandName == "classify.seqs")			{	command = new ClassifySeqsCommand(optionString);			}
+		else if(commandName == "chimera.ccode")			{	command = new ChimeraCcodeCommand(optionString);			}
+		else if(commandName == "chimera.check")			{	command = new ChimeraCheckCommand(optionString);			}
+		else if(commandName == "chimera.slayer")		{	command = new ChimeraSlayerCommand(optionString);			}
+		else if(commandName == "chimera.pintail")		{	command = new ChimeraPintailCommand(optionString);			}
+		else if(commandName == "chimera.bellerophon")	{	command = new ChimeraBellerophonCommand(optionString);		}
 		else if(commandName == "phylotype")				{	command = new PhylotypeCommand(optionString);				}
 		else if(commandName == "mgcluster")				{	command = new MGClusterCommand(optionString);				}
 		else if(commandName == "pre.cluster")			{	command = new PreClusterCommand(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											{	command = new NoCommand(optionString);						}
 
 		return command;