X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=63e0690f40cebb2b1ac0bf1b481a6848261c71bd;hb=1b49ed179327150ebf24d77b33d9b3e6872cc8c0;hp=a401177f74a97a3c61f9373a6390c249f24403a7;hpb=e74ac2023625728a7e1e57fa15004101a6270cd9;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index a401177..63e0690 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -48,7 +48,6 @@
 #include "reversecommand.h"
 #include "trimseqscommand.h"
 #include "mergefilecommand.h"
-#include "chimeraseqscommand.h"
 #include "listseqscommand.h"
 #include "getseqscommand.h"
 #include "removeseqscommand.h"
@@ -114,6 +113,10 @@
 #include "mantelcommand.h"
 #include "makefastqcommand.h"
 #include "anosimcommand.h"
+#include "getcurrentcommand.h"
+#include "setcurrentcommand.h"
+#include "sharedcommand.h"
+#include "getcommandinfocommand.h"
 
 /*******************************************************/
 
@@ -149,6 +152,7 @@ CommandFactory::CommandFactory(){
 	commands["read.dist"]			= "read.dist"; 
 	commands["read.otu"]			= "read.otu";
 	commands["read.tree"]			= "read.tree"; 
+	commands["make.shared"]			= "make.shared"; 
 	commands["bin.seqs"]			= "bin.seqs"; 
 	commands["get.oturep"]			= "get.oturep";
 	commands["cluster"]				= "cluster"; 
@@ -180,7 +184,7 @@ CommandFactory::CommandFactory(){
 	commands["trim.flows"]			= "trim.flows";
 	commands["list.seqs"]			= "list.seqs";
 	commands["get.seqs"]			= "get.seqs";
-	commands["remove.seqs"]			= "get.seqs";
+	commands["remove.seqs"]			= "remove.seqs";
 	commands["system"]				= "system";
 	commands["align.check"]			= "align.check";
 	commands["get.sharedseqs"]		= "get.sharedseqs";
@@ -231,13 +235,15 @@ CommandFactory::CommandFactory(){
 	commands["anosim"]				= "anosim";
 	commands["make.fastq"]			= "make.fastq";
 	commands["merge.groups"]		= "merge.groups";
+	commands["get.current"]			= "get.current";
+	commands["set.current"]			= "set.current";
+	commands["get.commandinfo"]		= "get.commandinfo";
 	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	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";
@@ -332,7 +338,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "trim.seqs")				{	command = new TrimSeqsCommand(optionString);				}
 		else if(commandName == "trim.flows")			{	command = new TrimFlowsCommand(optionString);				}
 		else if(commandName == "shhh.seqs")				{	command = new ShhherCommand(optionString);					}
-		else if(commandName == "chimera.seqs")			{	command = new ChimeraSeqsCommand(optionString);				}
 		else if(commandName == "list.seqs")				{	command = new ListSeqsCommand(optionString);				}
 		else if(commandName == "get.seqs")				{	command = new GetSeqsCommand(optionString);					}
 		else if(commandName == "remove.seqs")			{	command = new RemoveSeqsCommand(optionString);				}
@@ -396,7 +401,11 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "homova")				{	command = new HomovaCommand(optionString);					}
 		else if(commandName == "mantel")				{	command = new MantelCommand(optionString);					}
 		else if(commandName == "make.fastq")			{	command = new MakeFastQCommand(optionString);				}
+		else if(commandName == "get.current")			{	command = new GetCurrentCommand(optionString);				}
+		else if(commandName == "set.current")			{	command = new SetCurrentCommand(optionString);				}
 		else if(commandName == "anosim")				{	command = new AnosimCommand(optionString);					}
+		else if(commandName == "make.shared")			{	command = new SharedCommand(optionString);					}
+		else if(commandName == "get.commandinfo")		{	command = new GetCommandInfoCommand(optionString);			}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -465,7 +474,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "trim.seqs")				{	pipecommand = new TrimSeqsCommand(optionString);				}
 		else if(commandName == "trim.flows")			{	pipecommand = new TrimFlowsCommand(optionString);				}
 		else if(commandName == "shhh.seqs")				{	pipecommand = new ShhherCommand(optionString);					}
-		else if(commandName == "chimera.seqs")			{	pipecommand = new ChimeraSeqsCommand(optionString);				}
 		else if(commandName == "list.seqs")				{	pipecommand = new ListSeqsCommand(optionString);				}
 		else if(commandName == "get.seqs")				{	pipecommand = new GetSeqsCommand(optionString);					}
 		else if(commandName == "remove.seqs")			{	pipecommand = new RemoveSeqsCommand(optionString);				}
@@ -529,6 +537,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "mantel")				{	pipecommand = new MantelCommand(optionString);					}
 		else if(commandName == "anosim")				{	pipecommand = new AnosimCommand(optionString);					}
 		else if(commandName == "make.fastq")			{	pipecommand = new MakeFastQCommand(optionString);				}
+		else if(commandName == "get.current")			{	pipecommand = new GetCurrentCommand(optionString);				}
+		else if(commandName == "set.current")			{	pipecommand = new SetCurrentCommand(optionString);				}
+		else if(commandName == "make.shared")			{	pipecommand = new SharedCommand(optionString);					}
+		else if(commandName == "get.commandinfo")		{	pipecommand = new GetCommandInfoCommand(optionString);			}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -585,7 +597,6 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "trim.seqs")				{	shellcommand = new TrimSeqsCommand();				}
 		else if(commandName == "trim.flows")			{	shellcommand = new TrimFlowsCommand();				}
 		else if(commandName == "shhh.seqs")				{	shellcommand = new ShhherCommand();					}
-		else if(commandName == "chimera.seqs")			{	shellcommand = new ChimeraSeqsCommand();			}
 		else if(commandName == "list.seqs")				{	shellcommand = new ListSeqsCommand();				}
 		else if(commandName == "get.seqs")				{	shellcommand = new GetSeqsCommand();				}
 		else if(commandName == "remove.seqs")			{	shellcommand = new RemoveSeqsCommand();				}
@@ -649,6 +660,10 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "mantel")				{	shellcommand = new MantelCommand();					}
 		else if(commandName == "anosim")				{	shellcommand = new AnosimCommand();					}
 		else if(commandName == "make.fastq")			{	shellcommand = new MakeFastQCommand();				}
+		else if(commandName == "get.current")			{	shellcommand = new GetCurrentCommand();				}
+		else if(commandName == "set.current")			{	shellcommand = new SetCurrentCommand();				}
+		else if(commandName == "make.shared")			{	shellcommand = new SharedCommand();					}
+		else if(commandName == "get.commandinfo")		{	shellcommand = new GetCommandInfoCommand();			}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;