X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=56fd56b348bdb497cdb04b01d01f4c3a87901a61;hb=29351fe29c017d2225366418973ed0e000ce5293;hp=49d197c40b9fe215f8067fa8d8a8f6ddb262f45c;hpb=67b6343929b6dbed97c4b26c3bb849725d573f6d;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 49d197c..56fd56b 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -9,22 +9,30 @@
 
 #include "command.hpp"
 #include "readdistcommand.h"
+#include "readtreecommand.h"
 #include "readotucommand.h"
-#include "readlistcommand.h"
 #include "clustercommand.h"
 #include "parselistcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
+#include "getgroupcommand.h"
+#include "getlabelcommand.h"
+#include "getlinecommand.h"
 #include "rarefactcommand.h"
 #include "summarycommand.h"
 #include "summarysharedcommand.h"
 #include "rarefactsharedcommand.h"
-#include "nocommand.h"
 #include "quitcommand.h"
 #include "helpcommand.h"
 #include "commandfactory.hpp"
 #include "deconvolutecommand.h"
-#include <exception>
+#include "parsimonycommand.h"
+#include "unifracunweightedcommand.h"
+#include "unifracweightedcommand.h"
+#include "libshuffcommand.h"
+#include "heatmapcommand.h"
+#include "mothur.h"
+#include "nocommands.h"
 
 
 /***********************************************************/
@@ -33,7 +41,6 @@
 CommandFactory::CommandFactory(){
 	command = new NoCommand();
 }
-
 /***********************************************************/
 
 /***********************************************************/
@@ -49,20 +56,28 @@ Command* CommandFactory::getCommand(string commandName){
 	try {
 		delete command;   //delete the old command
 
-			 if(commandName == "read.dist")				{	command = new ReadDistCommand();		}
-		else if(commandName == "read.otu")				{	command = new ReadOtuCommand();			}
-		else if(commandName == "read.list")				{	command = new ReadListFileCommand();	}
-		else if(commandName == "cluster")				{	command = new ClusterCommand();			}
-		else if(commandName == "deconvolute")			{	command = new DeconvoluteCommand();		}
-		else if(commandName == "help")					{	command = new HelpCommand();			}
-		else if(commandName == "quit")					{	command = new QuitCommand();			}
-		else if(commandName == "collect.single")		{	command = new CollectCommand();			}
-		else if(commandName == "collect.shared")		{	command = new CollectSharedCommand();	}
-		else if(commandName == "rarefaction.single")	{	command = new RareFactCommand();		}
-		else if(commandName == "rarefaction.shared")	{	command = new RareFactSharedCommand();	}
-		else if(commandName == "summary.single")		{	command = new SummaryCommand();			}
-		else if(commandName == "summary.shared")		{	command = new SummarySharedCommand();	}
-		else											{	command = new NoCommand();				}
+			 if(commandName == "read.dist")				{	command = new ReadDistCommand();			}
+		else if(commandName == "read.otu")				{	command = new ReadOtuCommand();				}
+		else if(commandName == "read.tree")				{	command = new ReadTreeCommand();			}
+		else if(commandName == "cluster")				{	command = new ClusterCommand();				}
+		else if(commandName == "deconvolute")			{	command = new DeconvoluteCommand();			}
+		else if(commandName == "parsimony")				{	command = new ParsimonyCommand();			}
+		else if(commandName == "help")					{	command = new HelpCommand();				}
+		else if(commandName == "quit")					{	command = new QuitCommand();				}
+		else if(commandName == "collect.single")		{	command = new CollectCommand();				}
+		else if(commandName == "collect.shared")		{	command = new CollectSharedCommand();		}
+		else if(commandName == "rarefaction.single")	{	command = new RareFactCommand();			}
+		else if(commandName == "rarefaction.shared")	{	command = new RareFactSharedCommand();		}
+		else if(commandName == "summary.single")		{	command = new SummaryCommand();				}
+		else if(commandName == "summary.shared")		{	command = new SummarySharedCommand();		}
+		else if(commandName == "unifrac.weighted")		{	command = new UnifracWeightedCommand();		}
+		else if(commandName == "unifrac.unweighted")	{	command = new UnifracUnweightedCommand();	}
+		else if(commandName == "get.group")             {   command = new GetgroupCommand();			}
+		else if(commandName == "get.label")             {   command = new GetlabelCommand();			}
+		else if(commandName == "get.line")              {   command = new GetlineCommand();				}
+		else if(commandName == "libshuff")              {   command = new LibShuffCommand();			}
+		else if(commandName == "heatmap")				{   command = new HeatMapCommand();				}
+		else											{	command = new NoCommand();					}
 
 		return command;
 	}
@@ -78,4 +93,3 @@ Command* CommandFactory::getCommand(string commandName){
 }
 /***********************************************************/
 
-/***********************************************************/
\ No newline at end of file