X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=7670d412df334d2d656000cf07349aa404ffd21b;hb=66f474db0824eebab0cebd53992728a0e5c789ca;hp=224a4cc7761fe145da05c48297f36a46d29fe09c;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 224a4cc..7670d41 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -8,26 +8,30 @@
  */
 
 #include "command.hpp"
-#include "readdistphylipfilecommand.h"
-#include "readdistcolumnfilecommand.h"
-#include "readlistfilecommand.h"
-#include "readrabundfilecommand.h"
-#include "readsabundfilecommand.h"
-#include "readsharedfilecommand.h"
+#include "readdistcommand.h"
+#include "readtreecommand.h"
+#include "readotucommand.h"
 #include "clustercommand.h"
 #include "parselistcommand.h"
-#include "sharedcommand.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 <exception>
+#include "deconvolutecommand.h"
+#include "parsimonycommand.h"
+#include "unifracunweightedcommand.h"
+#include "unifracweightedcommand.h"
+#include "libshuffcommand.h"
+#include "mothur.h"
+#include "nocommands.h"
 
 
 /***********************************************************/
@@ -36,7 +40,6 @@
 CommandFactory::CommandFactory(){
 	command = new NoCommand();
 }
-
 /***********************************************************/
 
 /***********************************************************/
@@ -52,24 +55,27 @@ Command* CommandFactory::getCommand(string commandName){
 	try {
 		delete command;   //delete the old command
 
-			 if(commandName == "read.phylip")			{	command = new ReadDistPhylipFileCommand();	}
-		else if(commandName == "read.column")			{	command = new ReadDistColumnFileCommand();	}
-		else if(commandName == "read.list")				{	command = new ReadListFileCommand();	}
-		else if(commandName == "read.rabund")			{	command = new ReadRAbundFileCommand();	}
-		else if(commandName == "read.sabund")			{	command = new ReadSAbundFileCommand();	}
-		else if(commandName == "read.shared")			{	command = new ReadSharedFileCommand();	}
-		else if(commandName == "cluster")				{	command = new ClusterCommand();			}
-		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 == "shared")				{	command = new SharedCommand();			}
-		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 == "parselist")				{	command = new ParseListCommand();		}
-		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											{	command = new NoCommand();					}
 
 		return command;
 	}
@@ -85,4 +91,3 @@ Command* CommandFactory::getCommand(string commandName){
 }
 /***********************************************************/
 
-/***********************************************************/
\ No newline at end of file