X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=ea43c48e6b84e4c2e83de0c067e081c2a88da49f;hb=d5d2761f88b41f1006d0b700e0ab51e2ce48b875;hp=224a4cc7761fe145da05c48297f36a46d29fe09c;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 224a4cc..ea43c48 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -8,26 +8,39 @@
  */
 
 #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 "heatmapcommand.h"
+#include "filterseqscommand.h"
+#include "mothur.h"
+#include "venncommand.h"
+#include "nocommands.h"
+#include "binsequencecommand.h"
+#include "getoturepcommand.h"
+#include "treegroupscommand.h"
+#include "bootstrapsharedcommand.h"
+#include "concensuscommand.h"
+#include "distancecommand.h"
 
 
 /***********************************************************/
@@ -36,7 +49,6 @@
 CommandFactory::CommandFactory(){
 	command = new NoCommand();
 }
-
 /***********************************************************/
 
 /***********************************************************/
@@ -52,24 +64,36 @@ 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 if(commandName == "heatmap")				{   command = new HeatMapCommand();				}
+		else if(commandName == "filter.seqs")			{   command = new FilterSeqsCommand();          }
+		else if(commandName == "venn")					{   command = new VennCommand();				}
+		else if(commandName == "bin.seqs")				{   command = new BinSeqCommand();				}
+		else if(commandName == "get.oturep")			{   command = new GetOTURepCommand();			}
+		else if(commandName == "tree.shared")			{   command = new TreeGroupCommand();			}
+		else if(commandName == "bootstrap.shared")		{   command = new BootSharedCommand();			}
+		else if(commandName == "concensus")				{   command = new ConcensusCommand();			}
+		else if(commandName == "distance")				{   command = new DistanceCommand();			}
+		else											{	command = new NoCommand();					}
 
 		return command;
 	}
@@ -85,4 +109,3 @@ Command* CommandFactory::getCommand(string commandName){
 }
 /***********************************************************/
 
-/***********************************************************/
\ No newline at end of file