X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=7b3a5c024fa31655a22946f3b5b2a86af6ae5b79;hb=dc874a77f24b3808775e2ce7e39595c647a07f82;hp=ff156139ea3f3c1d67791d440113177fc261a700;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ff15613..7b3a5c0 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -31,12 +31,22 @@
 #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"
+#include "aligncommand.h"
+#include "matrixoutputcommand.h"
+#include "getsabundcommand.h"
+#include "getrabundcommand.h"
+#include "seqsummarycommand.h"
+#include "screenseqscommand.h"
 
 
 /***********************************************************/
@@ -60,7 +70,7 @@ Command* CommandFactory::getCommand(string commandName){
 	try {
 		delete command;   //delete the old command
 
-			 if(commandName == "read.dist")				{	command = new ReadDistCommand();			}
+		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();				}
@@ -79,13 +89,22 @@ Command* CommandFactory::getCommand(string commandName){
 		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 == "get.sabund")            {   command = new GetSAbundCommand();			}
+		else if(commandName == "get.rabund")            {   command = new GetRAbundCommand();			}
 		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 == "dist.shared")			{   command = new MatrixOutputCommand();		}
 		else if(commandName == "bootstrap.shared")		{   command = new BootSharedCommand();			}
+		else if(commandName == "concensus")				{   command = new ConcensusCommand();			}
+		else if(commandName == "dist.seqs")				{   command = new DistanceCommand();			}
+		else if(commandName == "align.seqs")			{   command = new AlignCommand();				}
+		else if(commandName == "summary.seqs")			{	command = new SeqSummaryCommand();			}
+		else if(commandName == "screen.seqs")			{	command = new ScreenSeqsCommand();			}
 		else											{	command = new NoCommand();					}
 
 		return command;