X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=21e7b54548a370065ab554d3a2b0f7b5c4887146;hb=0e14094b51dd81c07c6a56b7b51533eff2332339;hp=c03751518e3e9a2ab54da2e38be693e08a3d6c34;hpb=ec453945974b5c72af0bea042e3517312566d592;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index c037515..21e7b54 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -41,6 +41,9 @@
 #include "bootstrapsharedcommand.h"
 #include "concensuscommand.h"
 #include "distancecommand.h"
+#include "aligncommand.h"
+#include "getrepseqscommand.h"
+#include "matrixoutputcommand.h"
 
 
 /***********************************************************/
@@ -88,11 +91,14 @@ Command* CommandFactory::getCommand(string commandName){
 		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.repseqs")			{   command = new GetRepSeqsCommand();			}
 		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.seq")				{   command = new DistanceCommand();			}
+		else if(commandName == "dist.seqs")				{   command = new DistanceCommand();			}
+		else if(commandName == "align.seqs")			{   command = new AlignCommand();				}
 		else											{	command = new NoCommand();					}
 
 		return command;