X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=a559c81a4fc5a5703858be458d3e472420723f27;hb=986663e2220f6b043ee83d1699cfa081dc49cbed;hp=ea43c48e6b84e4c2e83de0c067e081c2a88da49f;hpb=d5d2761f88b41f1006d0b700e0ab51e2ce48b875;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ea43c48..a559c81 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -41,7 +41,13 @@
 #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"
+#include "reversecommand.h"
 
 /***********************************************************/
 
@@ -64,11 +70,11 @@ 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();				}
-		else if(commandName == "deconvolute")			{	command = new DeconvoluteCommand();			}
+		else if(commandName == "unique.seqs")			{	command = new DeconvoluteCommand();			}
 		else if(commandName == "parsimony")				{	command = new ParsimonyCommand();			}
 		else if(commandName == "help")					{	command = new HelpCommand();				}
 		else if(commandName == "quit")					{	command = new QuitCommand();				}
@@ -83,6 +89,8 @@ 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();          }
@@ -90,9 +98,14 @@ Command* CommandFactory::getCommand(string commandName){
 		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 == "distance")				{   command = new DistanceCommand();			}
+		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 if(commandName == "reverse.seqs")			{	command = new ReverseSeqsCommand();			}
 		else											{	command = new NoCommand();					}
 
 		return command;