X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=5a32ac1a526450b8d9408a88e0e57cc31e946720;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=8ab0a9529ba697aece318c7e11301f9e465b19c3;hpb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 8ab0a95..5a32ac1 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -148,6 +148,7 @@
 #include "makelefsecommand.h"
 #include "lefsecommand.h"
 #include "kruskalwalliscommand.h"
+#include "sracommand.h"
 
 /*******************************************************/
 
@@ -319,6 +320,7 @@ CommandFactory::CommandFactory(){
     commands["make.lefse"]          = "make.lefse";
     commands["lefse"]               = "lefse";
     commands["kruskal.wallis"]      = "kruskal.wallis";
+    commands["sra"]                 = "sra";
     
 
 }
@@ -408,7 +410,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 			else { optionString += "inputdir=" + inputDir; }
 		}
 		
-		if(commandName == "cluster")				{	command = new ClusterCommand(optionString);					}
+		if(commandName == "cluster")                    {	command = new ClusterCommand(optionString);					}
 		else if(commandName == "unique.seqs")			{	command = new DeconvoluteCommand(optionString);				}
 		else if(commandName == "parsimony")				{	command = new ParsimonyCommand(optionString);				}
 		else if(commandName == "help")					{	command = new HelpCommand(optionString);					}
@@ -533,7 +535,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "make.contigs")          {	command = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {	command = new LoadLogfileCommand(optionString);             }
         else if(commandName == "sff.multiple")          {	command = new SffMultipleCommand(optionString);             }
-        else if(commandName == "classify.rf")           {	command = new ClassifyRFSharedCommand(optionString);          }
+        else if(commandName == "classify.rf")           {	command = new ClassifyRFSharedCommand(optionString);        }
         else if(commandName == "filter.shared")         {	command = new FilterSharedCommand(optionString);            }
         else if(commandName == "primer.design")         {	command = new PrimerDesignCommand(optionString);            }
         else if(commandName == "get.dists")             {	command = new GetDistsCommand(optionString);                }
@@ -546,6 +548,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "make.lefse")			{	command = new MakeLefseCommand(optionString);				}
         else if(commandName == "lefse")                 {	command = new LefseCommand(optionString);                   }
         else if(commandName == "kruskal.wallis")        {	command = new KruskalWallisCommand(optionString);           }
+        else if(commandName == "sra")                   {	command = new SRACommand(optionString);                     }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -714,6 +717,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "make.lefse")			{	pipecommand = new MakeLefseCommand(optionString);				}
         else if(commandName == "lefse")                 {	pipecommand = new LefseCommand(optionString);                   }
         else if(commandName == "kruskal.wallis")        {	pipecommand = new KruskalWallisCommand(optionString);           }
+        else if(commandName == "sra")                   {	pipecommand = new SRACommand(optionString);                     }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -868,6 +872,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "make.lefse")			{	shellcommand = new MakeLefseCommand();				}
         else if(commandName == "lefse")                 {	shellcommand = new LefseCommand();                  }
         else if(commandName == "kruskal.wallis")        {	shellcommand = new KruskalWallisCommand();          }
+        else if(commandName == "sra")                   {	shellcommand = new SRACommand();                    }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;