X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=8c5c0faef60a480a189f98994afc250e4c36a8c6;hb=a89c6295ae9a35fcaaab7fa50dcb68360dd543b0;hp=c247f908ca190087e4a30bb05ea31d88a0e7fd6b;hpb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index c247f90..8c5c0fa 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -148,6 +148,9 @@
 #include "makelefsecommand.h"
 #include "lefsecommand.h"
 #include "kruskalwalliscommand.h"
+#include "sracommand.h"
+#include "mergesfffilecommand.h"
+#include "getmimarkspackagecommand.h"
 
 /*******************************************************/
 
@@ -319,6 +322,9 @@ CommandFactory::CommandFactory(){
     commands["make.lefse"]          = "make.lefse";
     commands["lefse"]               = "lefse";
     commands["kruskal.wallis"]      = "kruskal.wallis";
+    commands["sra"]                 = "sra";
+    commands["merge.sfffiles"]      = "merge.sfffiles";
+    commands["get.mimarkspackage"]  = "get.mimarkspackage";
     
 
 }
@@ -533,7 +539,7 @@ 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 +552,9 @@ 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 if(commandName == "merge.sfffiles")        {	command = new MergeSfffilesCommand(optionString);           }
+        else if(commandName == "get.mimarkspackage")    {	command = new GetMIMarksPackageCommand(optionString);       }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -714,6 +723,9 @@ 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 if(commandName == "merge.sfffiles")        {	pipecommand = new MergeSfffilesCommand(optionString);           }
+        else if(commandName == "get.mimarkspackage")    {	pipecommand = new GetMIMarksPackageCommand(optionString);       }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -868,6 +880,9 @@ 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 if(commandName == "merge.sfffiles")        {	shellcommand = new MergeSfffilesCommand();          }
+        else if(commandName == "get.mimarkspackage")    {	shellcommand = new GetMIMarksPackageCommand();      }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;