X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.cpp;h=e8e9c2754677ee639fce944fbc533d3bd9eb98db;hp=03c3e49ccff50f128c657780da2b9d8109289358;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=bcb6728939694811bf6a00ae6d568f783840edfd

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 03c3e49..e8e9c27 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -148,6 +148,8 @@
 #include "makelefsecommand.h"
 #include "lefsecommand.h"
 #include "kruskalwalliscommand.h"
+#include "sracommand.h"
+#include "mergesfffilecommand.h"
 
 /*******************************************************/
 
@@ -306,7 +308,7 @@ CommandFactory::CommandFactory(){
     commands["make.table"]          = "make.table";
     commands["sff.multiple"]        = "sff.multiple";
 	commands["quit"]				= "MPIEnabled"; 
-    commands["classifyrf.shared"]		= "classifyrf.shared"; 
+    commands["classify.rf"]         = "classify.rf"; 
     commands["filter.shared"]		= "filter.shared"; 
     commands["primer.design"]		= "primer.design";
     commands["get.dists"]           = "get.dists";
@@ -319,6 +321,8 @@ CommandFactory::CommandFactory(){
     commands["make.lefse"]          = "make.lefse";
     commands["lefse"]               = "lefse";
     commands["kruskal.wallis"]      = "kruskal.wallis";
+    commands["sra"]                 = "sra";
+    commands["merge.sfffiles"]      = "merge.sfffiles";
     
 
 }
@@ -408,7 +412,7 @@ 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 +537,7 @@ 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 == "classifyrf.shared")       {	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 +550,8 @@ 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											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -701,7 +707,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "make.contigs")          {	pipecommand = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {	pipecommand = new LoadLogfileCommand(optionString);             }
         else if(commandName == "sff.multiple")          {	pipecommand = new SffMultipleCommand(optionString);             }
-        else if(commandName == "classifyrf.shared")       {	pipecommand = new ClassifyRFSharedCommand(optionString);          }
+        else if(commandName == "classify.rf")           {	pipecommand = new ClassifyRFSharedCommand(optionString);        }
         else if(commandName == "filter.shared")         {	pipecommand = new FilterSharedCommand(optionString);            }
         else if(commandName == "primer.design")         {	pipecommand = new PrimerDesignCommand(optionString);            }
         else if(commandName == "get.dists")             {	pipecommand = new GetDistsCommand(optionString);                }
@@ -714,6 +720,8 @@ 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											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -855,7 +863,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "make.contigs")          {	shellcommand = new MakeContigsCommand();            }
         else if(commandName == "load.logfile")          {	shellcommand = new LoadLogfileCommand();            }
         else if(commandName == "sff.multiple")          {	shellcommand = new SffMultipleCommand();            }
-        else if(commandName == "classifyrf.shared")       {	shellcommand = new ClassifyRFSharedCommand();         }
+        else if(commandName == "classify.rf")           {	shellcommand = new ClassifyRFSharedCommand();       }
         else if(commandName == "filter.shared")         {	shellcommand = new FilterSharedCommand();           }
         else if(commandName == "primer.design")         {	shellcommand = new PrimerDesignCommand();           }
         else if(commandName == "get.dists")             {	shellcommand = new GetDistsCommand();               }
@@ -868,6 +876,8 @@ 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											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;