X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.cpp;h=e8e9c2754677ee639fce944fbc533d3bd9eb98db;hp=41a67297c4199ab819ef7f0498dfd27e6debd515;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=b25ede2ad307ae76f8a610443e0ec3ec69621ce7

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 41a6729..e8e9c27 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -135,7 +135,7 @@
 #include "makecontigscommand.h"
 #include "loadlogfilecommand.h"
 #include "sffmultiplecommand.h"
-#include "classifysharedcommand.h"
+#include "classifyrfsharedcommand.h"
 #include "filtersharedcommand.h"
 #include "primerdesigncommand.h"
 #include "getdistscommand.h"
@@ -148,6 +148,8 @@
 #include "makelefsecommand.h"
 #include "lefsecommand.h"
 #include "kruskalwalliscommand.h"
+#include "sracommand.h"
+#include "mergesfffilecommand.h"
 
 /*******************************************************/
 
@@ -306,19 +308,21 @@ CommandFactory::CommandFactory(){
     commands["make.table"]          = "make.table";
     commands["sff.multiple"]        = "sff.multiple";
 	commands["quit"]				= "MPIEnabled"; 
-    commands["classify.shared"]		= "classify.shared"; 
+    commands["classify.rf"]         = "classify.rf"; 
     commands["filter.shared"]		= "filter.shared"; 
     commands["primer.design"]		= "primer.design";
     commands["get.dists"]           = "get.dists";
     commands["remove.dists"]        = "remove.dists";
     commands["merge.taxsummary"]    = "merge.taxsummary";
-    commands["get.metacommunity"]   = "get.metacommunity";
+    commands["get.communitytype"]   = "get.communitytype";
     commands["sparcc"]              = "sparcc";
     commands["make.lookup"]         = "make.lookup";
     commands["rename.seqs"]         = "rename.seqs";
     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);					}
@@ -533,19 +537,21 @@ 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.shared")       {	command = new ClassifySharedCommand(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);                }
         else if(commandName == "remove.dists")          {	command = new RemoveDistsCommand(optionString);             }
         else if(commandName == "merge.taxsummary")      {	command = new MergeTaxSummaryCommand(optionString);         }
-        else if(commandName == "get.metacommunity")     {	command = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "get.communitytype")     {	command = new GetMetaCommunityCommand(optionString);        }
         else if(commandName == "sparcc")                {	command = new SparccCommand(optionString);                  }
         else if(commandName == "make.lookup")			{	command = new MakeLookupCommand(optionString);				}
         else if(commandName == "rename.seqs")			{	command = new RenameSeqsCommand(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;
@@ -701,19 +707,21 @@ 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 == "classify.shared")       {	pipecommand = new ClassifySharedCommand(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);                }
         else if(commandName == "remove.dists")          {	pipecommand = new RemoveDistsCommand(optionString);             }
         else if(commandName == "merge.taxsummary")      {	pipecommand = new MergeTaxSummaryCommand(optionString);         }
-        else if(commandName == "get.metacommunity")     {	pipecommand = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "get.communitytype")     {	pipecommand = new GetMetaCommunityCommand(optionString);        }
         else if(commandName == "sparcc")                {	pipecommand = new SparccCommand(optionString);                  }
         else if(commandName == "make.lookup")			{	pipecommand = new MakeLookupCommand(optionString);				}
         else if(commandName == "rename.seqs")			{	pipecommand = new RenameSeqsCommand(optionString);				}
         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;
@@ -855,19 +863,21 @@ 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 == "classify.shared")       {	shellcommand = new ClassifySharedCommand();         }
+        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();               }
         else if(commandName == "remove.dists")          {	shellcommand = new RemoveDistsCommand();            }
         else if(commandName == "merge.taxsummary")      {	shellcommand = new MergeTaxSummaryCommand();        }
-        else if(commandName == "get.metacommunity")     {	shellcommand = new GetMetaCommunityCommand();       }
+        else if(commandName == "get.communitytype")     {	shellcommand = new GetMetaCommunityCommand();       }
         else if(commandName == "sparcc")                {	shellcommand = new SparccCommand();                 }
         else if(commandName == "make.lookup")			{	shellcommand = new MakeLookupCommand();				}
         else if(commandName == "rename.seqs")			{	shellcommand = new RenameSeqsCommand();				}
         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;