fixes while testing 1.33.0

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 03c3e49ccff50f128c657780da2b9d8109289358..e8e9c2754677ee639fce944fbc533d3bd9eb98db 100644 (file)
--- 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;