fixes while testing 1.33.0

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index a0796a34fc243916081632e54a54233bef679a5f..e8e9c2754677ee639fce944fbc533d3bd9eb98db 100644 (file)
--- 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"
@@ -145,6 +145,11 @@
 #include "sparcccommand.h"
 #include "makelookupcommand.h"
 #include "renameseqscommand.h"
+#include "makelefsecommand.h"
+#include "lefsecommand.h"
+#include "kruskalwalliscommand.h"
+#include "sracommand.h"
+#include "mergesfffilecommand.h"
 
 /*******************************************************/
 
@@ -303,16 +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";
     
 
 }
@@ -402,7 +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);                                        }
@@ -527,16 +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;
@@ -692,16 +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;
@@ -843,16 +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;