added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs parameters to sffinfo to allow...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 1241a04e998537fe33446a1c9ba3d933e690e557..8653643a0e5f89058f95842bfdb134b711ab4de5 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -8,9 +8,6 @@
  */
 
 #include "command.hpp"
-#include "readdistcommand.h"
-#include "readtreecommand.h"
-#include "readotucommand.h"
 #include "clustercommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
@@ -133,7 +130,11 @@
 #include "makebiomcommand.h"
 #include "getcoremicrobiomecommand.h"
 #include "listotulabelscommand.h"
+#include "getotulabelscommand.h"
+#include "removeotulabelscommand.h"
 #include "makecontigscommand.h"
+#include "loadlogfilecommand.h"
+#include "sffmultiplecommand.h"
 
 /*******************************************************/
 
@@ -166,9 +167,6 @@ CommandFactory::CommandFactory(){
        append = false;
        
        //initialize list of valid commands
-       commands["read.dist"]                   = "read.dist"; 
-       commands["read.otu"]                    = "read.otu";
-       commands["read.tree"]                   = "read.tree"; 
        commands["make.shared"]                 = "make.shared"; 
        commands["bin.seqs"]                    = "bin.seqs"; 
        commands["get.oturep"]                  = "get.oturep";
@@ -288,7 +286,12 @@ CommandFactory::CommandFactory(){
     commands["make.biom"]           = "make.biom";
     commands["get.coremicrobiome"]  = "get.coremicrobiome";
     commands["list.otulabels"]      = "list.otulabels";
+    commands["get.otulabels"]       = "get.otulabels";
+    commands["remove.otulabels"]    = "remove.otulabels";
     commands["make.contigs"]        = "make.contigs";
+    commands["load.logfile"]        = "load.logfile";
+    commands["make.table"]          = "make.table";
+    commands["sff.multiple"]        = "sff.multiple";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -378,10 +381,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                        else { optionString += "inputdir=" + inputDir; }
                }
                
-               if(commandName == "read.dist")                                  {       command = new ReadDistCommand(optionString);                            }
-               else if(commandName == "read.otu")                              {       command = new ReadOtuCommand(optionString);                                     }
-               else if(commandName == "read.tree")                             {       command = new ReadTreeCommand(optionString);                            }
-               else 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);                                        }
@@ -485,7 +485,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "make.shared")                   {       command = new SharedCommand(optionString);                                      }
                else if(commandName == "get.commandinfo")               {       command = new GetCommandInfoCommand(optionString);                      }
                else if(commandName == "deunique.tree")                 {       command = new DeuniqueTreeCommand(optionString);                        }
-               else if(commandName == "count.seqs")                    {       command = new CountSeqsCommand(optionString);                           }
+               else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       command = new CountSeqsCommand(optionString);                           }
                else if(commandName == "count.groups")                  {       command = new CountGroupsCommand(optionString);                         }
                else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
                else if(commandName == "summary.tax")                   {       command = new SummaryTaxCommand(optionString);                          }
@@ -501,7 +501,11 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "make.biom")             {      command = new MakeBiomCommand(optionString);                }
         else if(commandName == "get.coremicrobiome")    {      command = new GetCoreMicroBiomeCommand(optionString);       }
         else if(commandName == "list.otulabels")        {      command = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "get.otulabels")         {      command = new GetOtuLabelsCommand(optionString);            }
+        else if(commandName == "remove.otulabels")      {      command = new RemoveOtuLabelsCommand(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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -533,10 +537,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                        else { optionString += "inputdir=" + inputDir; }
                }
                
-               if(commandName == "read.dist")                                  {       pipecommand = new ReadDistCommand(optionString);                                }
-               else if(commandName == "read.otu")                              {       pipecommand = new ReadOtuCommand(optionString);                                 }
-               else if(commandName == "read.tree")                             {       pipecommand = new ReadTreeCommand(optionString);                                }
-               else if(commandName == "cluster")                               {       pipecommand = new ClusterCommand(optionString);                                 }
+               if(commandName == "cluster")                            {       pipecommand = new ClusterCommand(optionString);                                 }
                else if(commandName == "unique.seqs")                   {       pipecommand = new DeconvoluteCommand(optionString);                             }
                else if(commandName == "parsimony")                             {       pipecommand = new ParsimonyCommand(optionString);                               }
                else if(commandName == "help")                                  {       pipecommand = new HelpCommand(optionString);                                    }
@@ -639,7 +640,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "make.shared")                   {       pipecommand = new SharedCommand(optionString);                                  }
                else if(commandName == "get.commandinfo")               {       pipecommand = new GetCommandInfoCommand(optionString);                  }
                else if(commandName == "deunique.tree")                 {       pipecommand = new DeuniqueTreeCommand(optionString);                    }
-               else if(commandName == "count.seqs")                    {       pipecommand = new CountSeqsCommand(optionString);                               }
+               else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       pipecommand = new CountSeqsCommand(optionString);                               }
                else if(commandName == "count.groups")                  {       pipecommand = new CountGroupsCommand(optionString);                             }
                else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
                else if(commandName == "summary.tax")                   {       pipecommand = new SummaryTaxCommand(optionString);                              }
@@ -655,7 +656,11 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "make.biom")             {      pipecommand = new MakeBiomCommand(optionString);                }
         else if(commandName == "get.coremicrobiome")    {      pipecommand = new GetCoreMicroBiomeCommand(optionString);       }
         else if(commandName == "list.otulabels")        {      pipecommand = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "get.otulabels")         {      pipecommand = new GetOtuLabelsCommand(optionString);            }
+        else if(commandName == "remove.otulabels")      {      pipecommand = new RemoveOtuLabelsCommand(optionString);         }
         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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -673,10 +678,7 @@ Command* CommandFactory::getCommand(string commandName){
        try {
                delete shellcommand;   //delete the old command
                
-               if(commandName == "read.dist")                                  {       shellcommand = new ReadDistCommand();                           }
-               else if(commandName == "read.otu")                              {       shellcommand = new ReadOtuCommand();                            }
-               else if(commandName == "read.tree")                             {       shellcommand = new ReadTreeCommand();                           }
-               else if(commandName == "cluster")                               {       shellcommand = new ClusterCommand();                            }
+               if(commandName == "cluster")                            {       shellcommand = new ClusterCommand();                            }
                else if(commandName == "unique.seqs")                   {       shellcommand = new DeconvoluteCommand();                        }
                else if(commandName == "parsimony")                             {       shellcommand = new ParsimonyCommand();                          }
                else if(commandName == "help")                                  {       shellcommand = new HelpCommand();                                       }
@@ -779,7 +781,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "make.shared")                   {       shellcommand = new SharedCommand();                                     }
                else if(commandName == "get.commandinfo")               {       shellcommand = new GetCommandInfoCommand();                     }
                else if(commandName == "deunique.tree")                 {       shellcommand = new DeuniqueTreeCommand();                       }
-               else if(commandName == "count.seqs")                    {       shellcommand = new CountSeqsCommand();                          }
+               else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       shellcommand = new CountSeqsCommand();                          }
                else if(commandName == "count.groups")                  {       shellcommand = new CountGroupsCommand();                        }
                else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
                else if(commandName == "summary.tax")                   {       shellcommand = new SummaryTaxCommand();                         }
@@ -795,7 +797,11 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "make.biom")             {      shellcommand = new MakeBiomCommand();               }
         else if(commandName == "get.coremicrobiome")    {      shellcommand = new GetCoreMicroBiomeCommand();      }
         else if(commandName == "list.otulabels")        {      shellcommand = new ListOtuLabelsCommand();          }
+        else if(commandName == "get.otulabels")         {      shellcommand = new GetOtuLabelsCommand();           }
+        else if(commandName == "remove.otulabels")      {      shellcommand = new RemoveOtuLabelsCommand();        }
         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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;