removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index e18e6ac1956e3f21f990d6c5b1c45be42dafebf9..a04ee160bb92870aa05865fc25e7504f8a689596 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -8,9 +8,9 @@
  */
 
 #include "command.hpp"
-#include "readdistcommand.h"
-#include "readtreecommand.h"
-#include "readotucommand.h"
+//#include "readdistcommand.h"
+//#include "readtreecommand.h"
+//#include "readotucommand.h"
 #include "clustercommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
@@ -48,7 +48,6 @@
 #include "reversecommand.h"
 #include "trimseqscommand.h"
 #include "mergefilecommand.h"
-#include "chimeraseqscommand.h"
 #include "listseqscommand.h"
 #include "getseqscommand.h"
 #include "removeseqscommand.h"
@@ -116,6 +115,7 @@
 #include "anosimcommand.h"
 #include "getcurrentcommand.h"
 #include "setcurrentcommand.h"
+#include "sharedcommand.h"
 
 /*******************************************************/
 
@@ -148,9 +148,10 @@ 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["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";
        commands["cluster"]                             = "cluster"; 
@@ -241,7 +242,6 @@ CommandFactory::CommandFactory(){
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
        commands["align.seqs"]                  = "MPIEnabled";
-       commands["chimera.seqs"]                = "chimera.seqs";
        commands["chimera.ccode"]               = "MPIEnabled";
        commands["chimera.check"]               = "MPIEnabled";
        commands["chimera.slayer"]              = "MPIEnabled";
@@ -297,10 +297,10 @@ 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 == "read.dist")                                        {       command = new ReadDistCommand(optionString);                            }
+               //else if(commandName == "read.otu")                            {       command = new ReadOtuCommand(optionString);                                     }
+               //else if(commandName == "read.tree")                           {       command = new ReadTreeCommand(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);                                        }
@@ -336,7 +336,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
                else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
                else if(commandName == "shhh.seqs")                             {       command = new ShhherCommand(optionString);                                      }
-               else if(commandName == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(optionString);                         }
                else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
                else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
                else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
@@ -403,6 +402,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "get.current")                   {       command = new GetCurrentCommand(optionString);                          }
                else if(commandName == "set.current")                   {       command = new SetCurrentCommand(optionString);                          }
                else if(commandName == "anosim")                                {       command = new AnosimCommand(optionString);                                      }
+               else if(commandName == "make.shared")                   {       command = new SharedCommand(optionString);                                      }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -432,10 +432,10 @@ 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 == "read.dist")                                        {       pipecommand = new ReadDistCommand(optionString);                                }
+               //else if(commandName == "read.otu")                            {       pipecommand = new ReadOtuCommand(optionString);                                 }
+               //else if(commandName == "read.tree")                           {       pipecommand = new ReadTreeCommand(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);                                    }
@@ -471,7 +471,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
                else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
                else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhherCommand(optionString);                                  }
-               else if(commandName == "chimera.seqs")                  {       pipecommand = new ChimeraSeqsCommand(optionString);                             }
                else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
                else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
                else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
@@ -537,6 +536,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "make.fastq")                    {       pipecommand = new MakeFastQCommand(optionString);                               }
                else if(commandName == "get.current")                   {       pipecommand = new GetCurrentCommand(optionString);                              }
                else if(commandName == "set.current")                   {       pipecommand = new SetCurrentCommand(optionString);                              }
+               else if(commandName == "make.shared")                   {       pipecommand = new SharedCommand(optionString);                                  }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -554,10 +554,10 @@ 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 == "read.dist")                                        {       shellcommand = new ReadDistCommand();                           }
+               //else if(commandName == "read.otu")                            {       shellcommand = new ReadOtuCommand();                            }
+               //else if(commandName == "read.tree")                           {       shellcommand = new ReadTreeCommand();                           }
+               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();                                       }
@@ -593,7 +593,6 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
                else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
                else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhherCommand();                                     }
-               else if(commandName == "chimera.seqs")                  {       shellcommand = new ChimeraSeqsCommand();                        }
                else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
                else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
                else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }
@@ -659,6 +658,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "make.fastq")                    {       shellcommand = new MakeFastQCommand();                          }
                else if(commandName == "get.current")                   {       shellcommand = new GetCurrentCommand();                         }
                else if(commandName == "set.current")                   {       shellcommand = new SetCurrentCommand();                         }
+               else if(commandName == "make.shared")                   {       shellcommand = new SharedCommand();                                     }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;