added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 2822d0b9920a0f5cc5005cf01ce653b38b9ede6d..54ff4a12d120ddcc482d84876ac53a04f6e3a04a 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"
@@ -136,6 +133,7 @@
 #include "getotulabelscommand.h"
 #include "removeotulabelscommand.h"
 #include "makecontigscommand.h"
+#include "loadlogfilecommand.h"
 
 /*******************************************************/
 
@@ -168,9 +166,6 @@ 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";
@@ -293,6 +288,7 @@ CommandFactory::CommandFactory(){
     commands["get.otulabels"]       = "get.otulabels";
     commands["remove.otulabels"]    = "remove.otulabels";
     commands["make.contigs"]        = "make.contigs";
+    commands["load.logfile"]        = "load.logfile";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -382,10 +378,7 @@ 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);                                        }
@@ -508,6 +501,7 @@ Command* CommandFactory::getCommand(string commandName, string 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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -539,10 +533,7 @@ 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);                                    }
@@ -664,6 +655,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -681,10 +673,7 @@ 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();                                       }
@@ -806,6 +795,7 @@ Command* CommandFactory::getCommand(string commandName){
         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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;