added classify.otu command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 9917b3cce2c2b4a48ac89ae4ab8a387921d1d74e..bd519eebfd6eaa24134dad9ac08f2193004e6386 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -76,6 +76,10 @@
 #include "makegroupcommand.h"
 #include "chopseqscommand.h"
 #include "clearcutcommand.h"
+#include "catchallcommand.h"
+#include "splitabundcommand.h"
+#include "clustersplitcommand.h"
+#include "classifyotucommand.h"
 
 /*******************************************************/
 
@@ -159,6 +163,10 @@ CommandFactory::CommandFactory(){
        commands["make.group"]                  = "make.group";
        commands["chop.seqs"]                   = "chop.seqs";
        commands["clearcut"]                    = "clearcut";
+       commands["catchall"]                    = "catchall";
+       commands["split.abund"]                 = "split.abund";
+       commands["cluster.split"]               = "cluster.split";
+       commands["classify.otu"]                = "classify.otu";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -243,7 +251,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                               }
                else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);                    }
                else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                              }
-               //else if(commandName == "consensus")                   {   command = new ConcensusCommand(optionString);                               }
+               else if(commandName == "consensus")                             {   command = new ConcensusCommand(optionString);                               }
                else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                                }
                else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                                   }
                else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                          }
@@ -279,6 +287,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
                else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
                else if(commandName == "clearcut")                              {       command = new ClearcutCommand(optionString);                            }
+               else if(commandName == "catchall")                              {       command = new CatchAllCommand(optionString);                            }
+               else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
+               else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
+               else if(commandName == "classify.otu")                  {       command = new ClassifyOtuCommand(optionString);                         }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -330,9 +342,9 @@ bool CommandFactory::isValidCommand(string command) {
 /***********************************************************************/
 void CommandFactory::printCommands(ostream& out) {
        try {   
-               out << "Valid commands are ";
+               out << "Valid commands are: ";
                for (it = commands.begin(); it != commands.end(); it++) {
-                       out << it->first << ", ";
+                       out << it->first << ",";
                }
                out << endl;
        }