working on megastats

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0bca8c0ee3db3706404b3fc5c4ff42b8c8f99388..bbdd61692b7e328937d526e887ef5f0590528f2e 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -79,6 +79,14 @@
 #include "catchallcommand.h"
 #include "splitabundcommand.h"
 #include "clustersplitcommand.h"
+#include "classifyotucommand.h"
+#include "degapseqscommand.h"
+#include "getrelabundcommand.h"
+#include "sensspeccommand.h"
+#include "sffinfocommand.h"
+#include "seqerrorcommand.h"
+#include "normalizesharedcommand.h"
+#include "metastatscommand.h"
 
 /*******************************************************/
 
@@ -164,7 +172,12 @@ CommandFactory::CommandFactory(){
        commands["clearcut"]                    = "clearcut";
        commands["catchall"]                    = "catchall";
        commands["split.abund"]                 = "split.abund";
-       commands["cluster.split"]               = "cluster.split";
+       commands["classify.otu"]                = "classify.otu";
+       commands["degap.seqs"]                  = "degap.seqs";
+       commands["get.relabund"]                = "get.relabund";
+       commands["sffinfo"]                             = "sffinfo";
+       commands["normalize.shared"]    = "normalize.shared";
+       commands["metastats"]                   = "metastats";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -177,6 +190,9 @@ CommandFactory::CommandFactory(){
        commands["chimera.bellerophon"] = "MPIEnabled";
        commands["screen.seqs"]                 = "MPIEnabled";
        commands["summary.seqs"]                = "MPIEnabled";
+       commands["cluster.split"]               = "MPIEnabled";
+       commands["sens.spec"]                   = "sens.spec";
+       commands["seq.error"]                   = "seq.error";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -249,7 +265,7 @@ 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);                          }
@@ -288,6 +304,14 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "degap.seqs")                    {       command = new DegapSeqsCommand(optionString);                           }
+               else if(commandName == "get.relabund")                  {       command = new GetRelAbundCommand(optionString);                         }
+               else if(commandName == "sens.spec")                             {       command = new SensSpecCommand(optionString);                            }
+               else if(commandName == "seq.error")                             {       command = new SeqErrorCommand(optionString);                            }
+               else if(commandName == "sffinfo")                               {       command = new SffInfoCommand(optionString);                                     }
+               else if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
+               else if(commandName == "metastats")                             {       command = new MetaStatsCommand(optionString);                           }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -339,9 +363,9 @@ 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;
        }