sens.spec changes

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index aaeec67f1b4eec4e2194fc014e87064c1d5c2b5c..725ce8cb7d2c4c9685e0f95ae6f67bc5cbb5fc83 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -71,6 +71,18 @@
 #include "chimeraslayercommand.h"
 #include "chimerapintailcommand.h"
 #include "chimerabellerophoncommand.h"
+#include "setlogfilecommand.h"
+#include "phylodiversitycommand.h"
+#include "makegroupcommand.h"
+#include "chopseqscommand.h"
+#include "clearcutcommand.h"
+#include "catchallcommand.h"
+#include "splitabundcommand.h"
+#include "clustersplitcommand.h"
+#include "classifyotucommand.h"
+#include "degapseqscommand.h"
+#include "getrelabundcommand.h"
+#include "sensspeccommand.h"
 
 /*******************************************************/
 
@@ -97,6 +109,8 @@ CommandFactory::CommandFactory(){
        command = new NoCommand(s);
        
        outputDir = ""; inputDir = "";
+       logFileName = "";
+       append = false;
        
        //initialize list of valid commands
        commands["read.dist"]                   = "read.dist"; 
@@ -127,9 +141,7 @@ CommandFactory::CommandFactory(){
        commands["get.rabund"]          = "get.rabund";
        commands["bootstrap.shared"]    = "bootstrap.shared";
        //commands["consensus"]                 = "consensus";
-       commands["help"]                                = "help"; 
-       commands["summary.seqs"]                = "summary.seqs";
-       commands["screen.seqs"]                 = "screen.seqs";
+       commands["help"]                                = "help";
        commands["reverse.seqs"]                = "reverse.seqs";
        commands["trim.seqs"]                   = "trim.seqs";
        commands["list.seqs"]                   = "list.seqs";
@@ -149,6 +161,16 @@ CommandFactory::CommandFactory(){
        commands["merge.files"]                 = "merge.files";
        commands["parse.list"]                  = "parse.list";
        commands["parse.sff"]                   = "parse.sff";
+       commands["set.logfile"]                 = "set.logfile";
+       commands["phylo.diversity"]             = "phylo.diversity";
+       commands["make.group"]                  = "make.group";
+       commands["chop.seqs"]                   = "chop.seqs";
+       commands["clearcut"]                    = "clearcut";
+       commands["catchall"]                    = "catchall";
+       commands["split.abund"]                 = "split.abund";
+       commands["classify.otu"]                = "classify.otu";
+       commands["degap.seqs"]                  = "degap.seqs";
+       commands["get.relabund"]                = "get.relabund";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -159,6 +181,10 @@ CommandFactory::CommandFactory(){
        commands["chimera.slayer"]              = "MPIEnabled";
        commands["chimera.pintail"]             = "MPIEnabled";
        commands["chimera.bellerophon"] = "MPIEnabled";
+       commands["screen.seqs"]                 = "MPIEnabled";
+       commands["summary.seqs"]                = "MPIEnabled";
+       commands["cluster.split"]               = "MPIEnabled";
+       commands["sens.spec"]                   = "sens.spec";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -231,7 +257,7 @@ 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);                          }
@@ -260,8 +286,20 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "pcoa")                                  {       command = new PCACommand(optionString);                                         }
                else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
                else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
+               else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
                else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
                else if(commandName == "parse.sff")                             {       command = new ParseSFFCommand(optionString);                            }
+               else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(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 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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -313,9 +351,9 @@ 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;
        }