added phylo.diversity command. added hard parameter to cluster, hcluster and read...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index aaeec67f1b4eec4e2194fc014e87064c1d5c2b5c..30b76f813f6710ff9c2cda0819305ca8837f7bf5 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -71,6 +71,8 @@
 #include "chimeraslayercommand.h"
 #include "chimerapintailcommand.h"
 #include "chimerabellerophoncommand.h"
+#include "setlogfilecommand.h"
+#include "phylodiversitycommand.h"
 
 /*******************************************************/
 
@@ -97,6 +99,8 @@ CommandFactory::CommandFactory(){
        command = new NoCommand(s);
        
        outputDir = ""; inputDir = "";
+       logFileName = "";
+       append = false;
        
        //initialize list of valid commands
        commands["read.dist"]                   = "read.dist"; 
@@ -127,9 +131,7 @@ 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 +151,8 @@ 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["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -159,6 +163,8 @@ CommandFactory::CommandFactory(){
        commands["chimera.slayer"]              = "MPIEnabled";
        commands["chimera.pintail"]             = "MPIEnabled";
        commands["chimera.bellerophon"] = "MPIEnabled";
+       commands["screen.seqs"]                 = "MPIEnabled";
+       commands["summary.seqs"]                = "MPIEnabled";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -260,8 +266,10 @@ 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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;