#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"
/*******************************************************/
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["cluster.split"] = "cluster.split";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
commands["filter.seqs"] = "MPIEnabled";
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); }
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 { command = new NoCommand(optionString); }
return command;