#include "catchallcommand.h"
#include "splitabundcommand.h"
#include "clustersplitcommand.h"
#include "catchallcommand.h"
#include "splitabundcommand.h"
#include "clustersplitcommand.h"
commands["clearcut"] = "clearcut";
commands["catchall"] = "catchall";
commands["split.abund"] = "split.abund";
commands["clearcut"] = "clearcut";
commands["catchall"] = "catchall";
commands["split.abund"] = "split.abund";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
commands["filter.seqs"] = "MPIEnabled";
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 == "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 == "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 == "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 == "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 == "clearcut") { command = new ClearcutCommand(optionString); }
else if(commandName == "catchall") { command = new CatchAllCommand(optionString); }
else if(commandName == "split.abund") { command = new SplitAbundCommand(optionString); }
/***********************************************************************/
void CommandFactory::printCommands(ostream& out) {
try {
/***********************************************************************/
void CommandFactory::printCommands(ostream& out) {
try {