#include "makecontigscommand.h"
#include "loadlogfilecommand.h"
#include "sffmultiplecommand.h"
#include "makecontigscommand.h"
#include "loadlogfilecommand.h"
#include "sffmultiplecommand.h"
#include "filtersharedcommand.h"
#include "primerdesigncommand.h"
#include "getdistscommand.h"
#include "filtersharedcommand.h"
#include "primerdesigncommand.h"
#include "getdistscommand.h"
#include "makelefsecommand.h"
#include "lefsecommand.h"
#include "kruskalwalliscommand.h"
#include "makelefsecommand.h"
#include "lefsecommand.h"
#include "kruskalwalliscommand.h"
commands["make.table"] = "make.table";
commands["sff.multiple"] = "sff.multiple";
commands["quit"] = "MPIEnabled";
commands["make.table"] = "make.table";
commands["sff.multiple"] = "sff.multiple";
commands["quit"] = "MPIEnabled";
commands["filter.shared"] = "filter.shared";
commands["primer.design"] = "primer.design";
commands["get.dists"] = "get.dists";
commands["filter.shared"] = "filter.shared";
commands["primer.design"] = "primer.design";
commands["get.dists"] = "get.dists";
commands["make.lefse"] = "make.lefse";
commands["lefse"] = "lefse";
commands["kruskal.wallis"] = "kruskal.wallis";
commands["make.lefse"] = "make.lefse";
commands["lefse"] = "lefse";
commands["kruskal.wallis"] = "kruskal.wallis";
else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
else if(commandName == "help") { command = new HelpCommand(optionString); }
else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
else if(commandName == "help") { command = new HelpCommand(optionString); }
else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
else if(commandName == "load.logfile") { command = new LoadLogfileCommand(optionString); }
else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
else if(commandName == "load.logfile") { command = new LoadLogfileCommand(optionString); }
else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
else if(commandName == "make.lefse") { command = new MakeLefseCommand(optionString); }
else if(commandName == "lefse") { command = new LefseCommand(optionString); }
else if(commandName == "kruskal.wallis") { command = new KruskalWallisCommand(optionString); }
else if(commandName == "make.lefse") { command = new MakeLefseCommand(optionString); }
else if(commandName == "lefse") { command = new LefseCommand(optionString); }
else if(commandName == "kruskal.wallis") { command = new KruskalWallisCommand(optionString); }
else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
else if(commandName == "load.logfile") { pipecommand = new LoadLogfileCommand(optionString); }
else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
else if(commandName == "load.logfile") { pipecommand = new LoadLogfileCommand(optionString); }
else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
else if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
else if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
else if(commandName == "make.lefse") { pipecommand = new MakeLefseCommand(optionString); }
else if(commandName == "lefse") { pipecommand = new LefseCommand(optionString); }
else if(commandName == "kruskal.wallis") { pipecommand = new KruskalWallisCommand(optionString); }
else if(commandName == "make.lefse") { pipecommand = new MakeLefseCommand(optionString); }
else if(commandName == "lefse") { pipecommand = new LefseCommand(optionString); }
else if(commandName == "kruskal.wallis") { pipecommand = new KruskalWallisCommand(optionString); }
else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
else if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); }
else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
else if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); }
else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
else if(commandName == "make.lefse") { shellcommand = new MakeLefseCommand(); }
else if(commandName == "lefse") { shellcommand = new LefseCommand(); }
else if(commandName == "kruskal.wallis") { shellcommand = new KruskalWallisCommand(); }
else if(commandName == "make.lefse") { shellcommand = new MakeLefseCommand(); }
else if(commandName == "lefse") { shellcommand = new LefseCommand(); }
else if(commandName == "kruskal.wallis") { shellcommand = new KruskalWallisCommand(); }