commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
else if(commandName == "pre.cluster") { command = new PreClusterCommand(optionString); }
else if(commandName == "pcoa") { command = new PCOACommand(optionString); }
else if(commandName == "pca") { command = new PCACommand(optionString); }
else if(commandName == "pre.cluster") { command = new PreClusterCommand(optionString); }
else if(commandName == "pcoa") { command = new PCOACommand(optionString); }
else if(commandName == "pca") { 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 == "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 == "pre.cluster") { pipecommand = new PreClusterCommand(optionString); }
else if(commandName == "pcoa") { pipecommand = new PCOACommand(optionString); }
else if(commandName == "pca") { pipecommand = new PCACommand(optionString); }
else if(commandName == "pre.cluster") { pipecommand = new PreClusterCommand(optionString); }
else if(commandName == "pcoa") { pipecommand = new PCOACommand(optionString); }
else if(commandName == "pca") { pipecommand = new PCACommand(optionString); }
else if(commandName == "otu.hierarchy") { pipecommand = new OtuHierarchyCommand(optionString); }
else if(commandName == "set.dir") { pipecommand = new SetDirectoryCommand(optionString); }
else if(commandName == "set.logfile") { pipecommand = new SetLogFileCommand(optionString); }
else if(commandName == "otu.hierarchy") { pipecommand = new OtuHierarchyCommand(optionString); }
else if(commandName == "set.dir") { pipecommand = new SetDirectoryCommand(optionString); }
else if(commandName == "set.logfile") { pipecommand = new SetLogFileCommand(optionString); }
else if(commandName == "pre.cluster") { shellcommand = new PreClusterCommand(); }
else if(commandName == "pcoa") { shellcommand = new PCOACommand(); }
else if(commandName == "pca") { shellcommand = new PCACommand(); }
else if(commandName == "pre.cluster") { shellcommand = new PreClusterCommand(); }
else if(commandName == "pcoa") { shellcommand = new PCOACommand(); }
else if(commandName == "pca") { shellcommand = new PCACommand(); }
else if(commandName == "otu.hierarchy") { shellcommand = new OtuHierarchyCommand(); }
else if(commandName == "set.dir") { shellcommand = new SetDirectoryCommand(); }
else if(commandName == "set.logfile") { shellcommand = new SetLogFileCommand(); }
else if(commandName == "otu.hierarchy") { shellcommand = new OtuHierarchyCommand(); }
else if(commandName == "set.dir") { shellcommand = new SetDirectoryCommand(); }
else if(commandName == "set.logfile") { shellcommand = new SetLogFileCommand(); }