#include "makecontigscommand.h"
#include "loadlogfilecommand.h"
#include "sffmultiplecommand.h"
-#include "classifysharedcommand.h"
+#include "classifyrfsharedcommand.h"
#include "filtersharedcommand.h"
#include "primerdesigncommand.h"
#include "getdistscommand.h"
commands["make.table"] = "make.table";
commands["sff.multiple"] = "sff.multiple";
commands["quit"] = "MPIEnabled";
- commands["classify.shared"] = "classify.shared";
+ commands["classify.rf"] = "classify.rf";
commands["filter.shared"] = "filter.shared";
commands["primer.design"] = "primer.design";
commands["get.dists"] = "get.dists";
else { optionString += "inputdir=" + inputDir; }
}
- if(commandName == "cluster") { command = new ClusterCommand(optionString); }
+ if(commandName == "cluster") { command = new ClusterCommand(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 == "classify.shared") { command = new ClassifySharedCommand(optionString); }
+ else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(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.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 == "classify.shared") { pipecommand = new ClassifySharedCommand(optionString); }
+ else if(commandName == "classify.rf") { pipecommand = new ClassifyRFSharedCommand(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.contigs") { shellcommand = new MakeContigsCommand(); }
else if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); }
else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
- else if(commandName == "classify.shared") { shellcommand = new ClassifySharedCommand(); }
+ else if(commandName == "classify.rf") { shellcommand = new ClassifyRFSharedCommand(); }
else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }