#include "createdatabasecommand.h"
#include "makebiomcommand.h"
#include "getcoremicrobiomecommand.h"
+#include "listotulabelscommand.h"
+#include "getotulabelscommand.h"
+#include "removeotulabelscommand.h"
+#include "makecontigscommand.h"
/*******************************************************/
commands["pcr.seqs"] = "pcr.seqs";
commands["create.database"] = "create.database";
commands["make.biom"] = "make.biom";
- commands["get.coremicrobiome"] = "get.coremicrobiome";
+ commands["get.coremicrobiome"] = "get.coremicrobiome";
+ commands["list.otulabels"] = "list.otulabels";
+ commands["get.otulabels"] = "get.otulabels";
+ commands["remove.otulabels"] = "remove.otulabels";
+ commands["make.contigs"] = "make.contigs";
commands["quit"] = "MPIEnabled";
}
else if(commandName == "create.database") { command = new CreateDatabaseCommand(optionString); }
else if(commandName == "make.biom") { command = new MakeBiomCommand(optionString); }
else if(commandName == "get.coremicrobiome") { command = new GetCoreMicroBiomeCommand(optionString); }
+ else if(commandName == "list.otulabels") { command = new ListOtuLabelsCommand(optionString); }
+ else if(commandName == "get.otulabels") { command = new GetOtuLabelsCommand(optionString); }
+ else if(commandName == "remove.otulabels") { command = new RemoveOtuLabelsCommand(optionString); }
+ else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
else if(commandName == "create.database") { pipecommand = new CreateDatabaseCommand(optionString); }
else if(commandName == "make.biom") { pipecommand = new MakeBiomCommand(optionString); }
else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); }
+ else if(commandName == "list.otulabels") { pipecommand = new ListOtuLabelsCommand(optionString); }
+ else if(commandName == "get.otulabels") { pipecommand = new GetOtuLabelsCommand(optionString); }
+ else if(commandName == "remove.otulabels") { pipecommand = new RemoveOtuLabelsCommand(optionString); }
+ else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
else if(commandName == "create.database") { shellcommand = new CreateDatabaseCommand(); }
else if(commandName == "make.biom") { shellcommand = new MakeBiomCommand(); }
else if(commandName == "get.coremicrobiome") { shellcommand = new GetCoreMicroBiomeCommand(); }
+ else if(commandName == "list.otulabels") { shellcommand = new ListOtuLabelsCommand(); }
+ else if(commandName == "get.otulabels") { shellcommand = new GetOtuLabelsCommand(); }
+ else if(commandName == "remove.otulabels") { shellcommand = new RemoveOtuLabelsCommand(); }
+ else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;