#include "catchallcommand.h"
#include "splitabundcommand.h"
#include "clustersplitcommand.h"
+#include "classifyotucommand.h"
+#include "degapseqscommand.h"
+#include "getrelabundcommand.h"
+#include "sensspeccommand.h"
/*******************************************************/
commands["clearcut"] = "clearcut";
commands["catchall"] = "catchall";
commands["split.abund"] = "split.abund";
- commands["cluster.split"] = "cluster.split";
+ commands["classify.otu"] = "classify.otu";
+ commands["degap.seqs"] = "degap.seqs";
+ commands["get.relabund"] = "get.relabund";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
commands["filter.seqs"] = "MPIEnabled";
commands["chimera.bellerophon"] = "MPIEnabled";
commands["screen.seqs"] = "MPIEnabled";
commands["summary.seqs"] = "MPIEnabled";
+ commands["cluster.split"] = "MPIEnabled";
+ commands["sens.spec"] = "sens.spec";
commands["quit"] = "MPIEnabled";
}
else if(commandName == "catchall") { command = new CatchAllCommand(optionString); }
else if(commandName == "split.abund") { command = new SplitAbundCommand(optionString); }
else if(commandName == "cluster.split") { command = new ClusterSplitCommand(optionString); }
+ else if(commandName == "classify.otu") { command = new ClassifyOtuCommand(optionString); }
+ else if(commandName == "degap.seqs") { command = new DegapSeqsCommand(optionString); }
+ else if(commandName == "get.relabund") { command = new GetRelAbundCommand(optionString); }
+ else if(commandName == "sens.spec") { command = new SensSpecCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
/***********************************************************************/
void CommandFactory::printCommands(ostream& out) {
try {
- out << "Valid commands are ";
+ out << "Valid commands are: ";
for (it = commands.begin(); it != commands.end(); it++) {
- out << it->first << ", ";
+ out << it->first << ",";
}
out << endl;
}