#include "catchallcommand.h"
#include "splitabundcommand.h"
#include "clustersplitcommand.h"
+#include "classifyotucommand.h"
/*******************************************************/
commands["clearcut"] = "clearcut";
commands["catchall"] = "catchall";
commands["split.abund"] = "split.abund";
- //commands["cluster.split"] = "cluster.split";
+ commands["cluster.split"] = "cluster.split";
+ commands["classify.otu"] = "classify.otu";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
commands["filter.seqs"] = "MPIEnabled";
else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
else if(commandName == "bootstrap.shared") { command = new BootSharedCommand(optionString); }
- //else if(commandName == "consensus") { command = new ConcensusCommand(optionString); }
+ else if(commandName == "consensus") { command = new ConcensusCommand(optionString); }
else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
else if(commandName == "clearcut") { command = new ClearcutCommand(optionString); }
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 == "cluster.split") { command = new ClusterSplitCommand(optionString); }
+ else if(commandName == "classify.otu") { command = new ClassifyOtuCommand(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;
}