#include "chimeraslayercommand.h"
#include "chimerapintailcommand.h"
#include "chimerabellerophoncommand.h"
+#include "setlogfilecommand.h"
+#include "phylodiversitycommand.h"
/*******************************************************/
command = new NoCommand(s);
outputDir = ""; inputDir = "";
+ logFileName = "";
+ append = false;
//initialize list of valid commands
commands["read.dist"] = "read.dist";
commands["get.rabund"] = "get.rabund";
commands["bootstrap.shared"] = "bootstrap.shared";
//commands["consensus"] = "consensus";
- commands["help"] = "help";
- commands["summary.seqs"] = "summary.seqs";
- commands["screen.seqs"] = "screen.seqs";
+ commands["help"] = "help";
commands["reverse.seqs"] = "reverse.seqs";
commands["trim.seqs"] = "trim.seqs";
commands["list.seqs"] = "list.seqs";
commands["merge.files"] = "merge.files";
commands["parse.list"] = "parse.list";
commands["parse.sff"] = "parse.sff";
+ commands["set.logfile"] = "set.logfile";
+ commands["phylo.diversity"] = "phylo.diversity";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
commands["filter.seqs"] = "MPIEnabled";
commands["chimera.slayer"] = "MPIEnabled";
commands["chimera.pintail"] = "MPIEnabled";
commands["chimera.bellerophon"] = "MPIEnabled";
+ commands["screen.seqs"] = "MPIEnabled";
+ commands["summary.seqs"] = "MPIEnabled";
commands["quit"] = "MPIEnabled";
}
else if(commandName == "pcoa") { 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 == "parse.list") { command = new ParseListCommand(optionString); }
else if(commandName == "parse.sff") { command = new ParseSFFCommand(optionString); }
+ else if(commandName == "phylo.diversity") { command = new PhyloDiversityCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;