*/
#include "command.hpp"
-//#include "readdistcommand.h"
-//#include "readtreecommand.h"
-//#include "readotucommand.h"
+#include "readdistcommand.h"
+#include "readtreecommand.h"
+#include "readotucommand.h"
#include "clustercommand.h"
#include "collectcommand.h"
#include "collectsharedcommand.h"
#include "getcurrentcommand.h"
#include "setcurrentcommand.h"
#include "sharedcommand.h"
+#include "getcommandinfocommand.h"
/*******************************************************/
append = false;
//initialize list of valid commands
- //commands["read.dist"] = "read.dist";
- //commands["read.otu"] = "read.otu";
- //commands["read.tree"] = "read.tree";
+ commands["read.dist"] = "read.dist";
+ commands["read.otu"] = "read.otu";
+ commands["read.tree"] = "read.tree";
commands["make.shared"] = "make.shared";
commands["bin.seqs"] = "bin.seqs";
commands["get.oturep"] = "get.oturep";
commands["trim.flows"] = "trim.flows";
commands["list.seqs"] = "list.seqs";
commands["get.seqs"] = "get.seqs";
- commands["remove.seqs"] = "get.seqs";
+ commands["remove.seqs"] = "remove.seqs";
commands["system"] = "system";
commands["align.check"] = "align.check";
commands["get.sharedseqs"] = "get.sharedseqs";
commands["merge.groups"] = "merge.groups";
commands["get.current"] = "get.current";
commands["set.current"] = "set.current";
+ commands["get.commandinfo"] = "get.commandinfo";
commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
else { optionString += "inputdir=" + inputDir; }
}
- //if(commandName == "read.dist") { command = new ReadDistCommand(optionString); }
- //else if(commandName == "read.otu") { command = new ReadOtuCommand(optionString); }
- //else if(commandName == "read.tree") { command = new ReadTreeCommand(optionString); }
- if(commandName == "cluster") { command = new ClusterCommand(optionString); }
+ if(commandName == "read.dist") { command = new ReadDistCommand(optionString); }
+ else if(commandName == "read.otu") { command = new ReadOtuCommand(optionString); }
+ else if(commandName == "read.tree") { command = new ReadTreeCommand(optionString); }
+ else 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 == "set.current") { command = new SetCurrentCommand(optionString); }
else if(commandName == "anosim") { command = new AnosimCommand(optionString); }
else if(commandName == "make.shared") { command = new SharedCommand(optionString); }
+ else if(commandName == "get.commandinfo") { command = new GetCommandInfoCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
else { optionString += "inputdir=" + inputDir; }
}
- //if(commandName == "read.dist") { pipecommand = new ReadDistCommand(optionString); }
- //else if(commandName == "read.otu") { pipecommand = new ReadOtuCommand(optionString); }
- //else if(commandName == "read.tree") { pipecommand = new ReadTreeCommand(optionString); }
- if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); }
+ if(commandName == "read.dist") { pipecommand = new ReadDistCommand(optionString); }
+ else if(commandName == "read.otu") { pipecommand = new ReadOtuCommand(optionString); }
+ else if(commandName == "read.tree") { pipecommand = new ReadTreeCommand(optionString); }
+ else if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); }
else if(commandName == "unique.seqs") { pipecommand = new DeconvoluteCommand(optionString); }
else if(commandName == "parsimony") { pipecommand = new ParsimonyCommand(optionString); }
else if(commandName == "help") { pipecommand = new HelpCommand(optionString); }
else if(commandName == "get.current") { pipecommand = new GetCurrentCommand(optionString); }
else if(commandName == "set.current") { pipecommand = new SetCurrentCommand(optionString); }
else if(commandName == "make.shared") { pipecommand = new SharedCommand(optionString); }
+ else if(commandName == "get.commandinfo") { pipecommand = new GetCommandInfoCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
try {
delete shellcommand; //delete the old command
- //if(commandName == "read.dist") { shellcommand = new ReadDistCommand(); }
- //else if(commandName == "read.otu") { shellcommand = new ReadOtuCommand(); }
- //else if(commandName == "read.tree") { shellcommand = new ReadTreeCommand(); }
- if(commandName == "cluster") { shellcommand = new ClusterCommand(); }
+ if(commandName == "read.dist") { shellcommand = new ReadDistCommand(); }
+ else if(commandName == "read.otu") { shellcommand = new ReadOtuCommand(); }
+ else if(commandName == "read.tree") { shellcommand = new ReadTreeCommand(); }
+ else if(commandName == "cluster") { shellcommand = new ClusterCommand(); }
else if(commandName == "unique.seqs") { shellcommand = new DeconvoluteCommand(); }
else if(commandName == "parsimony") { shellcommand = new ParsimonyCommand(); }
else if(commandName == "help") { shellcommand = new HelpCommand(); }
else if(commandName == "get.current") { shellcommand = new GetCurrentCommand(); }
else if(commandName == "set.current") { shellcommand = new SetCurrentCommand(); }
else if(commandName == "make.shared") { shellcommand = new SharedCommand(); }
+ else if(commandName == "get.commandinfo") { shellcommand = new GetCommandInfoCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;