*/
#include "command.hpp"
-#include "readdistcommand.h"
-#include "readtreecommand.h"
-#include "readotucommand.h"
#include "clustercommand.h"
#include "collectcommand.h"
#include "collectsharedcommand.h"
#include "getotulabelscommand.h"
#include "removeotulabelscommand.h"
#include "makecontigscommand.h"
+#include "loadlogfilecommand.h"
+#include "sffmultiplecommand.h"
+#include "classifysharedcommand.h"
/*******************************************************/
append = false;
//initialize list of valid commands
- 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["get.otulabels"] = "get.otulabels";
commands["remove.otulabels"] = "remove.otulabels";
commands["make.contigs"] = "make.contigs";
+ commands["load.logfile"] = "load.logfile";
+ commands["make.table"] = "make.table";
+ commands["sff.multiple"] = "sff.multiple";
commands["quit"] = "MPIEnabled";
+ commands["classify.shared"] = "classify.shared";
+
}
/***********************************************************/
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); }
- else if(commandName == "cluster") { command = new ClusterCommand(optionString); }
+ 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 == "make.shared") { command = new SharedCommand(optionString); }
else if(commandName == "get.commandinfo") { command = new GetCommandInfoCommand(optionString); }
else if(commandName == "deunique.tree") { command = new DeuniqueTreeCommand(optionString); }
- else if(commandName == "count.seqs") { command = new CountSeqsCommand(optionString); }
+ else if((commandName == "count.seqs") || (commandName == "make.table")) { command = new CountSeqsCommand(optionString); }
else if(commandName == "count.groups") { command = new CountGroupsCommand(optionString); }
else if(commandName == "clear.memory") { command = new ClearMemoryCommand(optionString); }
else if(commandName == "summary.tax") { command = new SummaryTaxCommand(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 if(commandName == "load.logfile") { command = new LoadLogfileCommand(optionString); }
+ else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
+ else if(commandName == "classify.shared") { command = new ClassifySharedCommand(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); }
- else if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); }
+ 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 == "make.shared") { pipecommand = new SharedCommand(optionString); }
else if(commandName == "get.commandinfo") { pipecommand = new GetCommandInfoCommand(optionString); }
else if(commandName == "deunique.tree") { pipecommand = new DeuniqueTreeCommand(optionString); }
- else if(commandName == "count.seqs") { pipecommand = new CountSeqsCommand(optionString); }
+ else if((commandName == "count.seqs") || (commandName == "make.table")) { pipecommand = new CountSeqsCommand(optionString); }
else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(optionString); }
else if(commandName == "clear.memory") { pipecommand = new ClearMemoryCommand(optionString); }
else if(commandName == "summary.tax") { pipecommand = new SummaryTaxCommand(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 if(commandName == "load.logfile") { pipecommand = new LoadLogfileCommand(optionString); }
+ else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
+ else if(commandName == "classify.shared") { pipecommand = new ClassifySharedCommand(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(); }
- else if(commandName == "cluster") { shellcommand = new ClusterCommand(); }
+ 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 == "make.shared") { shellcommand = new SharedCommand(); }
else if(commandName == "get.commandinfo") { shellcommand = new GetCommandInfoCommand(); }
else if(commandName == "deunique.tree") { shellcommand = new DeuniqueTreeCommand(); }
- else if(commandName == "count.seqs") { shellcommand = new CountSeqsCommand(); }
+ else if((commandName == "count.seqs") || (commandName == "make.table")) { shellcommand = new CountSeqsCommand(); }
else if(commandName == "count.groups") { shellcommand = new CountGroupsCommand(); }
else if(commandName == "clear.memory") { shellcommand = new ClearMemoryCommand(); }
else if(commandName == "summary.tax") { shellcommand = new SummaryTaxCommand(); }
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 if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); }
+ else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
+ else if(commandName == "classify.shared") { shellcommand = new ClassifySharedCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;