#include "binsequencecommand.h"
#include "getoturepcommand.h"
#include "treegroupscommand.h"
-#include "bootstrapsharedcommand.h"
-//#include "consensuscommand.h"
#include "distancecommand.h"
#include "aligncommand.h"
#include "matrixoutputcommand.h"
#include "classifytreecommand.h"
#include "cooccurrencecommand.h"
#include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
/*******************************************************/
commands["get.label"] = "get.label";
commands["get.sabund"] = "get.sabund";
commands["get.rabund"] = "get.rabund";
- commands["bootstrap.shared"] = "bootstrap.shared";
- //commands["consensus"] = "consensus";
commands["help"] = "help";
commands["reverse.seqs"] = "reverse.seqs";
commands["trim.seqs"] = "trim.seqs";
commands["classify.tree"] = "classify.tree";
commands["cooccurrence"] = "cooccurrence";
commands["pcr.seqs"] = "pcr.seqs";
+ commands["create.database"] = "create.database";
commands["quit"] = "MPIEnabled";
}
else if(commandName == "get.oturep") { command = new GetOTURepCommand(optionString); }
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 == "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 == "classify.tree") { command = new ClassifyTreeCommand(optionString); }
else if(commandName == "cooccurrence") { command = new CooccurrenceCommand(optionString); }
else if(commandName == "pcr.seqs") { command = new PcrSeqsCommand(optionString); }
+ else if(commandName == "create.database") { command = new CreateDatabaseCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
else if(commandName == "get.oturep") { pipecommand = new GetOTURepCommand(optionString); }
else if(commandName == "tree.shared") { pipecommand = new TreeGroupCommand(optionString); }
else if(commandName == "dist.shared") { pipecommand = new MatrixOutputCommand(optionString); }
- else if(commandName == "bootstrap.shared") { pipecommand = new BootSharedCommand(optionString); }
- else if(commandName == "consensus") { pipecommand = new ConcensusCommand(optionString); }
else if(commandName == "dist.seqs") { pipecommand = new DistanceCommand(optionString); }
else if(commandName == "align.seqs") { pipecommand = new AlignCommand(optionString); }
else if(commandName == "summary.seqs") { pipecommand = new SeqSummaryCommand(optionString); }
else if(commandName == "classify.tree") { pipecommand = new ClassifyTreeCommand(optionString); }
else if(commandName == "cooccurrence") { pipecommand = new CooccurrenceCommand(optionString); }
else if(commandName == "pcr.seqs") { pipecommand = new PcrSeqsCommand(optionString); }
+ else if(commandName == "create.database") { pipecommand = new CreateDatabaseCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
else if(commandName == "get.oturep") { shellcommand = new GetOTURepCommand(); }
else if(commandName == "tree.shared") { shellcommand = new TreeGroupCommand(); }
else if(commandName == "dist.shared") { shellcommand = new MatrixOutputCommand(); }
- else if(commandName == "bootstrap.shared") { shellcommand = new BootSharedCommand(); }
- else if(commandName == "consensus") { shellcommand = new ConcensusCommand(); }
else if(commandName == "dist.seqs") { shellcommand = new DistanceCommand(); }
else if(commandName == "align.seqs") { shellcommand = new AlignCommand(); }
else if(commandName == "summary.seqs") { shellcommand = new SeqSummaryCommand(); }
else if(commandName == "classify.tree") { shellcommand = new ClassifyTreeCommand(); }
else if(commandName == "cooccurrence") { shellcommand = new CooccurrenceCommand(); }
else if(commandName == "pcr.seqs") { shellcommand = new PcrSeqsCommand(); }
+ else if(commandName == "create.database") { shellcommand = new CreateDatabaseCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;