#include "parsefastaqcommand.h"
#include "pipelinepdscommand.h"
#include "deuniqueseqscommand.h"
-
+#include "pairwiseseqscommand.h"
+#include "clusterdoturcommand.h"
+#include "subsamplecommand.h"
+#include "removegroupscommand.h"
+#include "getgroupscommand.h"
+#include "getotuscommand.h"
+#include "removeotuscommand.h"
+#include "indicatorcommand.h"
+#include "consensusseqscommand.h"
/*******************************************************/
commands["remove.lineage"] = "remove.lineage";
commands["fastq.info"] = "fastq.info";
commands["deunique.seqs"] = "deunique.seqs";
+ commands["cluster.classic"] = "cluster.classic";
+ commands["sub.sample"] = "sub.sample";
+ commands["remove.groups"] = "remove.groups";
+ commands["get.groups"] = "get.groups";
+ commands["get.otus"] = "get.otus";
+ commands["remove.otus"] = "remove.otus";
+ commands["indicator"] = "indicator";
+ commands["consensus.seqs"] = "consensus.seqs";
+ commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
else if(commandName == "cluster.fragments") { command = new ClusterFragmentsCommand(optionString); }
else if(commandName == "get.lineage") { command = new GetLineageCommand(optionString); }
else if(commandName == "remove.lineage") { command = new RemoveLineageCommand(optionString); }
+ else if(commandName == "get.groups") { command = new GetGroupsCommand(optionString); }
+ else if(commandName == "remove.groups") { command = new RemoveGroupsCommand(optionString); }
+ else if(commandName == "get.otus") { command = new GetOtusCommand(optionString); }
+ else if(commandName == "remove.otus") { command = new RemoveOtusCommand(optionString); }
else if(commandName == "fastq.info") { command = new ParseFastaQCommand(optionString); }
else if(commandName == "pipeline.pds") { command = new PipelineCommand(optionString); }
else if(commandName == "deunique.seqs") { command = new DeUniqueSeqsCommand(optionString); }
+ else if(commandName == "pairwise.seqs") { command = new PairwiseSeqsCommand(optionString); }
+ else if(commandName == "cluster.classic") { command = new ClusterDoturCommand(optionString); }
+ else if(commandName == "sub.sample") { command = new SubSampleCommand(optionString); }
+ else if(commandName == "indicator") { command = new IndicatorCommand(optionString); }
+ else if(commandName == "consensus.seqs") { command = new ConsensusSeqsCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
else if(commandName == "split.groups") { pipecommand = new SplitGroupCommand(optionString); }
else if(commandName == "cluster.fragments") { pipecommand = new ClusterFragmentsCommand(optionString); }
else if(commandName == "get.lineage") { pipecommand = new GetLineageCommand(optionString); }
+ else if(commandName == "get.groups") { pipecommand = new GetGroupsCommand(optionString); }
else if(commandName == "remove.lineage") { pipecommand = new RemoveLineageCommand(optionString); }
+ else if(commandName == "remove.groups") { pipecommand = new RemoveGroupsCommand(optionString); }
+ else if(commandName == "get.otus") { pipecommand = new GetOtusCommand(optionString); }
+ else if(commandName == "remove.otus") { pipecommand = new RemoveOtusCommand(optionString); }
else if(commandName == "fastq.info") { pipecommand = new ParseFastaQCommand(optionString); }
else if(commandName == "deunique.seqs") { pipecommand = new DeUniqueSeqsCommand(optionString); }
+ else if(commandName == "pairwise.seqs") { pipecommand = new PairwiseSeqsCommand(optionString); }
+ else if(commandName == "cluster.classic") { pipecommand = new ClusterDoturCommand(optionString); }
+ else if(commandName == "sub.sample") { pipecommand = new SubSampleCommand(optionString); }
+ else if(commandName == "indicator") { pipecommand = new IndicatorCommand(optionString); }
+ else if(commandName == "consensus.seqs") { pipecommand = new ConsensusSeqsCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
else if(commandName == "cluster.fragments") { shellcommand = new ClusterFragmentsCommand(); }
else if(commandName == "get.lineage") { shellcommand = new GetLineageCommand(); }
else if(commandName == "remove.lineage") { shellcommand = new RemoveLineageCommand(); }
+ else if(commandName == "get.groups") { shellcommand = new GetGroupsCommand(); }
+ else if(commandName == "remove.groups") { shellcommand = new RemoveGroupsCommand(); }
+ else if(commandName == "get.otus") { shellcommand = new GetOtusCommand(); }
+ else if(commandName == "remove.otus") { shellcommand = new RemoveOtusCommand(); }
else if(commandName == "fastq.info") { shellcommand = new ParseFastaQCommand(); }
else if(commandName == "deunique.seqs") { shellcommand = new DeUniqueSeqsCommand(); }
+ else if(commandName == "pairwise.seqs") { shellcommand = new PairwiseSeqsCommand(); }
+ else if(commandName == "cluster.classic") { shellcommand = new ClusterDoturCommand(); }
+ else if(commandName == "sub.sample") { shellcommand = new SubSampleCommand(); }
+ else if(commandName == "indicator") { shellcommand = new IndicatorCommand(); }
+ else if(commandName == "consensus.seqs") { shellcommand = new ConsensusSeqsCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;