+}
+/***********************************************************/
+
+/***********************************************************/
+//This function calls the appropriate command fucntions based on user input.
+Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
+ try {
+ delete pipecommand; //delete the old command
+
+ checkForRedirects(optionString);
+
+ //user has opted to redirect output from dir where input files are located to some other place
+ if (outputDir != "") {
+ if (optionString != "") { optionString += ", outputdir=" + outputDir; }
+ else { optionString += "outputdir=" + outputDir; }
+ }
+
+ //user has opted to redirect input from dir where mothur.exe is located to some other place
+ if (inputDir != "") {
+ if (optionString != "") { optionString += ", inputdir=" + inputDir; }
+ else { optionString += "inputdir=" + inputDir; }
+ }
+
+ 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 == "quit") { pipecommand = new QuitCommand(optionString); }
+ else if(commandName == "collect.single") { pipecommand = new CollectCommand(optionString); }
+ else if(commandName == "collect.shared") { pipecommand = new CollectSharedCommand(optionString); }
+ else if(commandName == "rarefaction.single") { pipecommand = new RareFactCommand(optionString); }
+ else if(commandName == "rarefaction.shared") { pipecommand = new RareFactSharedCommand(optionString); }
+ else if(commandName == "summary.single") { pipecommand = new SummaryCommand(optionString); }
+ else if(commandName == "summary.shared") { pipecommand = new SummarySharedCommand(optionString); }
+ else if(commandName == "unifrac.weighted") { pipecommand = new UnifracWeightedCommand(optionString); }
+ else if(commandName == "unifrac.unweighted") { pipecommand = new UnifracUnweightedCommand(optionString); }
+ else if(commandName == "get.group") { pipecommand = new GetgroupCommand(optionString); }
+ else if(commandName == "get.label") { pipecommand = new GetlabelCommand(optionString); }
+ else if(commandName == "get.sabund") { pipecommand = new GetSAbundCommand(optionString); }
+ else if(commandName == "get.rabund") { pipecommand = new GetRAbundCommand(optionString); }
+ else if(commandName == "libshuff") { pipecommand = new LibShuffCommand(optionString); }
+ else if(commandName == "heatmap.bin") { pipecommand = new HeatMapCommand(optionString); }
+ else if(commandName == "heatmap.sim") { pipecommand = new HeatMapSimCommand(optionString); }
+ else if(commandName == "filter.seqs") { pipecommand = new FilterSeqsCommand(optionString); }
+ else if(commandName == "venn") { pipecommand = new VennCommand(optionString); }
+ else if(commandName == "bin.seqs") { pipecommand = new BinSeqCommand(optionString); }
+ 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 == "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 == "screen.seqs") { pipecommand = new ScreenSeqsCommand(optionString); }
+ else if(commandName == "reverse.seqs") { pipecommand = new ReverseSeqsCommand(optionString); }
+ else if(commandName == "trim.seqs") { pipecommand = new TrimSeqsCommand(optionString); }
+ else if(commandName == "trim.flows") { pipecommand = new TrimFlowsCommand(optionString); }
+ else if(commandName == "shhh.flows") { pipecommand = new ShhherCommand(optionString); }
+ else if(commandName == "list.seqs") { pipecommand = new ListSeqsCommand(optionString); }
+ else if(commandName == "get.seqs") { pipecommand = new GetSeqsCommand(optionString); }
+ else if(commandName == "remove.seqs") { pipecommand = new RemoveSeqsCommand(optionString); }
+ else if(commandName == "merge.files") { pipecommand = new MergeFileCommand(optionString); }
+ else if(commandName == "system") { pipecommand = new SystemCommand(optionString); }
+ else if(commandName == "align.check") { pipecommand = new AlignCheckCommand(optionString); }
+ else if(commandName == "get.sharedseqs") { pipecommand = new GetSharedOTUCommand(optionString); }
+ else if(commandName == "get.otulist") { pipecommand = new GetListCountCommand(optionString); }
+ else if(commandName == "hcluster") { pipecommand = new HClusterCommand(optionString); }
+ else if(commandName == "classify.seqs") { pipecommand = new ClassifySeqsCommand(optionString); }
+ else if(commandName == "chimera.ccode") { pipecommand = new ChimeraCcodeCommand(optionString); }
+ else if(commandName == "chimera.check") { pipecommand = new ChimeraCheckCommand(optionString); }
+ else if(commandName == "chimera.uchime") { pipecommand = new ChimeraUchimeCommand(optionString); }
+ else if(commandName == "chimera.slayer") { pipecommand = new ChimeraSlayerCommand(optionString); }
+ else if(commandName == "chimera.pintail") { pipecommand = new ChimeraPintailCommand(optionString); }
+ else if(commandName == "chimera.bellerophon") { pipecommand = new ChimeraBellerophonCommand(optionString); }
+ else if(commandName == "phylotype") { pipecommand = new PhylotypeCommand(optionString); }
+ else if(commandName == "mgcluster") { pipecommand = new MGClusterCommand(optionString); }
+ else if(commandName == "pre.cluster") { pipecommand = new PreClusterCommand(optionString); }
+ else if(commandName == "pcoa") { pipecommand = new PCOACommand(optionString); }
+ else if(commandName == "pca") { pipecommand = new PCACommand(optionString); }
+ else if(commandName == "nmds") { pipecommand = new NMDSCommand(optionString); }
+ else if(commandName == "otu.hierarchy") { pipecommand = new OtuHierarchyCommand(optionString); }
+ else if(commandName == "set.dir") { pipecommand = new SetDirectoryCommand(optionString); }
+ else if(commandName == "set.logfile") { pipecommand = new SetLogFileCommand(optionString); }
+ else if(commandName == "parse.list") { pipecommand = new ParseListCommand(optionString); }
+ else if(commandName == "phylo.diversity") { pipecommand = new PhyloDiversityCommand(optionString); }
+ else if(commandName == "make.group") { pipecommand = new MakeGroupCommand(optionString); }
+ else if(commandName == "chop.seqs") { pipecommand = new ChopSeqsCommand(optionString); }
+ else if(commandName == "clearcut") { pipecommand = new ClearcutCommand(optionString); }
+ else if(commandName == "catchall") { pipecommand = new CatchAllCommand(optionString); }
+ else if(commandName == "split.abund") { pipecommand = new SplitAbundCommand(optionString); }
+ else if(commandName == "cluster.split") { pipecommand = new ClusterSplitCommand(optionString); }
+ else if(commandName == "classify.otu") { pipecommand = new ClassifyOtuCommand(optionString); }
+ else if(commandName == "degap.seqs") { pipecommand = new DegapSeqsCommand(optionString); }
+ else if(commandName == "get.relabund") { pipecommand = new GetRelAbundCommand(optionString); }
+ else if(commandName == "sens.spec") { pipecommand = new SensSpecCommand(optionString); }
+ else if(commandName == "seq.error") { pipecommand = new SeqErrorCommand(optionString); }
+ else if(commandName == "sffinfo") { pipecommand = new SffInfoCommand(optionString); }
+ else if(commandName == "normalize.shared") { pipecommand = new NormalizeSharedCommand(optionString); }
+ else if(commandName == "metastats") { pipecommand = new MetaStatsCommand(optionString); }
+ 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 if(commandName == "corr.axes") { pipecommand = new CorrAxesCommand(optionString); }
+ else if(commandName == "remove.rare") { pipecommand = new RemoveRareCommand(optionString); }
+ else if(commandName == "merge.groups") { pipecommand = new MergeGroupsCommand(optionString); }
+ else if(commandName == "amova") { pipecommand = new AmovaCommand(optionString); }
+ else if(commandName == "homova") { pipecommand = new HomovaCommand(optionString); }
+ else if(commandName == "mantel") { pipecommand = new MantelCommand(optionString); }
+ else if(commandName == "anosim") { pipecommand = new AnosimCommand(optionString); }
+ else if(commandName == "make.fastq") { pipecommand = new MakeFastQCommand(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 if(commandName == "deunique.tree") { pipecommand = new DeuniqueTreeCommand(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 == "summary.qual") { pipecommand = new SummaryQualCommand(optionString); }
+ else if(commandName == "chimera.perseus") { pipecommand = new ChimeraPerseusCommand(optionString); }
+ else if(commandName == "shhh.seqs") { pipecommand = new ShhhSeqsCommand(optionString); }
+ else if(commandName == "otu.association") { pipecommand = new OTUAssociationCommand(optionString); }
+ else if(commandName == "sort.seqs") { pipecommand = new SortSeqsCommand(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 if(commandName == "make.biom") { pipecommand = new MakeBiomCommand(optionString); }
+ else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); }
+ else if(commandName == "list.otulabels") { pipecommand = new ListOtuLabelsCommand(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 if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
+ else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
+ else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
+ else if(commandName == "remove.dists") { pipecommand = new RemoveDistsCommand(optionString); }
+ else if(commandName == "merge.taxsummary") { pipecommand = new MergeTaxSummaryCommand(optionString); }
+ else if(commandName == "get.metacommunity") { pipecommand = new GetMetaCommunityCommand(optionString); }
+ else { pipecommand = new NoCommand(optionString); }
+
+ return pipecommand;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "getCommand");