+/***********************************************************/
+//This function calls the appropriate command fucntions based on user input, this is used by the pipeline command to check a users piepline for errors before running
+Command* CommandFactory::getCommand(string commandName){
+ try {
+ delete shellcommand; //delete the old command
+
+ 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 == "quit") { shellcommand = new QuitCommand(); }
+ else if(commandName == "collect.single") { shellcommand = new CollectCommand(); }
+ else if(commandName == "collect.shared") { shellcommand = new CollectSharedCommand(); }
+ else if(commandName == "rarefaction.single") { shellcommand = new RareFactCommand(); }
+ else if(commandName == "rarefaction.shared") { shellcommand = new RareFactSharedCommand(); }
+ else if(commandName == "summary.single") { shellcommand = new SummaryCommand(); }
+ else if(commandName == "summary.shared") { shellcommand = new SummarySharedCommand(); }
+ else if(commandName == "unifrac.weighted") { shellcommand = new UnifracWeightedCommand(); }
+ else if(commandName == "unifrac.unweighted") { shellcommand = new UnifracUnweightedCommand(); }
+ else if(commandName == "get.group") { shellcommand = new GetgroupCommand(); }
+ else if(commandName == "get.label") { shellcommand = new GetlabelCommand(); }
+ else if(commandName == "get.sabund") { shellcommand = new GetSAbundCommand(); }
+ else if(commandName == "get.rabund") { shellcommand = new GetRAbundCommand(); }
+ else if(commandName == "libshuff") { shellcommand = new LibShuffCommand(); }
+ else if(commandName == "heatmap.bin") { shellcommand = new HeatMapCommand(); }
+ else if(commandName == "heatmap.sim") { shellcommand = new HeatMapSimCommand(); }
+ else if(commandName == "filter.seqs") { shellcommand = new FilterSeqsCommand(); }
+ else if(commandName == "venn") { shellcommand = new VennCommand(); }
+ else if(commandName == "bin.seqs") { shellcommand = new BinSeqCommand(); }
+ 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 == "dist.seqs") { shellcommand = new DistanceCommand(); }
+ else if(commandName == "align.seqs") { shellcommand = new AlignCommand(); }
+ else if(commandName == "summary.seqs") { shellcommand = new SeqSummaryCommand(); }
+ else if(commandName == "screen.seqs") { shellcommand = new ScreenSeqsCommand(); }
+ else if(commandName == "reverse.seqs") { shellcommand = new ReverseSeqsCommand(); }
+ else if(commandName == "trim.seqs") { shellcommand = new TrimSeqsCommand(); }
+ else if(commandName == "trim.flows") { shellcommand = new TrimFlowsCommand(); }
+ else if(commandName == "shhh.flows") { shellcommand = new ShhherCommand(); }
+ else if(commandName == "list.seqs") { shellcommand = new ListSeqsCommand(); }
+ else if(commandName == "get.seqs") { shellcommand = new GetSeqsCommand(); }
+ else if(commandName == "remove.seqs") { shellcommand = new RemoveSeqsCommand(); }
+ else if(commandName == "merge.files") { shellcommand = new MergeFileCommand(); }
+ else if(commandName == "system") { shellcommand = new SystemCommand(); }
+ else if(commandName == "align.check") { shellcommand = new AlignCheckCommand(); }
+ else if(commandName == "get.sharedseqs") { shellcommand = new GetSharedOTUCommand(); }
+ else if(commandName == "get.otulist") { shellcommand = new GetListCountCommand(); }
+ else if(commandName == "hcluster") { shellcommand = new HClusterCommand(); }
+ else if(commandName == "classify.seqs") { shellcommand = new ClassifySeqsCommand(); }
+ else if(commandName == "chimera.ccode") { shellcommand = new ChimeraCcodeCommand(); }
+ else if(commandName == "chimera.check") { shellcommand = new ChimeraCheckCommand(); }
+ else if(commandName == "chimera.slayer") { shellcommand = new ChimeraSlayerCommand(); }
+ else if(commandName == "chimera.uchime") { shellcommand = new ChimeraUchimeCommand(); }
+ else if(commandName == "chimera.pintail") { shellcommand = new ChimeraPintailCommand(); }
+ else if(commandName == "chimera.bellerophon") { shellcommand = new ChimeraBellerophonCommand(); }
+ else if(commandName == "phylotype") { shellcommand = new PhylotypeCommand(); }
+ else if(commandName == "mgcluster") { shellcommand = new MGClusterCommand(); }
+ else if(commandName == "pre.cluster") { shellcommand = new PreClusterCommand(); }
+ else if(commandName == "pcoa") { shellcommand = new PCOACommand(); }
+ else if(commandName == "pca") { shellcommand = new PCACommand(); }
+ else if(commandName == "nmds") { shellcommand = new NMDSCommand(); }
+ else if(commandName == "otu.hierarchy") { shellcommand = new OtuHierarchyCommand(); }
+ else if(commandName == "set.dir") { shellcommand = new SetDirectoryCommand(); }
+ else if(commandName == "set.logfile") { shellcommand = new SetLogFileCommand(); }
+ else if(commandName == "parse.list") { shellcommand = new ParseListCommand(); }
+ else if(commandName == "phylo.diversity") { shellcommand = new PhyloDiversityCommand(); }
+ else if(commandName == "make.group") { shellcommand = new MakeGroupCommand(); }
+ else if(commandName == "chop.seqs") { shellcommand = new ChopSeqsCommand(); }
+ else if(commandName == "clearcut") { shellcommand = new ClearcutCommand(); }
+ else if(commandName == "catchall") { shellcommand = new CatchAllCommand(); }
+ else if(commandName == "split.abund") { shellcommand = new SplitAbundCommand(); }
+ else if(commandName == "cluster.split") { shellcommand = new ClusterSplitCommand(); }
+ else if(commandName == "classify.otu") { shellcommand = new ClassifyOtuCommand(); }
+ else if(commandName == "degap.seqs") { shellcommand = new DegapSeqsCommand(); }
+ else if(commandName == "get.relabund") { shellcommand = new GetRelAbundCommand(); }
+ else if(commandName == "sens.spec") { shellcommand = new SensSpecCommand(); }
+ else if(commandName == "seq.error") { shellcommand = new SeqErrorCommand(); }
+ else if(commandName == "sffinfo") { shellcommand = new SffInfoCommand(); }
+ else if(commandName == "normalize.shared") { shellcommand = new NormalizeSharedCommand(); }
+ else if(commandName == "metastats") { shellcommand = new MetaStatsCommand(); }
+ else if(commandName == "split.groups") { shellcommand = new SplitGroupCommand(); }
+ 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 if(commandName == "corr.axes") { shellcommand = new CorrAxesCommand(); }
+ else if(commandName == "remove.rare") { shellcommand = new RemoveRareCommand(); }
+ else if(commandName == "merge.groups") { shellcommand = new MergeGroupsCommand(); }
+ else if(commandName == "amova") { shellcommand = new AmovaCommand(); }
+ else if(commandName == "homova") { shellcommand = new HomovaCommand(); }
+ else if(commandName == "mantel") { shellcommand = new MantelCommand(); }
+ else if(commandName == "anosim") { shellcommand = new AnosimCommand(); }
+ else if(commandName == "make.fastq") { shellcommand = new MakeFastQCommand(); }
+ 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 if(commandName == "deunique.tree") { shellcommand = new DeuniqueTreeCommand(); }
+ 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 == "summary.qual") { shellcommand = new SummaryQualCommand(); }
+ else if(commandName == "chimera.perseus") { shellcommand = new ChimeraPerseusCommand(); }
+ else if(commandName == "shhh.seqs") { shellcommand = new ShhhSeqsCommand(); }
+ else if(commandName == "otu.association") { shellcommand = new OTUAssociationCommand(); }
+ else if(commandName == "sort.seqs") { shellcommand = new SortSeqsCommand(); }
+ 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 if(commandName == "make.biom") { shellcommand = new MakeBiomCommand(); }
+ else if(commandName == "get.coremicrobiome") { shellcommand = new GetCoreMicroBiomeCommand(); }
+ else if(commandName == "list.otulabels") { shellcommand = new ListOtuLabelsCommand(); }
+ 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 if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
+ else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
+ else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
+ else if(commandName == "remove.dists") { shellcommand = new RemoveDistsCommand(); }
+ else if(commandName == "merge.taxsummary") { shellcommand = new MergeTaxSummaryCommand(); }
+ else if(commandName == "get.metacommunity") { shellcommand = new GetMetaCommunityCommand(); }
+ else { shellcommand = new NoCommand(); }
+
+ return shellcommand;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "getCommand");
+ exit(1);
+ }
+}
+/***********************************************************
+//This function is used to interrupt a command
+Command* CommandFactory::getCommand(){
+ try {
+ delete command; //delete the old command
+
+ string s = "";
+ command = new NoCommand(s);
+
+ return command;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "getCommand");
+ exit(1);
+ }
+}
+***********************************************************************/
+bool CommandFactory::isValidCommand(string command) {
+ try {
+
+ //is the command in the map
+ if ((commands.find(command)) != (commands.end())) {
+ return true;
+ }else{
+ m->mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
+ for (it = commands.begin(); it != commands.end(); it++) {
+ m->mothurOut(it->first + ", ");
+ }
+ m->mothurOutEndLine();
+ return false;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "isValidCommand");
+ exit(1);
+ }
+}
+/***********************************************************************/
+bool CommandFactory::isValidCommand(string command, string noError) {
+ try {
+
+ //is the command in the map
+ if ((commands.find(command)) != (commands.end())) {
+ return true;
+ }else{
+ return false;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "isValidCommand");
+ exit(1);
+ }
+}
+/***********************************************************************/
+void CommandFactory::printCommands(ostream& out) {
+ try {
+ out << "Valid commands are: ";
+ for (it = commands.begin(); it != commands.end(); it++) {
+ out << it->first << ",";
+ }
+ out << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "printCommands");
+ exit(1);
+ }
+}
+/***********************************************************************/
+void CommandFactory::printCommandsCategories(ostream& out) {
+ try {
+ map<string, string> commands = getListCommands();
+ map<string, string>::iterator it;
+
+ map<string, string> categories;
+ map<string, string>::iterator itCat;
+ //loop through each command outputting info
+ for (it = commands.begin(); it != commands.end(); it++) {
+
+ Command* thisCommand = getCommand(it->first);
+
+ //don't add hidden commands
+ if (thisCommand->getCommandCategory() != "Hidden") {
+ itCat = categories.find(thisCommand->getCommandCategory());
+ if (itCat == categories.end()) {
+ categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
+ }else {
+ categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
+ }
+ }
+ }
+
+ for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
+ out << itCat->first << " commmands include: " << itCat->second << endl;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "printCommandsCategories");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+
+
+