commandfactory.cpp

   1 /*
   2  *  commandfactory.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 10/25/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "command.hpp"
  11 #include "clustercommand.h"
  12 #include "collectcommand.h"
  13 #include "collectsharedcommand.h"
  14 #include "getgroupcommand.h"
  15 #include "getlabelcommand.h"
  16 #include "rarefactcommand.h"
  17 #include "summarycommand.h"
  18 #include "summarysharedcommand.h"
  19 #include "rarefactsharedcommand.h"
  20 #include "quitcommand.h"
  21 #include "helpcommand.h"
  22 #include "commandfactory.hpp"
  23 #include "deconvolutecommand.h"
  24 #include "parsimonycommand.h"
  25 #include "unifracunweightedcommand.h"
  26 #include "unifracweightedcommand.h"
  27 #include "libshuffcommand.h"
  28 #include "heatmapcommand.h"
  29 #include "heatmapsimcommand.h"
  30 #include "filterseqscommand.h"
  31 #include "venncommand.h"
  32 #include "nocommands.h"
  33 #include "binsequencecommand.h"
  34 #include "getoturepcommand.h"
  35 #include "treegroupscommand.h"
  36 #include "distancecommand.h"
  37 #include "aligncommand.h"
  38 #include "matrixoutputcommand.h"
  39 #include "getsabundcommand.h"
  40 #include "getrabundcommand.h"
  41 #include "seqsummarycommand.h"
  42 #include "screenseqscommand.h"
  43 #include "reversecommand.h"
  44 #include "trimseqscommand.h"
  45 #include "mergefilecommand.h"
  46 #include "listseqscommand.h"
  47 #include "getseqscommand.h"
  48 #include "removeseqscommand.h"
  49 #include "systemcommand.h"
  50 #include "secondarystructurecommand.h"
  51 #include "getsharedotucommand.h"
  52 #include "getlistcountcommand.h"
  53 #include "hclustercommand.h"
  54 #include "classifyseqscommand.h"
  55 #include "phylotypecommand.h"
  56 #include "mgclustercommand.h"
  57 #include "preclustercommand.h"
  58 #include "pcoacommand.h"
  59 #include "otuhierarchycommand.h"
  60 #include "setdircommand.h"
  61 #include "parselistscommand.h"
  62 #include "chimeraccodecommand.h"
  63 #include "chimeracheckcommand.h"
  64 #include "chimeraslayercommand.h"
  65 #include "chimerapintailcommand.h"
  66 #include "chimerabellerophoncommand.h"
  67 #include "chimerauchimecommand.h"
  68 #include "setlogfilecommand.h"
  69 #include "phylodiversitycommand.h"
  70 #include "makegroupcommand.h"
  71 #include "chopseqscommand.h"
  72 #include "clearcutcommand.h"
  73 #include "catchallcommand.h"
  74 #include "splitabundcommand.h"
  75 #include "clustersplitcommand.h"
  76 #include "classifyotucommand.h"
  77 #include "degapseqscommand.h"
  78 #include "getrelabundcommand.h"
  79 #include "sensspeccommand.h"
  80 #include "sffinfocommand.h"
  81 #include "seqerrorcommand.h"
  82 #include "normalizesharedcommand.h"
  83 #include "metastatscommand.h"
  84 #include "splitgroupscommand.h"
  85 #include "clusterfragmentscommand.h"
  86 #include "getlineagecommand.h"
  87 #include "removelineagecommand.h"
  88 #include "parsefastaqcommand.h"
  89 #include "pipelinepdscommand.h"
  90 #include "deuniqueseqscommand.h"
  91 #include "pairwiseseqscommand.h"
  92 #include "clusterdoturcommand.h"
  93 #include "subsamplecommand.h"
  94 #include "removegroupscommand.h"
  95 #include "getgroupscommand.h"
  96 #include "getotuscommand.h"
  97 #include "removeotuscommand.h"
  98 #include "indicatorcommand.h"
  99 #include "consensusseqscommand.h"
 100 #include "trimflowscommand.h"
 101 #include "corraxescommand.h"
 102 #include "shhhercommand.h"
 103 #include "pcacommand.h"
 104 #include "nmdscommand.h"
 105 #include "removerarecommand.h"
 106 #include "mergegroupscommand.h"
 107 #include "amovacommand.h"
 108 #include "homovacommand.h"
 109 #include "mantelcommand.h"
 110 #include "makefastqcommand.h"
 111 #include "anosimcommand.h"
 112 #include "getcurrentcommand.h"
 113 #include "setcurrentcommand.h"
 114 #include "sharedcommand.h"
 115 #include "getcommandinfocommand.h"
 116 #include "deuniquetreecommand.h"
 117 #include "countseqscommand.h"
 118 #include "countgroupscommand.h"
 119 #include "clearmemorycommand.h"
 120 #include "summarytaxcommand.h"
 121 #include "chimeraperseuscommand.h"
 122 #include "shhhseqscommand.h"
 123 #include "summaryqualcommand.h"
 124 #include "otuassociationcommand.h"
 125 #include "sortseqscommand.h"
 126 #include "classifytreecommand.h"
 127 #include "cooccurrencecommand.h"
 128 #include "pcrseqscommand.h"
 129 #include "createdatabasecommand.h"
 130 #include "makebiomcommand.h"
 131 #include "getcoremicrobiomecommand.h"
 132 #include "listotulabelscommand.h"
 133 #include "getotulabelscommand.h"
 134 #include "removeotulabelscommand.h"
 135 #include "makecontigscommand.h"
 136 #include "loadlogfilecommand.h"
 137 #include "sffmultiplecommand.h"
 138 #include "classifyrfsharedcommand.h"
 139 #include "filtersharedcommand.h"
 140 #include "primerdesigncommand.h"
 141 #include "getdistscommand.h"
 142 #include "removedistscommand.h"
 143 #include "mergetaxsummarycommand.h"
 144 #include "getmetacommunitycommand.h"
 145 #include "sparcccommand.h"
 146 #include "makelookupcommand.h"
 147 #include "renameseqscommand.h"
 148 #include "makelefsecommand.h"
 149 #include "lefsecommand.h"
 150 #include "kruskalwalliscommand.h"
 151 #include "sracommand.h"
 152 #include "mergesfffilecommand.h"
 153
 154 /*******************************************************/
 155
 156 /******************************************************/
 157 CommandFactory* CommandFactory::getInstance() {
 158         if( _uniqueInstance == 0) {
 159                 _uniqueInstance = new CommandFactory();
 160         }
 161         return _uniqueInstance;
 162 }
 163 /***********************************************************/
 164
 165 /***********************************************************/
 166 //note: This class is resposible for knowing which commands are mpiEnabled,
 167 //If a command is not enabled only process 0 will execute the command.
 168 //This avoids redundant outputs on pieces of code we have not paralellized.
 169 //If you add mpi code to a existing command you need to modify the list below or the code will hang on MPI blocking commands like FIle_open.
 170 //example:  commands["dist.seqs"] = "MPIEnabled";
 171
 172 CommandFactory::CommandFactory(){
 173         string s = "";
 174         m = MothurOut::getInstance();
 175
 176         command = new NoCommand(s);
 177         shellcommand = new NoCommand(s);
 178         pipecommand = new NoCommand(s);
 179
 180         outputDir = ""; inputDir = "";
 181         logFileName = "";
 182         append = false;
 183
 184         //initialize list of valid commands
 185         commands["make.shared"]                 = "make.shared";
 186         commands["bin.seqs"]                    = "bin.seqs";
 187         commands["get.oturep"]                  = "get.oturep";
 188         commands["cluster"]                             = "cluster";
 189         commands["unique.seqs"]                 = "unique.seqs";
 190         commands["dist.shared"]                 = "dist.shared";
 191         commands["collect.single"]              = "collect.single";
 192         commands["collect.shared"]              = "collect.shared";
 193         commands["rarefaction.single"]  = "rarefaction.single";
 194         commands["rarefaction.shared"]  = "rarefaction.shared";
 195         commands["summary.single"]              = "summary.single";
 196         commands["summary.shared"]              = "summary.shared";
 197         commands["parsimony"]                   = "parsimony";
 198         commands["unifrac.weighted"]    = "unifrac.weighted";
 199         commands["unifrac.unweighted"]  = "unifrac.unweighted";
 200         commands["libshuff"]                    = "libshuff";
 201         commands["tree.shared"]                 = "tree.shared";
 202         commands["heatmap.bin"]                 = "heatmap.bin";
 203         commands["heatmap.sim"]                 = "heatmap.sim";
 204         commands["venn"]                                = "venn";
 205         commands["get.group"]           = "get.group";
 206         commands["get.label"]           = "get.label";
 207         commands["get.sabund"]          = "get.sabund";
 208         commands["get.rabund"]          = "get.rabund";
 209         commands["help"]                                = "help";
 210         commands["reverse.seqs"]                = "reverse.seqs";
 211         commands["trim.seqs"]                   = "trim.seqs";
 212         commands["trim.flows"]                  = "trim.flows";
 213         commands["list.seqs"]                   = "list.seqs";
 214         commands["get.seqs"]                    = "get.seqs";
 215         commands["remove.seqs"]                 = "remove.seqs";
 216         commands["system"]                              = "system";
 217         commands["align.check"]                 = "align.check";
 218         commands["get.sharedseqs"]              = "get.sharedseqs";
 219         commands["get.otulist"]                 = "get.otulist";
 220         commands["hcluster"]                    = "hcluster";
 221         commands["phylotype"]                   = "phylotype";
 222         commands["mgcluster"]                   = "mgcluster";
 223         commands["pre.cluster"]                 = "pre.cluster";
 224         commands["pcoa"]                                = "pcoa";
 225         commands["otu.hierarchy"]               = "otu.hierarchy";
 226         commands["set.dir"]                             = "MPIEnabled";
 227         commands["merge.files"]                 = "merge.files";
 228         commands["parse.list"]                  = "parse.list";
 229         commands["set.logfile"]                 = "set.logfile";
 230         commands["phylo.diversity"]             = "phylo.diversity";
 231         commands["make.group"]                  = "make.group";
 232         commands["chop.seqs"]                   = "chop.seqs";
 233         commands["clearcut"]                    = "clearcut";
 234         commands["catchall"]                    = "catchall";
 235         commands["split.abund"]                 = "split.abund";
 236         commands["classify.otu"]                = "classify.otu";
 237         commands["degap.seqs"]                  = "degap.seqs";
 238         commands["get.relabund"]                = "get.relabund";
 239         commands["sffinfo"]                             = "sffinfo";
 240         commands["normalize.shared"]    = "normalize.shared";
 241         commands["metastats"]                   = "metastats";
 242         commands["split.groups"]                = "split.groups";
 243         commands["cluster.fragments"]   = "cluster.fragments";
 244         commands["get.lineage"]                 = "get.lineage";
 245         commands["remove.lineage"]              = "remove.lineage";
 246         commands["fastq.info"]                  = "fastq.info";
 247         commands["deunique.seqs"]               = "deunique.seqs";
 248         commands["cluster.classic"]             = "cluster.classic";
 249         commands["sub.sample"]                  = "sub.sample";
 250         commands["remove.groups"]               = "remove.groups";
 251         commands["get.groups"]                  = "get.groups";
 252         commands["get.otus"]                    = "get.otus";
 253         commands["remove.otus"]                 = "remove.otus";
 254         commands["indicator"]                   = "indicator";
 255         commands["consensus.seqs"]              = "consensus.seqs";
 256         commands["corr.axes"]                   = "corr.axes";
 257         commands["pca"]                                 = "pca";
 258         commands["nmds"]                                = "nmds";
 259         commands["remove.rare"]                 = "remove.rare";
 260         commands["amova"]                               = "amova";
 261         commands["homova"]                              = "homova";
 262         commands["mantel"]                              = "mantel";
 263         commands["anosim"]                              = "anosim";
 264         commands["make.fastq"]                  = "make.fastq";
 265         commands["merge.groups"]                = "merge.groups";
 266         commands["get.current"]                 = "MPIEnabled";
 267         commands["set.current"]                 = "MPIEnabled";
 268         commands["get.commandinfo"]             = "get.commandinfo";
 269         commands["deunique.tree"]               = "deunique.tree";
 270         commands["count.seqs"]                  = "count.seqs";
 271         commands["count.groups"]                = "count.groups";
 272         commands["clear.memory"]                = "clear.memory";
 273         commands["pairwise.seqs"]               = "MPIEnabled";
 274         commands["pipeline.pds"]                = "MPIEnabled";
 275         commands["classify.seqs"]               = "MPIEnabled";
 276         commands["dist.seqs"]                   = "MPIEnabled";
 277         commands["filter.seqs"]                 = "MPIEnabled";
 278         commands["align.seqs"]                  = "MPIEnabled";
 279         commands["chimera.ccode"]               = "MPIEnabled";
 280         commands["chimera.check"]               = "MPIEnabled";
 281         commands["chimera.slayer"]              = "MPIEnabled";
 282         commands["chimera.uchime"]              = "chimera.uchime";
 283         commands["chimera.perseus"]             = "chimera.perseus";
 284         commands["chimera.pintail"]             = "MPIEnabled";
 285         commands["chimera.bellerophon"] = "MPIEnabled";
 286         commands["screen.seqs"]                 = "MPIEnabled";
 287         commands["summary.seqs"]                = "MPIEnabled";
 288         commands["cluster.split"]               = "MPIEnabled";
 289         commands["shhh.flows"]                  = "MPIEnabled";
 290         commands["sens.spec"]                   = "sens.spec";
 291         commands["seq.error"]                   = "seq.error";
 292         commands["summary.tax"]                 = "summary.tax";
 293         commands["summary.qual"]                = "summary.qual";
 294         commands["shhh.seqs"]                   = "shhh.seqs";
 295         commands["otu.association"]             = "otu.association";
 296     commands["sort.seqs"]           = "sort.seqs";
 297     commands["classify.tree"]       = "classify.tree";
 298     commands["cooccurrence"]        = "cooccurrence";
 299     commands["pcr.seqs"]            = "pcr.seqs";
 300     commands["create.database"]     = "create.database";
 301     commands["make.biom"]           = "make.biom";
 302     commands["get.coremicrobiome"]  = "get.coremicrobiome";
 303     commands["list.otulabels"]      = "list.otulabels";
 304     commands["get.otulabels"]       = "get.otulabels";
 305     commands["remove.otulabels"]    = "remove.otulabels";
 306     commands["make.contigs"]        = "make.contigs";
 307     commands["load.logfile"]        = "load.logfile";
 308     commands["make.table"]          = "make.table";
 309     commands["sff.multiple"]        = "sff.multiple";
 310         commands["quit"]                                = "MPIEnabled";
 311     commands["classify.rf"]         = "classify.rf";
 312     commands["filter.shared"]           = "filter.shared";
 313     commands["primer.design"]           = "primer.design";
 314     commands["get.dists"]           = "get.dists";
 315     commands["remove.dists"]        = "remove.dists";
 316     commands["merge.taxsummary"]    = "merge.taxsummary";
 317     commands["get.communitytype"]   = "get.communitytype";
 318     commands["sparcc"]              = "sparcc";
 319     commands["make.lookup"]         = "make.lookup";
 320     commands["rename.seqs"]         = "rename.seqs";
 321     commands["make.lefse"]          = "make.lefse";
 322     commands["lefse"]               = "lefse";
 323     commands["kruskal.wallis"]      = "kruskal.wallis";
 324     commands["sra"]                 = "sra";
 325     commands["merge.sfffiles"]      = "merge.sfffiles";
 326
 327
 328 }
 329 /***********************************************************/
 330
 331 /***********************************************************/
 332 bool CommandFactory::MPIEnabled(string commandName) {
 333         bool mpi = false;
 334         it = commands.find(commandName);
 335         if (it != commands.end()) {
 336                 if (it->second == "MPIEnabled") { return true; }
 337         }
 338         return mpi;
 339 }
 340 /***********************************************************/
 341
 342 /***********************************************************/
 343 CommandFactory::~CommandFactory(){
 344         _uniqueInstance = 0;
 345         delete command;
 346         delete shellcommand;
 347         delete pipecommand;
 348 }
 349 /***********************************************************/
 350
 351 /***********************************************************/
 352 int CommandFactory::checkForRedirects(string optionString) {
 353     try {
 354
 355         int pos = optionString.find("outputdir");
 356         if (pos != string::npos) { //user has set outputdir in command option string
 357             string outputOption = "";
 358             bool foundEquals = false;
 359             for(int i=pos;i<optionString.length();i++){
 360                 if(optionString[i] == ',')       { break;               }
 361                 else if(optionString[i] == '=')  { foundEquals = true;  }
 362                 if (foundEquals)       {   outputOption += optionString[i]; }
 363             }
 364             if(m->dirCheck(outputOption)){
 365                 setOutputDirectory(outputOption);
 366                 m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
 367             }
 368         }
 369
 370         pos = optionString.find("inputdir");
 371         if (pos != string::npos) { //user has set inputdir in command option string
 372             string intputOption = "";
 373             bool foundEquals = false;
 374             for(int i=pos;i<optionString.length();i++){
 375                 if(optionString[i] == ',')       { break;               }
 376                 else if(optionString[i] == '=')  { foundEquals = true;  }
 377                 if (foundEquals)       {   intputOption += optionString[i]; }
 378             }
 379             if(m->dirCheck(intputOption)){
 380                 setInputDirectory(intputOption);
 381                 m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
 382             }
 383         }
 384
 385         return 0;
 386         }
 387         catch(exception& e) {
 388                 m->errorOut(e, "CommandFactory", "getCommand");
 389                 exit(1);
 390         }
 391 }
 392 /***********************************************************/
 393
 394 /***********************************************************/
 395 //This function calls the appropriate command fucntions based on user input.
 396 Command* CommandFactory::getCommand(string commandName, string optionString){
 397         try {
 398
 399                 delete command;   //delete the old command
 400
 401         checkForRedirects(optionString);
 402
 403                 //user has opted to redirect output from dir where input files are located to some other place
 404                 if (outputDir != "") {
 405                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 406                         else { optionString += "outputdir=" + outputDir; }
 407                 }
 408
 409                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 410                 if (inputDir != "") {
 411                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 412                         else { optionString += "inputdir=" + inputDir; }
 413                 }
 414
 415                 if(commandName == "cluster")                    {       command = new ClusterCommand(optionString);                                     }
 416                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand(optionString);                         }
 417                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand(optionString);                           }
 418                 else if(commandName == "help")                                  {       command = new HelpCommand(optionString);                                        }
 419                 else if(commandName == "quit")                                  {       command = new QuitCommand(optionString);                                        }
 420                 else if(commandName == "collect.single")                {       command = new CollectCommand(optionString);                                     }
 421                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand(optionString);                       }
 422                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand(optionString);                            }
 423                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand(optionString);                      }
 424                 else if(commandName == "summary.single")                {       command = new SummaryCommand(optionString);                                     }
 425                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand(optionString);                       }
 426                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand(optionString);                     }
 427                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);           }
 428                 else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                                }
 429                 else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                                }
 430                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                               }
 431                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                               }
 432                 else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                                }
 433                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand(optionString);                                 }
 434                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand(optionString);                              }
 435                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand(optionString);                              }
 436                 else if(commandName == "venn")                                  {   command = new VennCommand(optionString);                                    }
 437                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand(optionString);                                  }
 438                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                               }
 439                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                               }
 440                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);                    }
 441                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                                }
 442                 else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                                   }
 443                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                          }
 444                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                          }
 445                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
 446                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
 447                 else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
 448                 else if(commandName == "shhh.flows")                    {       command = new ShhherCommand(optionString);                                      }
 449                 else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
 450                 else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
 451                 else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
 452                 else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                           }
 453                 else if(commandName == "system")                                {       command = new SystemCommand(optionString);                                      }
 454                 else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                          }
 455                 else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                        }
 456                 else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                        }
 457                 else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                            }
 458                 else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                        }
 459                 else if(commandName == "chimera.ccode")                 {       command = new ChimeraCcodeCommand(optionString);                        }
 460                 else if(commandName == "chimera.check")                 {       command = new ChimeraCheckCommand(optionString);                        }
 461                 else if(commandName == "chimera.slayer")                {       command = new ChimeraSlayerCommand(optionString);                       }
 462                 else if(commandName == "chimera.uchime")                {       command = new ChimeraUchimeCommand(optionString);                       }
 463                 else if(commandName == "chimera.pintail")               {       command = new ChimeraPintailCommand(optionString);                      }
 464                 else if(commandName == "chimera.bellerophon")   {       command = new ChimeraBellerophonCommand(optionString);          }
 465                 else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
 466                 else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                           }
 467                 else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                          }
 468                 else if(commandName == "pcoa")                                  {       command = new PCOACommand(optionString);                                        }
 469                 else if(commandName == "pca")                                   {       command = new PCACommand(optionString);                                         }
 470                 else if(commandName == "nmds")                                  {       command = new NMDSCommand(optionString);                                        }
 471                 else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
 472                 else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
 473                 else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
 474                 else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
 475                 else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
 476                 else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
 477                 else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
 478                 else if(commandName == "clearcut")                              {       command = new ClearcutCommand(optionString);                            }
 479                 else if(commandName == "catchall")                              {       command = new CatchAllCommand(optionString);                            }
 480                 else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
 481                 else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
 482                 else if(commandName == "classify.otu")                  {       command = new ClassifyOtuCommand(optionString);                         }
 483                 else if(commandName == "degap.seqs")                    {       command = new DegapSeqsCommand(optionString);                           }
 484                 else if(commandName == "get.relabund")                  {       command = new GetRelAbundCommand(optionString);                         }
 485                 else if(commandName == "sens.spec")                             {       command = new SensSpecCommand(optionString);                            }
 486                 else if(commandName == "seq.error")                             {       command = new SeqErrorCommand(optionString);                            }
 487                 else if(commandName == "sffinfo")                               {       command = new SffInfoCommand(optionString);                                     }
 488                 else if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
 489                 else if(commandName == "metastats")                             {       command = new MetaStatsCommand(optionString);                           }
 490                 else if(commandName == "split.groups")                  {       command = new SplitGroupCommand(optionString);                          }
 491                 else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
 492                 else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
 493                 else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
 494                 else if(commandName == "get.groups")                    {       command = new GetGroupsCommand(optionString);                           }
 495                 else if(commandName == "remove.groups")                 {       command = new RemoveGroupsCommand(optionString);                        }
 496                 else if(commandName == "get.otus")                              {       command = new GetOtusCommand(optionString);                                     }
 497                 else if(commandName == "remove.otus")                   {       command = new RemoveOtusCommand(optionString);                          }
 498                 else if(commandName == "fastq.info")                    {       command = new ParseFastaQCommand(optionString);                         }
 499                 else if(commandName == "pipeline.pds")                  {       command = new PipelineCommand(optionString);                            }
 500                 else if(commandName == "deunique.seqs")                 {       command = new DeUniqueSeqsCommand(optionString);                        }
 501                 else if(commandName == "pairwise.seqs")                 {       command = new PairwiseSeqsCommand(optionString);                        }
 502                 else if(commandName == "cluster.classic")               {       command = new ClusterDoturCommand(optionString);                        }
 503                 else if(commandName == "sub.sample")                    {       command = new SubSampleCommand(optionString);                           }
 504                 else if(commandName == "indicator")                             {       command = new IndicatorCommand(optionString);                           }
 505                 else if(commandName == "consensus.seqs")                {       command = new ConsensusSeqsCommand(optionString);                       }
 506                 else if(commandName == "corr.axes")                             {       command = new CorrAxesCommand(optionString);                            }
 507                 else if(commandName == "remove.rare")                   {       command = new RemoveRareCommand(optionString);                          }
 508                 else if(commandName == "merge.groups")                  {       command = new MergeGroupsCommand(optionString);                         }
 509                 else if(commandName == "amova")                                 {       command = new AmovaCommand(optionString);                                       }
 510                 else if(commandName == "homova")                                {       command = new HomovaCommand(optionString);                                      }
 511                 else if(commandName == "mantel")                                {       command = new MantelCommand(optionString);                                      }
 512                 else if(commandName == "make.fastq")                    {       command = new MakeFastQCommand(optionString);                           }
 513                 else if(commandName == "get.current")                   {       command = new GetCurrentCommand(optionString);                          }
 514                 else if(commandName == "set.current")                   {       command = new SetCurrentCommand(optionString);                          }
 515                 else if(commandName == "anosim")                                {       command = new AnosimCommand(optionString);                                      }
 516                 else if(commandName == "make.shared")                   {       command = new SharedCommand(optionString);                                      }
 517                 else if(commandName == "get.commandinfo")               {       command = new GetCommandInfoCommand(optionString);                      }
 518                 else if(commandName == "deunique.tree")                 {       command = new DeuniqueTreeCommand(optionString);                        }
 519                 else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       command = new CountSeqsCommand(optionString);                           }
 520                 else if(commandName == "count.groups")                  {       command = new CountGroupsCommand(optionString);                         }
 521                 else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
 522                 else if(commandName == "summary.tax")                   {       command = new SummaryTaxCommand(optionString);                          }
 523                 else if(commandName == "summary.qual")                  {       command = new SummaryQualCommand(optionString);                         }
 524                 else if(commandName == "chimera.perseus")               {       command = new ChimeraPerseusCommand(optionString);                      }
 525                 else if(commandName == "shhh.seqs")                             {       command = new ShhhSeqsCommand(optionString);                            }
 526                 else if(commandName == "otu.association")               {       command = new OTUAssociationCommand(optionString);                      }
 527         else if(commandName == "sort.seqs")             {       command = new SortSeqsCommand(optionString);                }
 528         else if(commandName == "classify.tree")         {       command = new ClassifyTreeCommand(optionString);            }
 529         else if(commandName == "cooccurrence")          {       command = new CooccurrenceCommand(optionString);            }
 530         else if(commandName == "pcr.seqs")              {       command = new PcrSeqsCommand(optionString);                 }
 531         else if(commandName == "create.database")       {       command = new CreateDatabaseCommand(optionString);          }
 532         else if(commandName == "make.biom")             {       command = new MakeBiomCommand(optionString);                }
 533         else if(commandName == "get.coremicrobiome")    {       command = new GetCoreMicroBiomeCommand(optionString);       }
 534         else if(commandName == "list.otulabels")        {       command = new ListOtuLabelsCommand(optionString);           }
 535         else if(commandName == "get.otulabels")         {       command = new GetOtuLabelsCommand(optionString);            }
 536         else if(commandName == "remove.otulabels")      {       command = new RemoveOtuLabelsCommand(optionString);         }
 537         else if(commandName == "make.contigs")          {       command = new MakeContigsCommand(optionString);             }
 538         else if(commandName == "load.logfile")          {       command = new LoadLogfileCommand(optionString);             }
 539         else if(commandName == "sff.multiple")          {       command = new SffMultipleCommand(optionString);             }
 540         else if(commandName == "classify.rf")           {       command = new ClassifyRFSharedCommand(optionString);        }
 541         else if(commandName == "filter.shared")         {       command = new FilterSharedCommand(optionString);            }
 542         else if(commandName == "primer.design")         {       command = new PrimerDesignCommand(optionString);            }
 543         else if(commandName == "get.dists")             {       command = new GetDistsCommand(optionString);                }
 544         else if(commandName == "remove.dists")          {       command = new RemoveDistsCommand(optionString);             }
 545         else if(commandName == "merge.taxsummary")      {       command = new MergeTaxSummaryCommand(optionString);         }
 546         else if(commandName == "get.communitytype")     {       command = new GetMetaCommunityCommand(optionString);        }
 547         else if(commandName == "sparcc")                {       command = new SparccCommand(optionString);                  }
 548         else if(commandName == "make.lookup")                   {       command = new MakeLookupCommand(optionString);                          }
 549         else if(commandName == "rename.seqs")                   {       command = new RenameSeqsCommand(optionString);                          }
 550         else if(commandName == "make.lefse")                    {       command = new MakeLefseCommand(optionString);                           }
 551         else if(commandName == "lefse")                 {       command = new LefseCommand(optionString);                   }
 552         else if(commandName == "kruskal.wallis")        {       command = new KruskalWallisCommand(optionString);           }
 553         else if(commandName == "sra")                   {       command = new SRACommand(optionString);                     }
 554         else if(commandName == "merge.sfffiles")        {       command = new MergeSfffilesCommand(optionString);           }
 555                 else                                                                                    {       command = new NoCommand(optionString);                                          }
 556
 557                 return command;
 558         }
 559         catch(exception& e) {
 560                 m->errorOut(e, "CommandFactory", "getCommand");
 561                 exit(1);
 562         }
 563 }
 564 /***********************************************************/
 565
 566 /***********************************************************/
 567 //This function calls the appropriate command fucntions based on user input.
 568 Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
 569         try {
 570                 delete pipecommand;   //delete the old command
 571
 572         checkForRedirects(optionString);
 573
 574                 //user has opted to redirect output from dir where input files are located to some other place
 575                 if (outputDir != "") {
 576                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 577                         else { optionString += "outputdir=" + outputDir; }
 578                 }
 579
 580                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 581                 if (inputDir != "") {
 582                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 583                         else { optionString += "inputdir=" + inputDir; }
 584                 }
 585
 586                 if(commandName == "cluster")                            {       pipecommand = new ClusterCommand(optionString);                                 }
 587                 else if(commandName == "unique.seqs")                   {       pipecommand = new DeconvoluteCommand(optionString);                             }
 588                 else if(commandName == "parsimony")                             {       pipecommand = new ParsimonyCommand(optionString);                               }
 589                 else if(commandName == "help")                                  {       pipecommand = new HelpCommand(optionString);                                    }
 590                 else if(commandName == "quit")                                  {       pipecommand = new QuitCommand(optionString);                                    }
 591                 else if(commandName == "collect.single")                {       pipecommand = new CollectCommand(optionString);                                 }
 592                 else if(commandName == "collect.shared")                {       pipecommand = new CollectSharedCommand(optionString);                   }
 593                 else if(commandName == "rarefaction.single")    {       pipecommand = new RareFactCommand(optionString);                                }
 594                 else if(commandName == "rarefaction.shared")    {       pipecommand = new RareFactSharedCommand(optionString);                  }
 595                 else if(commandName == "summary.single")                {       pipecommand = new SummaryCommand(optionString);                                 }
 596                 else if(commandName == "summary.shared")                {       pipecommand = new SummarySharedCommand(optionString);                   }
 597                 else if(commandName == "unifrac.weighted")              {       pipecommand = new UnifracWeightedCommand(optionString);                 }
 598                 else if(commandName == "unifrac.unweighted")    {       pipecommand = new UnifracUnweightedCommand(optionString);               }
 599                 else if(commandName == "get.group")             {   pipecommand = new GetgroupCommand(optionString);                            }
 600                 else if(commandName == "get.label")             {   pipecommand = new GetlabelCommand(optionString);                            }
 601                 else if(commandName == "get.sabund")            {   pipecommand = new GetSAbundCommand(optionString);                           }
 602                 else if(commandName == "get.rabund")            {   pipecommand = new GetRAbundCommand(optionString);                           }
 603                 else if(commandName == "libshuff")              {   pipecommand = new LibShuffCommand(optionString);                            }
 604                 else if(commandName == "heatmap.bin")                   {   pipecommand = new HeatMapCommand(optionString);                                     }
 605                 else if(commandName == "heatmap.sim")                   {   pipecommand = new HeatMapSimCommand(optionString);                          }
 606                 else if(commandName == "filter.seqs")                   {   pipecommand = new FilterSeqsCommand(optionString);                          }
 607                 else if(commandName == "venn")                                  {   pipecommand = new VennCommand(optionString);                                        }
 608                 else if(commandName == "bin.seqs")                              {   pipecommand = new BinSeqCommand(optionString);                                      }
 609                 else if(commandName == "get.oturep")                    {   pipecommand = new GetOTURepCommand(optionString);                           }
 610                 else if(commandName == "tree.shared")                   {   pipecommand = new TreeGroupCommand(optionString);                           }
 611                 else if(commandName == "dist.shared")                   {   pipecommand = new MatrixOutputCommand(optionString);                        }
 612                 else if(commandName == "dist.seqs")                             {   pipecommand = new DistanceCommand(optionString);                            }
 613                 else if(commandName == "align.seqs")                    {   pipecommand = new AlignCommand(optionString);                                       }
 614                 else if(commandName == "summary.seqs")                  {       pipecommand = new SeqSummaryCommand(optionString);                              }
 615                 else if(commandName == "screen.seqs")                   {       pipecommand = new ScreenSeqsCommand(optionString);                              }
 616                 else if(commandName == "reverse.seqs")                  {       pipecommand = new ReverseSeqsCommand(optionString);                             }
 617                 else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
 618                 else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
 619                 else if(commandName == "shhh.flows")                    {       pipecommand = new ShhherCommand(optionString);                                  }
 620                 else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
 621                 else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
 622                 else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
 623                 else if(commandName == "merge.files")                   {       pipecommand = new MergeFileCommand(optionString);                               }
 624                 else if(commandName == "system")                                {       pipecommand = new SystemCommand(optionString);                                  }
 625                 else if(commandName == "align.check")                   {       pipecommand = new AlignCheckCommand(optionString);                              }
 626                 else if(commandName == "get.sharedseqs")                {       pipecommand = new GetSharedOTUCommand(optionString);                    }
 627                 else if(commandName == "get.otulist")                   {       pipecommand = new GetListCountCommand(optionString);                    }
 628                 else if(commandName == "hcluster")                              {       pipecommand = new HClusterCommand(optionString);                                }
 629                 else if(commandName == "classify.seqs")                 {       pipecommand = new ClassifySeqsCommand(optionString);                    }
 630                 else if(commandName == "chimera.ccode")                 {       pipecommand = new ChimeraCcodeCommand(optionString);                    }
 631                 else if(commandName == "chimera.check")                 {       pipecommand = new ChimeraCheckCommand(optionString);                    }
 632                 else if(commandName == "chimera.uchime")                {       pipecommand = new ChimeraUchimeCommand(optionString);                   }
 633                 else if(commandName == "chimera.slayer")                {       pipecommand = new ChimeraSlayerCommand(optionString);                   }
 634                 else if(commandName == "chimera.pintail")               {       pipecommand = new ChimeraPintailCommand(optionString);                  }
 635                 else if(commandName == "chimera.bellerophon")   {       pipecommand = new ChimeraBellerophonCommand(optionString);              }
 636                 else if(commandName == "phylotype")                             {       pipecommand = new PhylotypeCommand(optionString);                               }
 637                 else if(commandName == "mgcluster")                             {       pipecommand = new MGClusterCommand(optionString);                               }
 638                 else if(commandName == "pre.cluster")                   {       pipecommand = new PreClusterCommand(optionString);                              }
 639                 else if(commandName == "pcoa")                                  {       pipecommand = new PCOACommand(optionString);                                    }
 640                 else if(commandName == "pca")                                   {       pipecommand = new PCACommand(optionString);                                             }
 641                 else if(commandName == "nmds")                                  {       pipecommand = new NMDSCommand(optionString);                                    }
 642                 else if(commandName == "otu.hierarchy")                 {       pipecommand = new OtuHierarchyCommand(optionString);                    }
 643                 else if(commandName == "set.dir")                               {       pipecommand = new SetDirectoryCommand(optionString);                    }
 644                 else if(commandName == "set.logfile")                   {       pipecommand = new SetLogFileCommand(optionString);                              }
 645                 else if(commandName == "parse.list")                    {       pipecommand = new ParseListCommand(optionString);                               }
 646                 else if(commandName == "phylo.diversity")               {       pipecommand = new PhyloDiversityCommand(optionString);                  }
 647                 else if(commandName == "make.group")                    {       pipecommand = new MakeGroupCommand(optionString);                               }
 648                 else if(commandName == "chop.seqs")                             {       pipecommand = new ChopSeqsCommand(optionString);                                }
 649                 else if(commandName == "clearcut")                              {       pipecommand = new ClearcutCommand(optionString);                                }
 650                 else if(commandName == "catchall")                              {       pipecommand = new CatchAllCommand(optionString);                                }
 651                 else if(commandName == "split.abund")                   {       pipecommand = new SplitAbundCommand(optionString);                              }
 652                 else if(commandName == "cluster.split")                 {       pipecommand = new ClusterSplitCommand(optionString);                    }
 653                 else if(commandName == "classify.otu")                  {       pipecommand = new ClassifyOtuCommand(optionString);                             }
 654                 else if(commandName == "degap.seqs")                    {       pipecommand = new DegapSeqsCommand(optionString);                               }
 655                 else if(commandName == "get.relabund")                  {       pipecommand = new GetRelAbundCommand(optionString);                             }
 656                 else if(commandName == "sens.spec")                             {       pipecommand = new SensSpecCommand(optionString);                                }
 657                 else if(commandName == "seq.error")                             {       pipecommand = new SeqErrorCommand(optionString);                                }
 658                 else if(commandName == "sffinfo")                               {       pipecommand = new SffInfoCommand(optionString);                                 }
 659                 else if(commandName == "normalize.shared")              {       pipecommand = new NormalizeSharedCommand(optionString);                 }
 660                 else if(commandName == "metastats")                             {       pipecommand = new MetaStatsCommand(optionString);                               }
 661                 else if(commandName == "split.groups")                  {       pipecommand = new SplitGroupCommand(optionString);                              }
 662                 else if(commandName == "cluster.fragments")             {       pipecommand = new ClusterFragmentsCommand(optionString);                }
 663                 else if(commandName == "get.lineage")                   {       pipecommand = new GetLineageCommand(optionString);                              }
 664                 else if(commandName == "get.groups")                    {       pipecommand = new GetGroupsCommand(optionString);                               }
 665                 else if(commandName == "remove.lineage")                {       pipecommand = new RemoveLineageCommand(optionString);                   }
 666                 else if(commandName == "remove.groups")                 {       pipecommand = new RemoveGroupsCommand(optionString);                    }
 667                 else if(commandName == "get.otus")                              {       pipecommand = new GetOtusCommand(optionString);                                 }
 668                 else if(commandName == "remove.otus")                   {       pipecommand = new RemoveOtusCommand(optionString);                              }
 669                 else if(commandName == "fastq.info")                    {       pipecommand = new ParseFastaQCommand(optionString);                             }
 670                 else if(commandName == "deunique.seqs")                 {       pipecommand = new DeUniqueSeqsCommand(optionString);                    }
 671                 else if(commandName == "pairwise.seqs")                 {       pipecommand = new PairwiseSeqsCommand(optionString);                    }
 672                 else if(commandName == "cluster.classic")               {       pipecommand = new ClusterDoturCommand(optionString);                    }
 673                 else if(commandName == "sub.sample")                    {       pipecommand = new SubSampleCommand(optionString);                               }
 674                 else if(commandName == "indicator")                             {       pipecommand = new IndicatorCommand(optionString);                               }
 675                 else if(commandName == "consensus.seqs")                {       pipecommand = new ConsensusSeqsCommand(optionString);                   }
 676                 else if(commandName == "corr.axes")                             {       pipecommand = new CorrAxesCommand(optionString);                                }
 677                 else if(commandName == "remove.rare")                   {       pipecommand = new RemoveRareCommand(optionString);                              }
 678                 else if(commandName == "merge.groups")                  {       pipecommand = new MergeGroupsCommand(optionString);                             }
 679                 else if(commandName == "amova")                                 {       pipecommand = new AmovaCommand(optionString);                                   }
 680                 else if(commandName == "homova")                                {       pipecommand = new HomovaCommand(optionString);                                  }
 681                 else if(commandName == "mantel")                                {       pipecommand = new MantelCommand(optionString);                                  }
 682                 else if(commandName == "anosim")                                {       pipecommand = new AnosimCommand(optionString);                                  }
 683                 else if(commandName == "make.fastq")                    {       pipecommand = new MakeFastQCommand(optionString);                               }
 684                 else if(commandName == "get.current")                   {       pipecommand = new GetCurrentCommand(optionString);                              }
 685                 else if(commandName == "set.current")                   {       pipecommand = new SetCurrentCommand(optionString);                              }
 686                 else if(commandName == "make.shared")                   {       pipecommand = new SharedCommand(optionString);                                  }
 687                 else if(commandName == "get.commandinfo")               {       pipecommand = new GetCommandInfoCommand(optionString);                  }
 688                 else if(commandName == "deunique.tree")                 {       pipecommand = new DeuniqueTreeCommand(optionString);                    }
 689                 else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       pipecommand = new CountSeqsCommand(optionString);                               }
 690                 else if(commandName == "count.groups")                  {       pipecommand = new CountGroupsCommand(optionString);                             }
 691                 else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
 692                 else if(commandName == "summary.tax")                   {       pipecommand = new SummaryTaxCommand(optionString);                              }
 693                 else if(commandName == "summary.qual")                  {       pipecommand = new SummaryQualCommand(optionString);                             }
 694                 else if(commandName == "chimera.perseus")               {       pipecommand = new ChimeraPerseusCommand(optionString);                  }
 695                 else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhhSeqsCommand(optionString);                                }
 696                 else if(commandName == "otu.association")               {       pipecommand = new OTUAssociationCommand(optionString);                  }
 697         else if(commandName == "sort.seqs")             {       pipecommand = new SortSeqsCommand(optionString);                }
 698         else if(commandName == "classify.tree")         {       pipecommand = new ClassifyTreeCommand(optionString);            }
 699         else if(commandName == "cooccurrence")          {       pipecommand = new CooccurrenceCommand(optionString);            }
 700         else if(commandName == "pcr.seqs")              {       pipecommand = new PcrSeqsCommand(optionString);                 }
 701         else if(commandName == "create.database")       {       pipecommand = new CreateDatabaseCommand(optionString);          }
 702         else if(commandName == "make.biom")             {       pipecommand = new MakeBiomCommand(optionString);                }
 703         else if(commandName == "get.coremicrobiome")    {       pipecommand = new GetCoreMicroBiomeCommand(optionString);       }
 704         else if(commandName == "list.otulabels")        {       pipecommand = new ListOtuLabelsCommand(optionString);           }
 705         else if(commandName == "get.otulabels")         {       pipecommand = new GetOtuLabelsCommand(optionString);            }
 706         else if(commandName == "remove.otulabels")      {       pipecommand = new RemoveOtuLabelsCommand(optionString);         }
 707         else if(commandName == "make.contigs")          {       pipecommand = new MakeContigsCommand(optionString);             }
 708         else if(commandName == "load.logfile")          {       pipecommand = new LoadLogfileCommand(optionString);             }
 709         else if(commandName == "sff.multiple")          {       pipecommand = new SffMultipleCommand(optionString);             }
 710         else if(commandName == "classify.rf")           {       pipecommand = new ClassifyRFSharedCommand(optionString);        }
 711         else if(commandName == "filter.shared")         {       pipecommand = new FilterSharedCommand(optionString);            }
 712         else if(commandName == "primer.design")         {       pipecommand = new PrimerDesignCommand(optionString);            }
 713         else if(commandName == "get.dists")             {       pipecommand = new GetDistsCommand(optionString);                }
 714         else if(commandName == "remove.dists")          {       pipecommand = new RemoveDistsCommand(optionString);             }
 715         else if(commandName == "merge.taxsummary")      {       pipecommand = new MergeTaxSummaryCommand(optionString);         }
 716         else if(commandName == "get.communitytype")     {       pipecommand = new GetMetaCommunityCommand(optionString);        }
 717         else if(commandName == "sparcc")                {       pipecommand = new SparccCommand(optionString);                  }
 718         else if(commandName == "make.lookup")                   {       pipecommand = new MakeLookupCommand(optionString);                              }
 719         else if(commandName == "rename.seqs")                   {       pipecommand = new RenameSeqsCommand(optionString);                              }
 720         else if(commandName == "make.lefse")                    {       pipecommand = new MakeLefseCommand(optionString);                               }
 721         else if(commandName == "lefse")                 {       pipecommand = new LefseCommand(optionString);                   }
 722         else if(commandName == "kruskal.wallis")        {       pipecommand = new KruskalWallisCommand(optionString);           }
 723         else if(commandName == "sra")                   {       pipecommand = new SRACommand(optionString);                     }
 724         else if(commandName == "merge.sfffiles")        {       pipecommand = new MergeSfffilesCommand(optionString);           }
 725                 else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 726
 727                 return pipecommand;
 728         }
 729         catch(exception& e) {
 730                 m->errorOut(e, "CommandFactory", "getCommand");
 731                 exit(1);
 732         }
 733 }
 734 /***********************************************************/
 735
 736 /***********************************************************/
 737 //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
 738 Command* CommandFactory::getCommand(string commandName){
 739         try {
 740                 delete shellcommand;   //delete the old command
 741
 742                 if(commandName == "cluster")                            {       shellcommand = new ClusterCommand();                            }
 743                 else if(commandName == "unique.seqs")                   {       shellcommand = new DeconvoluteCommand();                        }
 744                 else if(commandName == "parsimony")                             {       shellcommand = new ParsimonyCommand();                          }
 745                 else if(commandName == "help")                                  {       shellcommand = new HelpCommand();                                       }
 746                 else if(commandName == "quit")                                  {       shellcommand = new QuitCommand();                                       }
 747                 else if(commandName == "collect.single")                {       shellcommand = new CollectCommand();                            }
 748                 else if(commandName == "collect.shared")                {       shellcommand = new CollectSharedCommand();                      }
 749                 else if(commandName == "rarefaction.single")    {       shellcommand = new RareFactCommand();                           }
 750                 else if(commandName == "rarefaction.shared")    {       shellcommand = new RareFactSharedCommand();                     }
 751                 else if(commandName == "summary.single")                {       shellcommand = new SummaryCommand();                            }
 752                 else if(commandName == "summary.shared")                {       shellcommand = new SummarySharedCommand();                      }
 753                 else if(commandName == "unifrac.weighted")              {       shellcommand = new UnifracWeightedCommand();            }
 754                 else if(commandName == "unifrac.unweighted")    {       shellcommand = new UnifracUnweightedCommand();          }
 755                 else if(commandName == "get.group")             {   shellcommand = new GetgroupCommand();                               }
 756                 else if(commandName == "get.label")             {   shellcommand = new GetlabelCommand();                               }
 757                 else if(commandName == "get.sabund")            {   shellcommand = new GetSAbundCommand();                              }
 758                 else if(commandName == "get.rabund")            {   shellcommand = new GetRAbundCommand();                              }
 759                 else if(commandName == "libshuff")              {   shellcommand = new LibShuffCommand();                               }
 760                 else if(commandName == "heatmap.bin")                   {   shellcommand = new HeatMapCommand();                                }
 761                 else if(commandName == "heatmap.sim")                   {   shellcommand = new HeatMapSimCommand();                             }
 762                 else if(commandName == "filter.seqs")                   {   shellcommand = new FilterSeqsCommand();                             }
 763                 else if(commandName == "venn")                                  {   shellcommand = new VennCommand();                                   }
 764                 else if(commandName == "bin.seqs")                              {   shellcommand = new BinSeqCommand();                                 }
 765                 else if(commandName == "get.oturep")                    {   shellcommand = new GetOTURepCommand();                              }
 766                 else if(commandName == "tree.shared")                   {   shellcommand = new TreeGroupCommand();                              }
 767                 else if(commandName == "dist.shared")                   {   shellcommand = new MatrixOutputCommand();                   }
 768                 else if(commandName == "dist.seqs")                             {   shellcommand = new DistanceCommand();                               }
 769                 else if(commandName == "align.seqs")                    {   shellcommand = new AlignCommand();                                  }
 770                 else if(commandName == "summary.seqs")                  {       shellcommand = new SeqSummaryCommand();                         }
 771                 else if(commandName == "screen.seqs")                   {       shellcommand = new ScreenSeqsCommand();                         }
 772                 else if(commandName == "reverse.seqs")                  {       shellcommand = new ReverseSeqsCommand();                        }
 773                 else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
 774                 else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
 775                 else if(commandName == "shhh.flows")                    {       shellcommand = new ShhherCommand();                                     }
 776                 else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
 777                 else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
 778                 else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }
 779                 else if(commandName == "merge.files")                   {       shellcommand = new MergeFileCommand();                          }
 780                 else if(commandName == "system")                                {       shellcommand = new SystemCommand();                                     }
 781                 else if(commandName == "align.check")                   {       shellcommand = new AlignCheckCommand();                         }
 782                 else if(commandName == "get.sharedseqs")                {       shellcommand = new GetSharedOTUCommand();                       }
 783                 else if(commandName == "get.otulist")                   {       shellcommand = new GetListCountCommand();                       }
 784                 else if(commandName == "hcluster")                              {       shellcommand = new HClusterCommand();                           }
 785                 else if(commandName == "classify.seqs")                 {       shellcommand = new ClassifySeqsCommand();                       }
 786                 else if(commandName == "chimera.ccode")                 {       shellcommand = new ChimeraCcodeCommand();                       }
 787                 else if(commandName == "chimera.check")                 {       shellcommand = new ChimeraCheckCommand();                       }
 788                 else if(commandName == "chimera.slayer")                {       shellcommand = new ChimeraSlayerCommand();                      }
 789                 else if(commandName == "chimera.uchime")                {       shellcommand = new ChimeraUchimeCommand();                      }
 790                 else if(commandName == "chimera.pintail")               {       shellcommand = new ChimeraPintailCommand();                     }
 791                 else if(commandName == "chimera.bellerophon")   {       shellcommand = new ChimeraBellerophonCommand();         }
 792                 else if(commandName == "phylotype")                             {       shellcommand = new PhylotypeCommand();                          }
 793                 else if(commandName == "mgcluster")                             {       shellcommand = new MGClusterCommand();                          }
 794                 else if(commandName == "pre.cluster")                   {       shellcommand = new PreClusterCommand();                         }
 795                 else if(commandName == "pcoa")                                  {       shellcommand = new PCOACommand();                                       }
 796                 else if(commandName == "pca")                                   {       shellcommand = new PCACommand();                                        }
 797                 else if(commandName == "nmds")                                  {       shellcommand = new NMDSCommand();                                       }
 798                 else if(commandName == "otu.hierarchy")                 {       shellcommand = new OtuHierarchyCommand();                       }
 799                 else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
 800                 else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }
 801                 else if(commandName == "parse.list")                    {       shellcommand = new ParseListCommand();                          }
 802                 else if(commandName == "phylo.diversity")               {       shellcommand = new PhyloDiversityCommand();                     }
 803                 else if(commandName == "make.group")                    {       shellcommand = new MakeGroupCommand();                          }
 804                 else if(commandName == "chop.seqs")                             {       shellcommand = new ChopSeqsCommand();                           }
 805                 else if(commandName == "clearcut")                              {       shellcommand = new ClearcutCommand();                           }
 806                 else if(commandName == "catchall")                              {       shellcommand = new CatchAllCommand();                           }
 807                 else if(commandName == "split.abund")                   {       shellcommand = new SplitAbundCommand();                         }
 808                 else if(commandName == "cluster.split")                 {       shellcommand = new ClusterSplitCommand();                       }
 809                 else if(commandName == "classify.otu")                  {       shellcommand = new ClassifyOtuCommand();                        }
 810                 else if(commandName == "degap.seqs")                    {       shellcommand = new DegapSeqsCommand();                          }
 811                 else if(commandName == "get.relabund")                  {       shellcommand = new GetRelAbundCommand();                        }
 812                 else if(commandName == "sens.spec")                             {       shellcommand = new SensSpecCommand();                           }
 813                 else if(commandName == "seq.error")                             {       shellcommand = new SeqErrorCommand();                           }
 814                 else if(commandName == "sffinfo")                               {       shellcommand = new SffInfoCommand();                            }
 815                 else if(commandName == "normalize.shared")              {       shellcommand = new NormalizeSharedCommand();            }
 816                 else if(commandName == "metastats")                             {       shellcommand = new MetaStatsCommand();                          }
 817                 else if(commandName == "split.groups")                  {       shellcommand = new SplitGroupCommand();                         }
 818                 else if(commandName == "cluster.fragments")             {       shellcommand = new ClusterFragmentsCommand();           }
 819                 else if(commandName == "get.lineage")                   {       shellcommand = new GetLineageCommand();                         }
 820                 else if(commandName == "remove.lineage")                {       shellcommand = new RemoveLineageCommand();                      }
 821                 else if(commandName == "get.groups")                    {       shellcommand = new GetGroupsCommand();                          }
 822                 else if(commandName == "remove.groups")                 {       shellcommand = new RemoveGroupsCommand();                       }
 823                 else if(commandName == "get.otus")                              {       shellcommand = new GetOtusCommand();                            }
 824                 else if(commandName == "remove.otus")                   {       shellcommand = new RemoveOtusCommand();                         }
 825                 else if(commandName == "fastq.info")                    {       shellcommand = new ParseFastaQCommand();                        }
 826                 else if(commandName == "deunique.seqs")                 {       shellcommand = new DeUniqueSeqsCommand();                       }
 827                 else if(commandName == "pairwise.seqs")                 {       shellcommand = new PairwiseSeqsCommand();                       }
 828                 else if(commandName == "cluster.classic")               {       shellcommand = new ClusterDoturCommand();                       }
 829                 else if(commandName == "sub.sample")                    {       shellcommand = new SubSampleCommand();                          }
 830                 else if(commandName == "indicator")                             {       shellcommand = new IndicatorCommand();                          }
 831                 else if(commandName == "consensus.seqs")                {       shellcommand = new ConsensusSeqsCommand();                      }
 832                 else if(commandName == "corr.axes")                             {       shellcommand = new CorrAxesCommand();                           }
 833                 else if(commandName == "remove.rare")                   {       shellcommand = new RemoveRareCommand();                         }
 834                 else if(commandName == "merge.groups")                  {       shellcommand = new MergeGroupsCommand();                        }
 835                 else if(commandName == "amova")                                 {       shellcommand = new AmovaCommand();                                      }
 836                 else if(commandName == "homova")                                {       shellcommand = new HomovaCommand();                                     }
 837                 else if(commandName == "mantel")                                {       shellcommand = new MantelCommand();                                     }
 838                 else if(commandName == "anosim")                                {       shellcommand = new AnosimCommand();                                     }
 839                 else if(commandName == "make.fastq")                    {       shellcommand = new MakeFastQCommand();                          }
 840                 else if(commandName == "get.current")                   {       shellcommand = new GetCurrentCommand();                         }
 841                 else if(commandName == "set.current")                   {       shellcommand = new SetCurrentCommand();                         }
 842                 else if(commandName == "make.shared")                   {       shellcommand = new SharedCommand();                                     }
 843                 else if(commandName == "get.commandinfo")               {       shellcommand = new GetCommandInfoCommand();                     }
 844                 else if(commandName == "deunique.tree")                 {       shellcommand = new DeuniqueTreeCommand();                       }
 845                 else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       shellcommand = new CountSeqsCommand();                          }
 846                 else if(commandName == "count.groups")                  {       shellcommand = new CountGroupsCommand();                        }
 847                 else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
 848                 else if(commandName == "summary.tax")                   {       shellcommand = new SummaryTaxCommand();                         }
 849                 else if(commandName == "summary.qual")                  {       shellcommand = new SummaryQualCommand();                        }
 850                 else if(commandName == "chimera.perseus")               {       shellcommand = new ChimeraPerseusCommand();                     }
 851                 else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhhSeqsCommand();                           }
 852                 else if(commandName == "otu.association")               {       shellcommand = new OTUAssociationCommand();                     }
 853         else if(commandName == "sort.seqs")             {       shellcommand = new SortSeqsCommand();               }
 854         else if(commandName == "classify.tree")         {       shellcommand = new ClassifyTreeCommand();           }
 855         else if(commandName == "cooccurrence")          {       shellcommand = new CooccurrenceCommand();           }
 856         else if(commandName == "pcr.seqs")              {       shellcommand = new PcrSeqsCommand();                }
 857         else if(commandName == "create.database")       {       shellcommand = new CreateDatabaseCommand();         }
 858         else if(commandName == "make.biom")             {       shellcommand = new MakeBiomCommand();               }
 859         else if(commandName == "get.coremicrobiome")    {       shellcommand = new GetCoreMicroBiomeCommand();      }
 860         else if(commandName == "list.otulabels")        {       shellcommand = new ListOtuLabelsCommand();          }
 861         else if(commandName == "get.otulabels")         {       shellcommand = new GetOtuLabelsCommand();           }
 862         else if(commandName == "remove.otulabels")      {       shellcommand = new RemoveOtuLabelsCommand();        }
 863         else if(commandName == "make.contigs")          {       shellcommand = new MakeContigsCommand();            }
 864         else if(commandName == "load.logfile")          {       shellcommand = new LoadLogfileCommand();            }
 865         else if(commandName == "sff.multiple")          {       shellcommand = new SffMultipleCommand();            }
 866         else if(commandName == "classify.rf")           {       shellcommand = new ClassifyRFSharedCommand();       }
 867         else if(commandName == "filter.shared")         {       shellcommand = new FilterSharedCommand();           }
 868         else if(commandName == "primer.design")         {       shellcommand = new PrimerDesignCommand();           }
 869         else if(commandName == "get.dists")             {       shellcommand = new GetDistsCommand();               }
 870         else if(commandName == "remove.dists")          {       shellcommand = new RemoveDistsCommand();            }
 871         else if(commandName == "merge.taxsummary")      {       shellcommand = new MergeTaxSummaryCommand();        }
 872         else if(commandName == "get.communitytype")     {       shellcommand = new GetMetaCommunityCommand();       }
 873         else if(commandName == "sparcc")                {       shellcommand = new SparccCommand();                 }
 874         else if(commandName == "make.lookup")                   {       shellcommand = new MakeLookupCommand();                         }
 875         else if(commandName == "rename.seqs")                   {       shellcommand = new RenameSeqsCommand();                         }
 876         else if(commandName == "make.lefse")                    {       shellcommand = new MakeLefseCommand();                          }
 877         else if(commandName == "lefse")                 {       shellcommand = new LefseCommand();                  }
 878         else if(commandName == "kruskal.wallis")        {       shellcommand = new KruskalWallisCommand();          }
 879         else if(commandName == "sra")                   {       shellcommand = new SRACommand();                    }
 880         else if(commandName == "merge.sfffiles")        {       shellcommand = new MergeSfffilesCommand();          }
 881                 else                                                                                    {       shellcommand = new NoCommand();                                         }
 882
 883                 return shellcommand;
 884         }
 885         catch(exception& e) {
 886                 m->errorOut(e, "CommandFactory", "getCommand");
 887                 exit(1);
 888         }
 889 }
 890 /***********************************************************
 891 //This function is used to interrupt a command
 892 Command* CommandFactory::getCommand(){
 893         try {
 894                 delete command;   //delete the old command
 895
 896                 string s = "";
 897             command = new NoCommand(s);
 898
 899                 return command;
 900         }
 901         catch(exception& e) {
 902                 m->errorOut(e, "CommandFactory", "getCommand");
 903                 exit(1);
 904         }
 905 }
 906 ***********************************************************************/
 907 bool CommandFactory::isValidCommand(string command) {
 908         try {
 909
 910                 //is the command in the map
 911                 if ((commands.find(command)) != (commands.end())) {
 912                         return true;
 913                 }else{
 914                         m->mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
 915                         for (it = commands.begin(); it != commands.end(); it++) {
 916                                 m->mothurOut(it->first + ", ");
 917                         }
 918                         m->mothurOutEndLine();
 919                         return false;
 920                 }
 921
 922         }
 923         catch(exception& e) {
 924                 m->errorOut(e, "CommandFactory", "isValidCommand");
 925                 exit(1);
 926         }
 927 }
 928 /***********************************************************************/
 929 bool CommandFactory::isValidCommand(string command, string noError) {
 930         try {
 931
 932                 //is the command in the map
 933                 if ((commands.find(command)) != (commands.end())) {
 934                         return true;
 935                 }else{
 936                         return false;
 937                 }
 938
 939         }
 940         catch(exception& e) {
 941                 m->errorOut(e, "CommandFactory", "isValidCommand");
 942                 exit(1);
 943         }
 944 }
 945 /***********************************************************************/
 946 void CommandFactory::printCommands(ostream& out) {
 947         try {
 948                 out << "Valid commands are: ";
 949                 for (it = commands.begin(); it != commands.end(); it++) {
 950                         out << it->first << ",";
 951                 }
 952                 out << endl;
 953         }
 954         catch(exception& e) {
 955                 m->errorOut(e, "CommandFactory", "printCommands");
 956                 exit(1);
 957         }
 958 }
 959 /***********************************************************************/
 960 void CommandFactory::printCommandsCategories(ostream& out) {
 961     try {
 962         map<string, string> commands = getListCommands();
 963         map<string, string>::iterator it;
 964
 965         map<string, string> categories;
 966         map<string, string>::iterator itCat;
 967         //loop through each command outputting info
 968         for (it = commands.begin(); it != commands.end(); it++) {
 969
 970             Command* thisCommand = getCommand(it->first);
 971
 972             //don't add hidden commands
 973             if (thisCommand->getCommandCategory() != "Hidden") {
 974                 itCat = categories.find(thisCommand->getCommandCategory());
 975                 if (itCat == categories.end()) {
 976                     categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
 977                 }else {
 978                     categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
 979                 }
 980             }
 981         }
 982
 983         for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
 984             out << itCat->first << " commmands include: " << itCat->second << endl;
 985         }
 986
 987     }
 988         catch(exception& e) {
 989                 m->errorOut(e, "CommandFactory", "printCommandsCategories");
 990                 exit(1);
 991         }
 992 }
 993
 994 /***********************************************************************/
 995
 996
 997
 998