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 "classifysharedcommand.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
 149 /*******************************************************/
 150
 151 /******************************************************/
 152 CommandFactory* CommandFactory::getInstance() {
 153         if( _uniqueInstance == 0) {
 154                 _uniqueInstance = new CommandFactory();
 155         }
 156         return _uniqueInstance;
 157 }
 158 /***********************************************************/
 159
 160 /***********************************************************/
 161 //note: This class is resposible for knowing which commands are mpiEnabled,
 162 //If a command is not enabled only process 0 will execute the command.
 163 //This avoids redundant outputs on pieces of code we have not paralellized.
 164 //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.
 165 //example:  commands["dist.seqs"] = "MPIEnabled";
 166
 167 CommandFactory::CommandFactory(){
 168         string s = "";
 169         m = MothurOut::getInstance();
 170
 171         command = new NoCommand(s);
 172         shellcommand = new NoCommand(s);
 173         pipecommand = new NoCommand(s);
 174
 175         outputDir = ""; inputDir = "";
 176         logFileName = "";
 177         append = false;
 178
 179         //initialize list of valid commands
 180         commands["make.shared"]                 = "make.shared";
 181         commands["bin.seqs"]                    = "bin.seqs";
 182         commands["get.oturep"]                  = "get.oturep";
 183         commands["cluster"]                             = "cluster";
 184         commands["unique.seqs"]                 = "unique.seqs";
 185         commands["dist.shared"]                 = "dist.shared";
 186         commands["collect.single"]              = "collect.single";
 187         commands["collect.shared"]              = "collect.shared";
 188         commands["rarefaction.single"]  = "rarefaction.single";
 189         commands["rarefaction.shared"]  = "rarefaction.shared";
 190         commands["summary.single"]              = "summary.single";
 191         commands["summary.shared"]              = "summary.shared";
 192         commands["parsimony"]                   = "parsimony";
 193         commands["unifrac.weighted"]    = "unifrac.weighted";
 194         commands["unifrac.unweighted"]  = "unifrac.unweighted";
 195         commands["libshuff"]                    = "libshuff";
 196         commands["tree.shared"]                 = "tree.shared";
 197         commands["heatmap.bin"]                 = "heatmap.bin";
 198         commands["heatmap.sim"]                 = "heatmap.sim";
 199         commands["venn"]                                = "venn";
 200         commands["get.group"]           = "get.group";
 201         commands["get.label"]           = "get.label";
 202         commands["get.sabund"]          = "get.sabund";
 203         commands["get.rabund"]          = "get.rabund";
 204         commands["help"]                                = "help";
 205         commands["reverse.seqs"]                = "reverse.seqs";
 206         commands["trim.seqs"]                   = "trim.seqs";
 207         commands["trim.flows"]                  = "trim.flows";
 208         commands["list.seqs"]                   = "list.seqs";
 209         commands["get.seqs"]                    = "get.seqs";
 210         commands["remove.seqs"]                 = "remove.seqs";
 211         commands["system"]                              = "system";
 212         commands["align.check"]                 = "align.check";
 213         commands["get.sharedseqs"]              = "get.sharedseqs";
 214         commands["get.otulist"]                 = "get.otulist";
 215         commands["hcluster"]                    = "hcluster";
 216         commands["phylotype"]                   = "phylotype";
 217         commands["mgcluster"]                   = "mgcluster";
 218         commands["pre.cluster"]                 = "pre.cluster";
 219         commands["pcoa"]                                = "pcoa";
 220         commands["otu.hierarchy"]               = "otu.hierarchy";
 221         commands["set.dir"]                             = "MPIEnabled";
 222         commands["merge.files"]                 = "merge.files";
 223         commands["parse.list"]                  = "parse.list";
 224         commands["set.logfile"]                 = "set.logfile";
 225         commands["phylo.diversity"]             = "phylo.diversity";
 226         commands["make.group"]                  = "make.group";
 227         commands["chop.seqs"]                   = "chop.seqs";
 228         commands["clearcut"]                    = "clearcut";
 229         commands["catchall"]                    = "catchall";
 230         commands["split.abund"]                 = "split.abund";
 231         commands["classify.otu"]                = "classify.otu";
 232         commands["degap.seqs"]                  = "degap.seqs";
 233         commands["get.relabund"]                = "get.relabund";
 234         commands["sffinfo"]                             = "sffinfo";
 235         commands["normalize.shared"]    = "normalize.shared";
 236         commands["metastats"]                   = "metastats";
 237         commands["split.groups"]                = "split.groups";
 238         commands["cluster.fragments"]   = "cluster.fragments";
 239         commands["get.lineage"]                 = "get.lineage";
 240         commands["remove.lineage"]              = "remove.lineage";
 241         commands["fastq.info"]                  = "fastq.info";
 242         commands["deunique.seqs"]               = "deunique.seqs";
 243         commands["cluster.classic"]             = "cluster.classic";
 244         commands["sub.sample"]                  = "sub.sample";
 245         commands["remove.groups"]               = "remove.groups";
 246         commands["get.groups"]                  = "get.groups";
 247         commands["get.otus"]                    = "get.otus";
 248         commands["remove.otus"]                 = "remove.otus";
 249         commands["indicator"]                   = "indicator";
 250         commands["consensus.seqs"]              = "consensus.seqs";
 251         commands["corr.axes"]                   = "corr.axes";
 252         commands["pca"]                                 = "pca";
 253         commands["nmds"]                                = "nmds";
 254         commands["remove.rare"]                 = "remove.rare";
 255         commands["amova"]                               = "amova";
 256         commands["homova"]                              = "homova";
 257         commands["mantel"]                              = "mantel";
 258         commands["anosim"]                              = "anosim";
 259         commands["make.fastq"]                  = "make.fastq";
 260         commands["merge.groups"]                = "merge.groups";
 261         commands["get.current"]                 = "MPIEnabled";
 262         commands["set.current"]                 = "MPIEnabled";
 263         commands["get.commandinfo"]             = "get.commandinfo";
 264         commands["deunique.tree"]               = "deunique.tree";
 265         commands["count.seqs"]                  = "count.seqs";
 266         commands["count.groups"]                = "count.groups";
 267         commands["clear.memory"]                = "clear.memory";
 268         commands["pairwise.seqs"]               = "MPIEnabled";
 269         commands["pipeline.pds"]                = "MPIEnabled";
 270         commands["classify.seqs"]               = "MPIEnabled";
 271         commands["dist.seqs"]                   = "MPIEnabled";
 272         commands["filter.seqs"]                 = "MPIEnabled";
 273         commands["align.seqs"]                  = "MPIEnabled";
 274         commands["chimera.ccode"]               = "MPIEnabled";
 275         commands["chimera.check"]               = "MPIEnabled";
 276         commands["chimera.slayer"]              = "MPIEnabled";
 277         commands["chimera.uchime"]              = "chimera.uchime";
 278         commands["chimera.perseus"]             = "chimera.perseus";
 279         commands["chimera.pintail"]             = "MPIEnabled";
 280         commands["chimera.bellerophon"] = "MPIEnabled";
 281         commands["screen.seqs"]                 = "MPIEnabled";
 282         commands["summary.seqs"]                = "MPIEnabled";
 283         commands["cluster.split"]               = "MPIEnabled";
 284         commands["shhh.flows"]                  = "MPIEnabled";
 285         commands["sens.spec"]                   = "sens.spec";
 286         commands["seq.error"]                   = "seq.error";
 287         commands["summary.tax"]                 = "summary.tax";
 288         commands["summary.qual"]                = "summary.qual";
 289         commands["shhh.seqs"]                   = "shhh.seqs";
 290         commands["otu.association"]             = "otu.association";
 291     commands["sort.seqs"]           = "sort.seqs";
 292     commands["classify.tree"]       = "classify.tree";
 293     commands["cooccurrence"]        = "cooccurrence";
 294     commands["pcr.seqs"]            = "pcr.seqs";
 295     commands["create.database"]     = "create.database";
 296     commands["make.biom"]           = "make.biom";
 297     commands["get.coremicrobiome"]  = "get.coremicrobiome";
 298     commands["list.otulabels"]      = "list.otulabels";
 299     commands["get.otulabels"]       = "get.otulabels";
 300     commands["remove.otulabels"]    = "remove.otulabels";
 301     commands["make.contigs"]        = "make.contigs";
 302     commands["load.logfile"]        = "load.logfile";
 303     commands["make.table"]          = "make.table";
 304     commands["sff.multiple"]        = "sff.multiple";
 305         commands["quit"]                                = "MPIEnabled";
 306     commands["classify.shared"]         = "classify.shared";
 307     commands["filter.shared"]           = "filter.shared";
 308     commands["primer.design"]           = "primer.design";
 309     commands["get.dists"]           = "get.dists";
 310     commands["remove.dists"]        = "remove.dists";
 311     commands["merge.taxsummary"]    = "merge.taxsummary";
 312     commands["get.metacommunity"]   = "get.metacommunity";
 313     commands["sparcc"]              = "sparcc";
 314     commands["make.lookup"]         = "make.lookup";
 315     commands["rename.seqs"]         = "rename.seqs";
 316
 317
 318 }
 319 /***********************************************************/
 320
 321 /***********************************************************/
 322 bool CommandFactory::MPIEnabled(string commandName) {
 323         bool mpi = false;
 324         it = commands.find(commandName);
 325         if (it != commands.end()) {
 326                 if (it->second == "MPIEnabled") { return true; }
 327         }
 328         return mpi;
 329 }
 330 /***********************************************************/
 331
 332 /***********************************************************/
 333 CommandFactory::~CommandFactory(){
 334         _uniqueInstance = 0;
 335         delete command;
 336         delete shellcommand;
 337         delete pipecommand;
 338 }
 339 /***********************************************************/
 340
 341 /***********************************************************/
 342 int CommandFactory::checkForRedirects(string optionString) {
 343     try {
 344
 345         int pos = optionString.find("outputdir");
 346         if (pos != string::npos) { //user has set outputdir in command option string
 347             string outputOption = "";
 348             bool foundEquals = false;
 349             for(int i=pos;i<optionString.length();i++){
 350                 if(optionString[i] == ',')       { break;               }
 351                 else if(optionString[i] == '=')  { foundEquals = true;  }
 352                 if (foundEquals)       {   outputOption += optionString[i]; }
 353             }
 354             if(m->dirCheck(outputOption)){
 355                 setOutputDirectory(outputOption);
 356                 m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
 357             }
 358         }
 359
 360         pos = optionString.find("inputdir");
 361         if (pos != string::npos) { //user has set inputdir in command option string
 362             string intputOption = "";
 363             bool foundEquals = false;
 364             for(int i=pos;i<optionString.length();i++){
 365                 if(optionString[i] == ',')       { break;               }
 366                 else if(optionString[i] == '=')  { foundEquals = true;  }
 367                 if (foundEquals)       {   intputOption += optionString[i]; }
 368             }
 369             if(m->dirCheck(intputOption)){
 370                 setInputDirectory(intputOption);
 371                 m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
 372             }
 373         }
 374
 375         return 0;
 376         }
 377         catch(exception& e) {
 378                 m->errorOut(e, "CommandFactory", "getCommand");
 379                 exit(1);
 380         }
 381 }
 382 /***********************************************************/
 383
 384 /***********************************************************/
 385 //This function calls the appropriate command fucntions based on user input.
 386 Command* CommandFactory::getCommand(string commandName, string optionString){
 387         try {
 388
 389                 delete command;   //delete the old command
 390
 391         checkForRedirects(optionString);
 392
 393                 //user has opted to redirect output from dir where input files are located to some other place
 394                 if (outputDir != "") {
 395                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 396                         else { optionString += "outputdir=" + outputDir; }
 397                 }
 398
 399                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 400                 if (inputDir != "") {
 401                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 402                         else { optionString += "inputdir=" + inputDir; }
 403                 }
 404
 405                 if(commandName == "cluster")                            {       command = new ClusterCommand(optionString);                                     }
 406                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand(optionString);                         }
 407                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand(optionString);                           }
 408                 else if(commandName == "help")                                  {       command = new HelpCommand(optionString);                                        }
 409                 else if(commandName == "quit")                                  {       command = new QuitCommand(optionString);                                        }
 410                 else if(commandName == "collect.single")                {       command = new CollectCommand(optionString);                                     }
 411                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand(optionString);                       }
 412                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand(optionString);                            }
 413                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand(optionString);                      }
 414                 else if(commandName == "summary.single")                {       command = new SummaryCommand(optionString);                                     }
 415                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand(optionString);                       }
 416                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand(optionString);                     }
 417                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);           }
 418                 else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                                }
 419                 else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                                }
 420                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                               }
 421                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                               }
 422                 else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                                }
 423                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand(optionString);                                 }
 424                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand(optionString);                              }
 425                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand(optionString);                              }
 426                 else if(commandName == "venn")                                  {   command = new VennCommand(optionString);                                    }
 427                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand(optionString);                                  }
 428                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                               }
 429                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                               }
 430                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);                    }
 431                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                                }
 432                 else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                                   }
 433                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                          }
 434                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                          }
 435                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
 436                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
 437                 else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
 438                 else if(commandName == "shhh.flows")                    {       command = new ShhherCommand(optionString);                                      }
 439                 else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
 440                 else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
 441                 else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
 442                 else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                           }
 443                 else if(commandName == "system")                                {       command = new SystemCommand(optionString);                                      }
 444                 else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                          }
 445                 else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                        }
 446                 else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                        }
 447                 else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                            }
 448                 else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                        }
 449                 else if(commandName == "chimera.ccode")                 {       command = new ChimeraCcodeCommand(optionString);                        }
 450                 else if(commandName == "chimera.check")                 {       command = new ChimeraCheckCommand(optionString);                        }
 451                 else if(commandName == "chimera.slayer")                {       command = new ChimeraSlayerCommand(optionString);                       }
 452                 else if(commandName == "chimera.uchime")                {       command = new ChimeraUchimeCommand(optionString);                       }
 453                 else if(commandName == "chimera.pintail")               {       command = new ChimeraPintailCommand(optionString);                      }
 454                 else if(commandName == "chimera.bellerophon")   {       command = new ChimeraBellerophonCommand(optionString);          }
 455                 else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
 456                 else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                           }
 457                 else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                          }
 458                 else if(commandName == "pcoa")                                  {       command = new PCOACommand(optionString);                                        }
 459                 else if(commandName == "pca")                                   {       command = new PCACommand(optionString);                                         }
 460                 else if(commandName == "nmds")                                  {       command = new NMDSCommand(optionString);                                        }
 461                 else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
 462                 else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
 463                 else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
 464                 else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
 465                 else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
 466                 else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
 467                 else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
 468                 else if(commandName == "clearcut")                              {       command = new ClearcutCommand(optionString);                            }
 469                 else if(commandName == "catchall")                              {       command = new CatchAllCommand(optionString);                            }
 470                 else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
 471                 else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
 472                 else if(commandName == "classify.otu")                  {       command = new ClassifyOtuCommand(optionString);                         }
 473                 else if(commandName == "degap.seqs")                    {       command = new DegapSeqsCommand(optionString);                           }
 474                 else if(commandName == "get.relabund")                  {       command = new GetRelAbundCommand(optionString);                         }
 475                 else if(commandName == "sens.spec")                             {       command = new SensSpecCommand(optionString);                            }
 476                 else if(commandName == "seq.error")                             {       command = new SeqErrorCommand(optionString);                            }
 477                 else if(commandName == "sffinfo")                               {       command = new SffInfoCommand(optionString);                                     }
 478                 else if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
 479                 else if(commandName == "metastats")                             {       command = new MetaStatsCommand(optionString);                           }
 480                 else if(commandName == "split.groups")                  {       command = new SplitGroupCommand(optionString);                          }
 481                 else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
 482                 else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
 483                 else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
 484                 else if(commandName == "get.groups")                    {       command = new GetGroupsCommand(optionString);                           }
 485                 else if(commandName == "remove.groups")                 {       command = new RemoveGroupsCommand(optionString);                        }
 486                 else if(commandName == "get.otus")                              {       command = new GetOtusCommand(optionString);                                     }
 487                 else if(commandName == "remove.otus")                   {       command = new RemoveOtusCommand(optionString);                          }
 488                 else if(commandName == "fastq.info")                    {       command = new ParseFastaQCommand(optionString);                         }
 489                 else if(commandName == "pipeline.pds")                  {       command = new PipelineCommand(optionString);                            }
 490                 else if(commandName == "deunique.seqs")                 {       command = new DeUniqueSeqsCommand(optionString);                        }
 491                 else if(commandName == "pairwise.seqs")                 {       command = new PairwiseSeqsCommand(optionString);                        }
 492                 else if(commandName == "cluster.classic")               {       command = new ClusterDoturCommand(optionString);                        }
 493                 else if(commandName == "sub.sample")                    {       command = new SubSampleCommand(optionString);                           }
 494                 else if(commandName == "indicator")                             {       command = new IndicatorCommand(optionString);                           }
 495                 else if(commandName == "consensus.seqs")                {       command = new ConsensusSeqsCommand(optionString);                       }
 496                 else if(commandName == "corr.axes")                             {       command = new CorrAxesCommand(optionString);                            }
 497                 else if(commandName == "remove.rare")                   {       command = new RemoveRareCommand(optionString);                          }
 498                 else if(commandName == "merge.groups")                  {       command = new MergeGroupsCommand(optionString);                         }
 499                 else if(commandName == "amova")                                 {       command = new AmovaCommand(optionString);                                       }
 500                 else if(commandName == "homova")                                {       command = new HomovaCommand(optionString);                                      }
 501                 else if(commandName == "mantel")                                {       command = new MantelCommand(optionString);                                      }
 502                 else if(commandName == "make.fastq")                    {       command = new MakeFastQCommand(optionString);                           }
 503                 else if(commandName == "get.current")                   {       command = new GetCurrentCommand(optionString);                          }
 504                 else if(commandName == "set.current")                   {       command = new SetCurrentCommand(optionString);                          }
 505                 else if(commandName == "anosim")                                {       command = new AnosimCommand(optionString);                                      }
 506                 else if(commandName == "make.shared")                   {       command = new SharedCommand(optionString);                                      }
 507                 else if(commandName == "get.commandinfo")               {       command = new GetCommandInfoCommand(optionString);                      }
 508                 else if(commandName == "deunique.tree")                 {       command = new DeuniqueTreeCommand(optionString);                        }
 509                 else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       command = new CountSeqsCommand(optionString);                           }
 510                 else if(commandName == "count.groups")                  {       command = new CountGroupsCommand(optionString);                         }
 511                 else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
 512                 else if(commandName == "summary.tax")                   {       command = new SummaryTaxCommand(optionString);                          }
 513                 else if(commandName == "summary.qual")                  {       command = new SummaryQualCommand(optionString);                         }
 514                 else if(commandName == "chimera.perseus")               {       command = new ChimeraPerseusCommand(optionString);                      }
 515                 else if(commandName == "shhh.seqs")                             {       command = new ShhhSeqsCommand(optionString);                            }
 516                 else if(commandName == "otu.association")               {       command = new OTUAssociationCommand(optionString);                      }
 517         else if(commandName == "sort.seqs")             {       command = new SortSeqsCommand(optionString);                }
 518         else if(commandName == "classify.tree")         {       command = new ClassifyTreeCommand(optionString);            }
 519         else if(commandName == "cooccurrence")          {       command = new CooccurrenceCommand(optionString);            }
 520         else if(commandName == "pcr.seqs")              {       command = new PcrSeqsCommand(optionString);                 }
 521         else if(commandName == "create.database")       {       command = new CreateDatabaseCommand(optionString);          }
 522         else if(commandName == "make.biom")             {       command = new MakeBiomCommand(optionString);                }
 523         else if(commandName == "get.coremicrobiome")    {       command = new GetCoreMicroBiomeCommand(optionString);       }
 524         else if(commandName == "list.otulabels")        {       command = new ListOtuLabelsCommand(optionString);           }
 525         else if(commandName == "get.otulabels")         {       command = new GetOtuLabelsCommand(optionString);            }
 526         else if(commandName == "remove.otulabels")      {       command = new RemoveOtuLabelsCommand(optionString);         }
 527         else if(commandName == "make.contigs")          {       command = new MakeContigsCommand(optionString);             }
 528         else if(commandName == "load.logfile")          {       command = new LoadLogfileCommand(optionString);             }
 529         else if(commandName == "sff.multiple")          {       command = new SffMultipleCommand(optionString);             }
 530         else if(commandName == "classify.shared")       {       command = new ClassifySharedCommand(optionString);          }
 531         else if(commandName == "filter.shared")         {       command = new FilterSharedCommand(optionString);            }
 532         else if(commandName == "primer.design")         {       command = new PrimerDesignCommand(optionString);            }
 533         else if(commandName == "get.dists")             {       command = new GetDistsCommand(optionString);                }
 534         else if(commandName == "remove.dists")          {       command = new RemoveDistsCommand(optionString);             }
 535         else if(commandName == "merge.taxsummary")      {       command = new MergeTaxSummaryCommand(optionString);         }
 536         else if(commandName == "get.metacommunity")     {       command = new GetMetaCommunityCommand(optionString);        }
 537         else if(commandName == "sparcc")                {       command = new SparccCommand(optionString);                  }
 538         else if(commandName == "make.lookup")                   {       command = new MakeLookupCommand(optionString);                          }
 539         else if(commandName == "rename.seqs")                   {       command = new RenameSeqsCommand(optionString);                          }
 540                 else                                                                                    {       command = new NoCommand(optionString);                                          }
 541
 542                 return command;
 543         }
 544         catch(exception& e) {
 545                 m->errorOut(e, "CommandFactory", "getCommand");
 546                 exit(1);
 547         }
 548 }
 549 /***********************************************************/
 550
 551 /***********************************************************/
 552 //This function calls the appropriate command fucntions based on user input.
 553 Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
 554         try {
 555                 delete pipecommand;   //delete the old command
 556
 557         checkForRedirects(optionString);
 558
 559                 //user has opted to redirect output from dir where input files are located to some other place
 560                 if (outputDir != "") {
 561                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 562                         else { optionString += "outputdir=" + outputDir; }
 563                 }
 564
 565                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 566                 if (inputDir != "") {
 567                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 568                         else { optionString += "inputdir=" + inputDir; }
 569                 }
 570
 571                 if(commandName == "cluster")                            {       pipecommand = new ClusterCommand(optionString);                                 }
 572                 else if(commandName == "unique.seqs")                   {       pipecommand = new DeconvoluteCommand(optionString);                             }
 573                 else if(commandName == "parsimony")                             {       pipecommand = new ParsimonyCommand(optionString);                               }
 574                 else if(commandName == "help")                                  {       pipecommand = new HelpCommand(optionString);                                    }
 575                 else if(commandName == "quit")                                  {       pipecommand = new QuitCommand(optionString);                                    }
 576                 else if(commandName == "collect.single")                {       pipecommand = new CollectCommand(optionString);                                 }
 577                 else if(commandName == "collect.shared")                {       pipecommand = new CollectSharedCommand(optionString);                   }
 578                 else if(commandName == "rarefaction.single")    {       pipecommand = new RareFactCommand(optionString);                                }
 579                 else if(commandName == "rarefaction.shared")    {       pipecommand = new RareFactSharedCommand(optionString);                  }
 580                 else if(commandName == "summary.single")                {       pipecommand = new SummaryCommand(optionString);                                 }
 581                 else if(commandName == "summary.shared")                {       pipecommand = new SummarySharedCommand(optionString);                   }
 582                 else if(commandName == "unifrac.weighted")              {       pipecommand = new UnifracWeightedCommand(optionString);                 }
 583                 else if(commandName == "unifrac.unweighted")    {       pipecommand = new UnifracUnweightedCommand(optionString);               }
 584                 else if(commandName == "get.group")             {   pipecommand = new GetgroupCommand(optionString);                            }
 585                 else if(commandName == "get.label")             {   pipecommand = new GetlabelCommand(optionString);                            }
 586                 else if(commandName == "get.sabund")            {   pipecommand = new GetSAbundCommand(optionString);                           }
 587                 else if(commandName == "get.rabund")            {   pipecommand = new GetRAbundCommand(optionString);                           }
 588                 else if(commandName == "libshuff")              {   pipecommand = new LibShuffCommand(optionString);                            }
 589                 else if(commandName == "heatmap.bin")                   {   pipecommand = new HeatMapCommand(optionString);                                     }
 590                 else if(commandName == "heatmap.sim")                   {   pipecommand = new HeatMapSimCommand(optionString);                          }
 591                 else if(commandName == "filter.seqs")                   {   pipecommand = new FilterSeqsCommand(optionString);                          }
 592                 else if(commandName == "venn")                                  {   pipecommand = new VennCommand(optionString);                                        }
 593                 else if(commandName == "bin.seqs")                              {   pipecommand = new BinSeqCommand(optionString);                                      }
 594                 else if(commandName == "get.oturep")                    {   pipecommand = new GetOTURepCommand(optionString);                           }
 595                 else if(commandName == "tree.shared")                   {   pipecommand = new TreeGroupCommand(optionString);                           }
 596                 else if(commandName == "dist.shared")                   {   pipecommand = new MatrixOutputCommand(optionString);                        }
 597                 else if(commandName == "dist.seqs")                             {   pipecommand = new DistanceCommand(optionString);                            }
 598                 else if(commandName == "align.seqs")                    {   pipecommand = new AlignCommand(optionString);                                       }
 599                 else if(commandName == "summary.seqs")                  {       pipecommand = new SeqSummaryCommand(optionString);                              }
 600                 else if(commandName == "screen.seqs")                   {       pipecommand = new ScreenSeqsCommand(optionString);                              }
 601                 else if(commandName == "reverse.seqs")                  {       pipecommand = new ReverseSeqsCommand(optionString);                             }
 602                 else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
 603                 else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
 604                 else if(commandName == "shhh.flows")                    {       pipecommand = new ShhherCommand(optionString);                                  }
 605                 else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
 606                 else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
 607                 else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
 608                 else if(commandName == "merge.files")                   {       pipecommand = new MergeFileCommand(optionString);                               }
 609                 else if(commandName == "system")                                {       pipecommand = new SystemCommand(optionString);                                  }
 610                 else if(commandName == "align.check")                   {       pipecommand = new AlignCheckCommand(optionString);                              }
 611                 else if(commandName == "get.sharedseqs")                {       pipecommand = new GetSharedOTUCommand(optionString);                    }
 612                 else if(commandName == "get.otulist")                   {       pipecommand = new GetListCountCommand(optionString);                    }
 613                 else if(commandName == "hcluster")                              {       pipecommand = new HClusterCommand(optionString);                                }
 614                 else if(commandName == "classify.seqs")                 {       pipecommand = new ClassifySeqsCommand(optionString);                    }
 615                 else if(commandName == "chimera.ccode")                 {       pipecommand = new ChimeraCcodeCommand(optionString);                    }
 616                 else if(commandName == "chimera.check")                 {       pipecommand = new ChimeraCheckCommand(optionString);                    }
 617                 else if(commandName == "chimera.uchime")                {       pipecommand = new ChimeraUchimeCommand(optionString);                   }
 618                 else if(commandName == "chimera.slayer")                {       pipecommand = new ChimeraSlayerCommand(optionString);                   }
 619                 else if(commandName == "chimera.pintail")               {       pipecommand = new ChimeraPintailCommand(optionString);                  }
 620                 else if(commandName == "chimera.bellerophon")   {       pipecommand = new ChimeraBellerophonCommand(optionString);              }
 621                 else if(commandName == "phylotype")                             {       pipecommand = new PhylotypeCommand(optionString);                               }
 622                 else if(commandName == "mgcluster")                             {       pipecommand = new MGClusterCommand(optionString);                               }
 623                 else if(commandName == "pre.cluster")                   {       pipecommand = new PreClusterCommand(optionString);                              }
 624                 else if(commandName == "pcoa")                                  {       pipecommand = new PCOACommand(optionString);                                    }
 625                 else if(commandName == "pca")                                   {       pipecommand = new PCACommand(optionString);                                             }
 626                 else if(commandName == "nmds")                                  {       pipecommand = new NMDSCommand(optionString);                                    }
 627                 else if(commandName == "otu.hierarchy")                 {       pipecommand = new OtuHierarchyCommand(optionString);                    }
 628                 else if(commandName == "set.dir")                               {       pipecommand = new SetDirectoryCommand(optionString);                    }
 629                 else if(commandName == "set.logfile")                   {       pipecommand = new SetLogFileCommand(optionString);                              }
 630                 else if(commandName == "parse.list")                    {       pipecommand = new ParseListCommand(optionString);                               }
 631                 else if(commandName == "phylo.diversity")               {       pipecommand = new PhyloDiversityCommand(optionString);                  }
 632                 else if(commandName == "make.group")                    {       pipecommand = new MakeGroupCommand(optionString);                               }
 633                 else if(commandName == "chop.seqs")                             {       pipecommand = new ChopSeqsCommand(optionString);                                }
 634                 else if(commandName == "clearcut")                              {       pipecommand = new ClearcutCommand(optionString);                                }
 635                 else if(commandName == "catchall")                              {       pipecommand = new CatchAllCommand(optionString);                                }
 636                 else if(commandName == "split.abund")                   {       pipecommand = new SplitAbundCommand(optionString);                              }
 637                 else if(commandName == "cluster.split")                 {       pipecommand = new ClusterSplitCommand(optionString);                    }
 638                 else if(commandName == "classify.otu")                  {       pipecommand = new ClassifyOtuCommand(optionString);                             }
 639                 else if(commandName == "degap.seqs")                    {       pipecommand = new DegapSeqsCommand(optionString);                               }
 640                 else if(commandName == "get.relabund")                  {       pipecommand = new GetRelAbundCommand(optionString);                             }
 641                 else if(commandName == "sens.spec")                             {       pipecommand = new SensSpecCommand(optionString);                                }
 642                 else if(commandName == "seq.error")                             {       pipecommand = new SeqErrorCommand(optionString);                                }
 643                 else if(commandName == "sffinfo")                               {       pipecommand = new SffInfoCommand(optionString);                                 }
 644                 else if(commandName == "normalize.shared")              {       pipecommand = new NormalizeSharedCommand(optionString);                 }
 645                 else if(commandName == "metastats")                             {       pipecommand = new MetaStatsCommand(optionString);                               }
 646                 else if(commandName == "split.groups")                  {       pipecommand = new SplitGroupCommand(optionString);                              }
 647                 else if(commandName == "cluster.fragments")             {       pipecommand = new ClusterFragmentsCommand(optionString);                }
 648                 else if(commandName == "get.lineage")                   {       pipecommand = new GetLineageCommand(optionString);                              }
 649                 else if(commandName == "get.groups")                    {       pipecommand = new GetGroupsCommand(optionString);                               }
 650                 else if(commandName == "remove.lineage")                {       pipecommand = new RemoveLineageCommand(optionString);                   }
 651                 else if(commandName == "remove.groups")                 {       pipecommand = new RemoveGroupsCommand(optionString);                    }
 652                 else if(commandName == "get.otus")                              {       pipecommand = new GetOtusCommand(optionString);                                 }
 653                 else if(commandName == "remove.otus")                   {       pipecommand = new RemoveOtusCommand(optionString);                              }
 654                 else if(commandName == "fastq.info")                    {       pipecommand = new ParseFastaQCommand(optionString);                             }
 655                 else if(commandName == "deunique.seqs")                 {       pipecommand = new DeUniqueSeqsCommand(optionString);                    }
 656                 else if(commandName == "pairwise.seqs")                 {       pipecommand = new PairwiseSeqsCommand(optionString);                    }
 657                 else if(commandName == "cluster.classic")               {       pipecommand = new ClusterDoturCommand(optionString);                    }
 658                 else if(commandName == "sub.sample")                    {       pipecommand = new SubSampleCommand(optionString);                               }
 659                 else if(commandName == "indicator")                             {       pipecommand = new IndicatorCommand(optionString);                               }
 660                 else if(commandName == "consensus.seqs")                {       pipecommand = new ConsensusSeqsCommand(optionString);                   }
 661                 else if(commandName == "corr.axes")                             {       pipecommand = new CorrAxesCommand(optionString);                                }
 662                 else if(commandName == "remove.rare")                   {       pipecommand = new RemoveRareCommand(optionString);                              }
 663                 else if(commandName == "merge.groups")                  {       pipecommand = new MergeGroupsCommand(optionString);                             }
 664                 else if(commandName == "amova")                                 {       pipecommand = new AmovaCommand(optionString);                                   }
 665                 else if(commandName == "homova")                                {       pipecommand = new HomovaCommand(optionString);                                  }
 666                 else if(commandName == "mantel")                                {       pipecommand = new MantelCommand(optionString);                                  }
 667                 else if(commandName == "anosim")                                {       pipecommand = new AnosimCommand(optionString);                                  }
 668                 else if(commandName == "make.fastq")                    {       pipecommand = new MakeFastQCommand(optionString);                               }
 669                 else if(commandName == "get.current")                   {       pipecommand = new GetCurrentCommand(optionString);                              }
 670                 else if(commandName == "set.current")                   {       pipecommand = new SetCurrentCommand(optionString);                              }
 671                 else if(commandName == "make.shared")                   {       pipecommand = new SharedCommand(optionString);                                  }
 672                 else if(commandName == "get.commandinfo")               {       pipecommand = new GetCommandInfoCommand(optionString);                  }
 673                 else if(commandName == "deunique.tree")                 {       pipecommand = new DeuniqueTreeCommand(optionString);                    }
 674                 else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       pipecommand = new CountSeqsCommand(optionString);                               }
 675                 else if(commandName == "count.groups")                  {       pipecommand = new CountGroupsCommand(optionString);                             }
 676                 else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
 677                 else if(commandName == "summary.tax")                   {       pipecommand = new SummaryTaxCommand(optionString);                              }
 678                 else if(commandName == "summary.qual")                  {       pipecommand = new SummaryQualCommand(optionString);                             }
 679                 else if(commandName == "chimera.perseus")               {       pipecommand = new ChimeraPerseusCommand(optionString);                  }
 680                 else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhhSeqsCommand(optionString);                                }
 681                 else if(commandName == "otu.association")               {       pipecommand = new OTUAssociationCommand(optionString);                  }
 682         else if(commandName == "sort.seqs")             {       pipecommand = new SortSeqsCommand(optionString);                }
 683         else if(commandName == "classify.tree")         {       pipecommand = new ClassifyTreeCommand(optionString);            }
 684         else if(commandName == "cooccurrence")          {       pipecommand = new CooccurrenceCommand(optionString);            }
 685         else if(commandName == "pcr.seqs")              {       pipecommand = new PcrSeqsCommand(optionString);                 }
 686         else if(commandName == "create.database")       {       pipecommand = new CreateDatabaseCommand(optionString);          }
 687         else if(commandName == "make.biom")             {       pipecommand = new MakeBiomCommand(optionString);                }
 688         else if(commandName == "get.coremicrobiome")    {       pipecommand = new GetCoreMicroBiomeCommand(optionString);       }
 689         else if(commandName == "list.otulabels")        {       pipecommand = new ListOtuLabelsCommand(optionString);           }
 690         else if(commandName == "get.otulabels")         {       pipecommand = new GetOtuLabelsCommand(optionString);            }
 691         else if(commandName == "remove.otulabels")      {       pipecommand = new RemoveOtuLabelsCommand(optionString);         }
 692         else if(commandName == "make.contigs")          {       pipecommand = new MakeContigsCommand(optionString);             }
 693         else if(commandName == "load.logfile")          {       pipecommand = new LoadLogfileCommand(optionString);             }
 694         else if(commandName == "sff.multiple")          {       pipecommand = new SffMultipleCommand(optionString);             }
 695         else if(commandName == "classify.shared")       {       pipecommand = new ClassifySharedCommand(optionString);          }
 696         else if(commandName == "filter.shared")         {       pipecommand = new FilterSharedCommand(optionString);            }
 697         else if(commandName == "primer.design")         {       pipecommand = new PrimerDesignCommand(optionString);            }
 698         else if(commandName == "get.dists")             {       pipecommand = new GetDistsCommand(optionString);                }
 699         else if(commandName == "remove.dists")          {       pipecommand = new RemoveDistsCommand(optionString);             }
 700         else if(commandName == "merge.taxsummary")      {       pipecommand = new MergeTaxSummaryCommand(optionString);         }
 701         else if(commandName == "get.metacommunity")     {       pipecommand = new GetMetaCommunityCommand(optionString);        }
 702         else if(commandName == "sparcc")                {       pipecommand = new SparccCommand(optionString);                  }
 703         else if(commandName == "make.lookup")                   {       pipecommand = new MakeLookupCommand(optionString);                              }
 704         else if(commandName == "rename.seqs")                   {       pipecommand = new RenameSeqsCommand(optionString);                              }
 705                 else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 706
 707                 return pipecommand;
 708         }
 709         catch(exception& e) {
 710                 m->errorOut(e, "CommandFactory", "getCommand");
 711                 exit(1);
 712         }
 713 }
 714 /***********************************************************/
 715
 716 /***********************************************************/
 717 //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
 718 Command* CommandFactory::getCommand(string commandName){
 719         try {
 720                 delete shellcommand;   //delete the old command
 721
 722                 if(commandName == "cluster")                            {       shellcommand = new ClusterCommand();                            }
 723                 else if(commandName == "unique.seqs")                   {       shellcommand = new DeconvoluteCommand();                        }
 724                 else if(commandName == "parsimony")                             {       shellcommand = new ParsimonyCommand();                          }
 725                 else if(commandName == "help")                                  {       shellcommand = new HelpCommand();                                       }
 726                 else if(commandName == "quit")                                  {       shellcommand = new QuitCommand();                                       }
 727                 else if(commandName == "collect.single")                {       shellcommand = new CollectCommand();                            }
 728                 else if(commandName == "collect.shared")                {       shellcommand = new CollectSharedCommand();                      }
 729                 else if(commandName == "rarefaction.single")    {       shellcommand = new RareFactCommand();                           }
 730                 else if(commandName == "rarefaction.shared")    {       shellcommand = new RareFactSharedCommand();                     }
 731                 else if(commandName == "summary.single")                {       shellcommand = new SummaryCommand();                            }
 732                 else if(commandName == "summary.shared")                {       shellcommand = new SummarySharedCommand();                      }
 733                 else if(commandName == "unifrac.weighted")              {       shellcommand = new UnifracWeightedCommand();            }
 734                 else if(commandName == "unifrac.unweighted")    {       shellcommand = new UnifracUnweightedCommand();          }
 735                 else if(commandName == "get.group")             {   shellcommand = new GetgroupCommand();                               }
 736                 else if(commandName == "get.label")             {   shellcommand = new GetlabelCommand();                               }
 737                 else if(commandName == "get.sabund")            {   shellcommand = new GetSAbundCommand();                              }
 738                 else if(commandName == "get.rabund")            {   shellcommand = new GetRAbundCommand();                              }
 739                 else if(commandName == "libshuff")              {   shellcommand = new LibShuffCommand();                               }
 740                 else if(commandName == "heatmap.bin")                   {   shellcommand = new HeatMapCommand();                                }
 741                 else if(commandName == "heatmap.sim")                   {   shellcommand = new HeatMapSimCommand();                             }
 742                 else if(commandName == "filter.seqs")                   {   shellcommand = new FilterSeqsCommand();                             }
 743                 else if(commandName == "venn")                                  {   shellcommand = new VennCommand();                                   }
 744                 else if(commandName == "bin.seqs")                              {   shellcommand = new BinSeqCommand();                                 }
 745                 else if(commandName == "get.oturep")                    {   shellcommand = new GetOTURepCommand();                              }
 746                 else if(commandName == "tree.shared")                   {   shellcommand = new TreeGroupCommand();                              }
 747                 else if(commandName == "dist.shared")                   {   shellcommand = new MatrixOutputCommand();                   }
 748                 else if(commandName == "dist.seqs")                             {   shellcommand = new DistanceCommand();                               }
 749                 else if(commandName == "align.seqs")                    {   shellcommand = new AlignCommand();                                  }
 750                 else if(commandName == "summary.seqs")                  {       shellcommand = new SeqSummaryCommand();                         }
 751                 else if(commandName == "screen.seqs")                   {       shellcommand = new ScreenSeqsCommand();                         }
 752                 else if(commandName == "reverse.seqs")                  {       shellcommand = new ReverseSeqsCommand();                        }
 753                 else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
 754                 else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
 755                 else if(commandName == "shhh.flows")                    {       shellcommand = new ShhherCommand();                                     }
 756                 else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
 757                 else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
 758                 else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }
 759                 else if(commandName == "merge.files")                   {       shellcommand = new MergeFileCommand();                          }
 760                 else if(commandName == "system")                                {       shellcommand = new SystemCommand();                                     }
 761                 else if(commandName == "align.check")                   {       shellcommand = new AlignCheckCommand();                         }
 762                 else if(commandName == "get.sharedseqs")                {       shellcommand = new GetSharedOTUCommand();                       }
 763                 else if(commandName == "get.otulist")                   {       shellcommand = new GetListCountCommand();                       }
 764                 else if(commandName == "hcluster")                              {       shellcommand = new HClusterCommand();                           }
 765                 else if(commandName == "classify.seqs")                 {       shellcommand = new ClassifySeqsCommand();                       }
 766                 else if(commandName == "chimera.ccode")                 {       shellcommand = new ChimeraCcodeCommand();                       }
 767                 else if(commandName == "chimera.check")                 {       shellcommand = new ChimeraCheckCommand();                       }
 768                 else if(commandName == "chimera.slayer")                {       shellcommand = new ChimeraSlayerCommand();                      }
 769                 else if(commandName == "chimera.uchime")                {       shellcommand = new ChimeraUchimeCommand();                      }
 770                 else if(commandName == "chimera.pintail")               {       shellcommand = new ChimeraPintailCommand();                     }
 771                 else if(commandName == "chimera.bellerophon")   {       shellcommand = new ChimeraBellerophonCommand();         }
 772                 else if(commandName == "phylotype")                             {       shellcommand = new PhylotypeCommand();                          }
 773                 else if(commandName == "mgcluster")                             {       shellcommand = new MGClusterCommand();                          }
 774                 else if(commandName == "pre.cluster")                   {       shellcommand = new PreClusterCommand();                         }
 775                 else if(commandName == "pcoa")                                  {       shellcommand = new PCOACommand();                                       }
 776                 else if(commandName == "pca")                                   {       shellcommand = new PCACommand();                                        }
 777                 else if(commandName == "nmds")                                  {       shellcommand = new NMDSCommand();                                       }
 778                 else if(commandName == "otu.hierarchy")                 {       shellcommand = new OtuHierarchyCommand();                       }
 779                 else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
 780                 else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }
 781                 else if(commandName == "parse.list")                    {       shellcommand = new ParseListCommand();                          }
 782                 else if(commandName == "phylo.diversity")               {       shellcommand = new PhyloDiversityCommand();                     }
 783                 else if(commandName == "make.group")                    {       shellcommand = new MakeGroupCommand();                          }
 784                 else if(commandName == "chop.seqs")                             {       shellcommand = new ChopSeqsCommand();                           }
 785                 else if(commandName == "clearcut")                              {       shellcommand = new ClearcutCommand();                           }
 786                 else if(commandName == "catchall")                              {       shellcommand = new CatchAllCommand();                           }
 787                 else if(commandName == "split.abund")                   {       shellcommand = new SplitAbundCommand();                         }
 788                 else if(commandName == "cluster.split")                 {       shellcommand = new ClusterSplitCommand();                       }
 789                 else if(commandName == "classify.otu")                  {       shellcommand = new ClassifyOtuCommand();                        }
 790                 else if(commandName == "degap.seqs")                    {       shellcommand = new DegapSeqsCommand();                          }
 791                 else if(commandName == "get.relabund")                  {       shellcommand = new GetRelAbundCommand();                        }
 792                 else if(commandName == "sens.spec")                             {       shellcommand = new SensSpecCommand();                           }
 793                 else if(commandName == "seq.error")                             {       shellcommand = new SeqErrorCommand();                           }
 794                 else if(commandName == "sffinfo")                               {       shellcommand = new SffInfoCommand();                            }
 795                 else if(commandName == "normalize.shared")              {       shellcommand = new NormalizeSharedCommand();            }
 796                 else if(commandName == "metastats")                             {       shellcommand = new MetaStatsCommand();                          }
 797                 else if(commandName == "split.groups")                  {       shellcommand = new SplitGroupCommand();                         }
 798                 else if(commandName == "cluster.fragments")             {       shellcommand = new ClusterFragmentsCommand();           }
 799                 else if(commandName == "get.lineage")                   {       shellcommand = new GetLineageCommand();                         }
 800                 else if(commandName == "remove.lineage")                {       shellcommand = new RemoveLineageCommand();                      }
 801                 else if(commandName == "get.groups")                    {       shellcommand = new GetGroupsCommand();                          }
 802                 else if(commandName == "remove.groups")                 {       shellcommand = new RemoveGroupsCommand();                       }
 803                 else if(commandName == "get.otus")                              {       shellcommand = new GetOtusCommand();                            }
 804                 else if(commandName == "remove.otus")                   {       shellcommand = new RemoveOtusCommand();                         }
 805                 else if(commandName == "fastq.info")                    {       shellcommand = new ParseFastaQCommand();                        }
 806                 else if(commandName == "deunique.seqs")                 {       shellcommand = new DeUniqueSeqsCommand();                       }
 807                 else if(commandName == "pairwise.seqs")                 {       shellcommand = new PairwiseSeqsCommand();                       }
 808                 else if(commandName == "cluster.classic")               {       shellcommand = new ClusterDoturCommand();                       }
 809                 else if(commandName == "sub.sample")                    {       shellcommand = new SubSampleCommand();                          }
 810                 else if(commandName == "indicator")                             {       shellcommand = new IndicatorCommand();                          }
 811                 else if(commandName == "consensus.seqs")                {       shellcommand = new ConsensusSeqsCommand();                      }
 812                 else if(commandName == "corr.axes")                             {       shellcommand = new CorrAxesCommand();                           }
 813                 else if(commandName == "remove.rare")                   {       shellcommand = new RemoveRareCommand();                         }
 814                 else if(commandName == "merge.groups")                  {       shellcommand = new MergeGroupsCommand();                        }
 815                 else if(commandName == "amova")                                 {       shellcommand = new AmovaCommand();                                      }
 816                 else if(commandName == "homova")                                {       shellcommand = new HomovaCommand();                                     }
 817                 else if(commandName == "mantel")                                {       shellcommand = new MantelCommand();                                     }
 818                 else if(commandName == "anosim")                                {       shellcommand = new AnosimCommand();                                     }
 819                 else if(commandName == "make.fastq")                    {       shellcommand = new MakeFastQCommand();                          }
 820                 else if(commandName == "get.current")                   {       shellcommand = new GetCurrentCommand();                         }
 821                 else if(commandName == "set.current")                   {       shellcommand = new SetCurrentCommand();                         }
 822                 else if(commandName == "make.shared")                   {       shellcommand = new SharedCommand();                                     }
 823                 else if(commandName == "get.commandinfo")               {       shellcommand = new GetCommandInfoCommand();                     }
 824                 else if(commandName == "deunique.tree")                 {       shellcommand = new DeuniqueTreeCommand();                       }
 825                 else if((commandName == "count.seqs") || (commandName == "make.table"))                 {       shellcommand = new CountSeqsCommand();                          }
 826                 else if(commandName == "count.groups")                  {       shellcommand = new CountGroupsCommand();                        }
 827                 else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
 828                 else if(commandName == "summary.tax")                   {       shellcommand = new SummaryTaxCommand();                         }
 829                 else if(commandName == "summary.qual")                  {       shellcommand = new SummaryQualCommand();                        }
 830                 else if(commandName == "chimera.perseus")               {       shellcommand = new ChimeraPerseusCommand();                     }
 831                 else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhhSeqsCommand();                           }
 832                 else if(commandName == "otu.association")               {       shellcommand = new OTUAssociationCommand();                     }
 833         else if(commandName == "sort.seqs")             {       shellcommand = new SortSeqsCommand();               }
 834         else if(commandName == "classify.tree")         {       shellcommand = new ClassifyTreeCommand();           }
 835         else if(commandName == "cooccurrence")          {       shellcommand = new CooccurrenceCommand();           }
 836         else if(commandName == "pcr.seqs")              {       shellcommand = new PcrSeqsCommand();                }
 837         else if(commandName == "create.database")       {       shellcommand = new CreateDatabaseCommand();         }
 838         else if(commandName == "make.biom")             {       shellcommand = new MakeBiomCommand();               }
 839         else if(commandName == "get.coremicrobiome")    {       shellcommand = new GetCoreMicroBiomeCommand();      }
 840         else if(commandName == "list.otulabels")        {       shellcommand = new ListOtuLabelsCommand();          }
 841         else if(commandName == "get.otulabels")         {       shellcommand = new GetOtuLabelsCommand();           }
 842         else if(commandName == "remove.otulabels")      {       shellcommand = new RemoveOtuLabelsCommand();        }
 843         else if(commandName == "make.contigs")          {       shellcommand = new MakeContigsCommand();            }
 844         else if(commandName == "load.logfile")          {       shellcommand = new LoadLogfileCommand();            }
 845         else if(commandName == "sff.multiple")          {       shellcommand = new SffMultipleCommand();            }
 846         else if(commandName == "classify.shared")       {       shellcommand = new ClassifySharedCommand();         }
 847         else if(commandName == "filter.shared")         {       shellcommand = new FilterSharedCommand();           }
 848         else if(commandName == "primer.design")         {       shellcommand = new PrimerDesignCommand();           }
 849         else if(commandName == "get.dists")             {       shellcommand = new GetDistsCommand();               }
 850         else if(commandName == "remove.dists")          {       shellcommand = new RemoveDistsCommand();            }
 851         else if(commandName == "merge.taxsummary")      {       shellcommand = new MergeTaxSummaryCommand();        }
 852         else if(commandName == "get.metacommunity")     {       shellcommand = new GetMetaCommunityCommand();       }
 853         else if(commandName == "sparcc")                {       shellcommand = new SparccCommand();                 }
 854         else if(commandName == "make.lookup")                   {       shellcommand = new MakeLookupCommand();                         }
 855         else if(commandName == "rename.seqs")                   {       shellcommand = new RenameSeqsCommand();                         }
 856                 else                                                                                    {       shellcommand = new NoCommand();                                         }
 857
 858                 return shellcommand;
 859         }
 860         catch(exception& e) {
 861                 m->errorOut(e, "CommandFactory", "getCommand");
 862                 exit(1);
 863         }
 864 }
 865 /***********************************************************
 866 //This function is used to interrupt a command
 867 Command* CommandFactory::getCommand(){
 868         try {
 869                 delete command;   //delete the old command
 870
 871                 string s = "";
 872             command = new NoCommand(s);
 873
 874                 return command;
 875         }
 876         catch(exception& e) {
 877                 m->errorOut(e, "CommandFactory", "getCommand");
 878                 exit(1);
 879         }
 880 }
 881 ***********************************************************************/
 882 bool CommandFactory::isValidCommand(string command) {
 883         try {
 884
 885                 //is the command in the map
 886                 if ((commands.find(command)) != (commands.end())) {
 887                         return true;
 888                 }else{
 889                         m->mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
 890                         for (it = commands.begin(); it != commands.end(); it++) {
 891                                 m->mothurOut(it->first + ", ");
 892                         }
 893                         m->mothurOutEndLine();
 894                         return false;
 895                 }
 896
 897         }
 898         catch(exception& e) {
 899                 m->errorOut(e, "CommandFactory", "isValidCommand");
 900                 exit(1);
 901         }
 902 }
 903 /***********************************************************************/
 904 bool CommandFactory::isValidCommand(string command, string noError) {
 905         try {
 906
 907                 //is the command in the map
 908                 if ((commands.find(command)) != (commands.end())) {
 909                         return true;
 910                 }else{
 911                         return false;
 912                 }
 913
 914         }
 915         catch(exception& e) {
 916                 m->errorOut(e, "CommandFactory", "isValidCommand");
 917                 exit(1);
 918         }
 919 }
 920 /***********************************************************************/
 921 void CommandFactory::printCommands(ostream& out) {
 922         try {
 923                 out << "Valid commands are: ";
 924                 for (it = commands.begin(); it != commands.end(); it++) {
 925                         out << it->first << ",";
 926                 }
 927                 out << endl;
 928         }
 929         catch(exception& e) {
 930                 m->errorOut(e, "CommandFactory", "printCommands");
 931                 exit(1);
 932         }
 933 }
 934 /***********************************************************************/
 935 void CommandFactory::printCommandsCategories(ostream& out) {
 936     try {
 937         map<string, string> commands = getListCommands();
 938         map<string, string>::iterator it;
 939
 940         map<string, string> categories;
 941         map<string, string>::iterator itCat;
 942         //loop through each command outputting info
 943         for (it = commands.begin(); it != commands.end(); it++) {
 944
 945             Command* thisCommand = getCommand(it->first);
 946
 947             //don't add hidden commands
 948             if (thisCommand->getCommandCategory() != "Hidden") {
 949                 itCat = categories.find(thisCommand->getCommandCategory());
 950                 if (itCat == categories.end()) {
 951                     categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
 952                 }else {
 953                     categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
 954                 }
 955             }
 956         }
 957
 958         for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
 959             out << itCat->first << " commmands include: " << itCat->second << endl;
 960         }
 961
 962     }
 963         catch(exception& e) {
 964                 m->errorOut(e, "CommandFactory", "printCommandsCategories");
 965                 exit(1);
 966         }
 967 }
 968
 969 /***********************************************************************/
 970
 971
 972
 973