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
 138 /*******************************************************/
 139
 140 /******************************************************/
 141 CommandFactory* CommandFactory::getInstance() {
 142         if( _uniqueInstance == 0) {
 143                 _uniqueInstance = new CommandFactory();
 144         }
 145         return _uniqueInstance;
 146 }
 147 /***********************************************************/
 148
 149 /***********************************************************/
 150 //note: This class is resposible for knowing which commands are mpiEnabled,
 151 //If a command is not enabled only process 0 will execute the command.
 152 //This avoids redundant outputs on pieces of code we have not paralellized.
 153 //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.
 154 //example:  commands["dist.seqs"] = "MPIEnabled";
 155
 156 CommandFactory::CommandFactory(){
 157         string s = "";
 158         m = MothurOut::getInstance();
 159
 160         command = new NoCommand(s);
 161         shellcommand = new NoCommand(s);
 162         pipecommand = new NoCommand(s);
 163
 164         outputDir = ""; inputDir = "";
 165         logFileName = "";
 166         append = false;
 167
 168         //initialize list of valid commands
 169         commands["make.shared"]                 = "make.shared";
 170         commands["bin.seqs"]                    = "bin.seqs";
 171         commands["get.oturep"]                  = "get.oturep";
 172         commands["cluster"]                             = "cluster";
 173         commands["unique.seqs"]                 = "unique.seqs";
 174         commands["dist.shared"]                 = "dist.shared";
 175         commands["collect.single"]              = "collect.single";
 176         commands["collect.shared"]              = "collect.shared";
 177         commands["rarefaction.single"]  = "rarefaction.single";
 178         commands["rarefaction.shared"]  = "rarefaction.shared";
 179         commands["summary.single"]              = "summary.single";
 180         commands["summary.shared"]              = "summary.shared";
 181         commands["parsimony"]                   = "parsimony";
 182         commands["unifrac.weighted"]    = "unifrac.weighted";
 183         commands["unifrac.unweighted"]  = "unifrac.unweighted";
 184         commands["libshuff"]                    = "libshuff";
 185         commands["tree.shared"]                 = "tree.shared";
 186         commands["heatmap.bin"]                 = "heatmap.bin";
 187         commands["heatmap.sim"]                 = "heatmap.sim";
 188         commands["venn"]                                = "venn";
 189         commands["get.group"]           = "get.group";
 190         commands["get.label"]           = "get.label";
 191         commands["get.sabund"]          = "get.sabund";
 192         commands["get.rabund"]          = "get.rabund";
 193         commands["help"]                                = "help";
 194         commands["reverse.seqs"]                = "reverse.seqs";
 195         commands["trim.seqs"]                   = "trim.seqs";
 196         commands["trim.flows"]                  = "trim.flows";
 197         commands["list.seqs"]                   = "list.seqs";
 198         commands["get.seqs"]                    = "get.seqs";
 199         commands["remove.seqs"]                 = "remove.seqs";
 200         commands["system"]                              = "system";
 201         commands["align.check"]                 = "align.check";
 202         commands["get.sharedseqs"]              = "get.sharedseqs";
 203         commands["get.otulist"]                 = "get.otulist";
 204         commands["hcluster"]                    = "hcluster";
 205         commands["phylotype"]                   = "phylotype";
 206         commands["mgcluster"]                   = "mgcluster";
 207         commands["pre.cluster"]                 = "pre.cluster";
 208         commands["pcoa"]                                = "pcoa";
 209         commands["otu.hierarchy"]               = "otu.hierarchy";
 210         commands["set.dir"]                             = "MPIEnabled";
 211         commands["merge.files"]                 = "merge.files";
 212         commands["parse.list"]                  = "parse.list";
 213         commands["set.logfile"]                 = "set.logfile";
 214         commands["phylo.diversity"]             = "phylo.diversity";
 215         commands["make.group"]                  = "make.group";
 216         commands["chop.seqs"]                   = "chop.seqs";
 217         commands["clearcut"]                    = "clearcut";
 218         commands["catchall"]                    = "catchall";
 219         commands["split.abund"]                 = "split.abund";
 220         commands["classify.otu"]                = "classify.otu";
 221         commands["degap.seqs"]                  = "degap.seqs";
 222         commands["get.relabund"]                = "get.relabund";
 223         commands["sffinfo"]                             = "sffinfo";
 224         commands["normalize.shared"]    = "normalize.shared";
 225         commands["metastats"]                   = "metastats";
 226         commands["split.groups"]                = "split.groups";
 227         commands["cluster.fragments"]   = "cluster.fragments";
 228         commands["get.lineage"]                 = "get.lineage";
 229         commands["remove.lineage"]              = "remove.lineage";
 230         commands["fastq.info"]                  = "fastq.info";
 231         commands["deunique.seqs"]               = "deunique.seqs";
 232         commands["cluster.classic"]             = "cluster.classic";
 233         commands["sub.sample"]                  = "sub.sample";
 234         commands["remove.groups"]               = "remove.groups";
 235         commands["get.groups"]                  = "get.groups";
 236         commands["get.otus"]                    = "get.otus";
 237         commands["remove.otus"]                 = "remove.otus";
 238         commands["indicator"]                   = "indicator";
 239         commands["consensus.seqs"]              = "consensus.seqs";
 240         commands["corr.axes"]                   = "corr.axes";
 241         commands["pca"]                                 = "pca";
 242         commands["nmds"]                                = "nmds";
 243         commands["remove.rare"]                 = "remove.rare";
 244         commands["amova"]                               = "amova";
 245         commands["homova"]                              = "homova";
 246         commands["mantel"]                              = "mantel";
 247         commands["anosim"]                              = "anosim";
 248         commands["make.fastq"]                  = "make.fastq";
 249         commands["merge.groups"]                = "merge.groups";
 250         commands["get.current"]                 = "MPIEnabled";
 251         commands["set.current"]                 = "MPIEnabled";
 252         commands["get.commandinfo"]             = "get.commandinfo";
 253         commands["deunique.tree"]               = "deunique.tree";
 254         commands["count.seqs"]                  = "count.seqs";
 255         commands["count.groups"]                = "count.groups";
 256         commands["clear.memory"]                = "clear.memory";
 257         commands["pairwise.seqs"]               = "MPIEnabled";
 258         commands["pipeline.pds"]                = "MPIEnabled";
 259         commands["classify.seqs"]               = "MPIEnabled";
 260         commands["dist.seqs"]                   = "MPIEnabled";
 261         commands["filter.seqs"]                 = "MPIEnabled";
 262         commands["align.seqs"]                  = "MPIEnabled";
 263         commands["chimera.ccode"]               = "MPIEnabled";
 264         commands["chimera.check"]               = "MPIEnabled";
 265         commands["chimera.slayer"]              = "MPIEnabled";
 266         commands["chimera.uchime"]              = "chimera.uchime";
 267         commands["chimera.perseus"]             = "chimera.perseus";
 268         commands["chimera.pintail"]             = "MPIEnabled";
 269         commands["chimera.bellerophon"] = "MPIEnabled";
 270         commands["screen.seqs"]                 = "MPIEnabled";
 271         commands["summary.seqs"]                = "MPIEnabled";
 272         commands["cluster.split"]               = "MPIEnabled";
 273         commands["shhh.flows"]                  = "MPIEnabled";
 274         commands["sens.spec"]                   = "sens.spec";
 275         commands["seq.error"]                   = "seq.error";
 276         commands["summary.tax"]                 = "summary.tax";
 277         commands["summary.qual"]                = "summary.qual";
 278         commands["shhh.seqs"]                   = "shhh.seqs";
 279         commands["otu.association"]             = "otu.association";
 280     commands["sort.seqs"]           = "sort.seqs";
 281     commands["classify.tree"]       = "classify.tree";
 282     commands["cooccurrence"]        = "cooccurrence";
 283     commands["pcr.seqs"]            = "pcr.seqs";
 284     commands["create.database"]     = "create.database";
 285     commands["make.biom"]           = "make.biom";
 286     commands["get.coremicrobiome"]  = "get.coremicrobiome";
 287     commands["list.otulabels"]      = "list.otulabels";
 288     commands["get.otulabels"]       = "get.otulabels";
 289     commands["remove.otulabels"]    = "remove.otulabels";
 290     commands["make.contigs"]        = "make.contigs";
 291     commands["load.logfile"]        = "load.logfile";
 292         commands["quit"]                                = "MPIEnabled";
 293
 294 }
 295 /***********************************************************/
 296
 297 /***********************************************************/
 298 bool CommandFactory::MPIEnabled(string commandName) {
 299         bool mpi = false;
 300         it = commands.find(commandName);
 301         if (it != commands.end()) {
 302                 if (it->second == "MPIEnabled") { return true; }
 303         }
 304         return mpi;
 305 }
 306 /***********************************************************/
 307
 308 /***********************************************************/
 309 CommandFactory::~CommandFactory(){
 310         _uniqueInstance = 0;
 311         delete command;
 312         delete shellcommand;
 313         delete pipecommand;
 314 }
 315 /***********************************************************/
 316
 317 /***********************************************************/
 318 int CommandFactory::checkForRedirects(string optionString) {
 319     try {
 320
 321         int pos = optionString.find("outputdir");
 322         if (pos != string::npos) { //user has set outputdir in command option string
 323             string outputOption = "";
 324             bool foundEquals = false;
 325             for(int i=pos;i<optionString.length();i++){
 326                 if(optionString[i] == ',')       { break;               }
 327                 else if(optionString[i] == '=')  { foundEquals = true;  }
 328                 if (foundEquals)       {   outputOption += optionString[i]; }
 329             }
 330             if(m->dirCheck(outputOption)){
 331                 setOutputDirectory(outputOption);
 332                 m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
 333             }
 334         }
 335
 336         pos = optionString.find("inputdir");
 337         if (pos != string::npos) { //user has set inputdir in command option string
 338             string intputOption = "";
 339             bool foundEquals = false;
 340             for(int i=pos;i<optionString.length();i++){
 341                 if(optionString[i] == ',')       { break;               }
 342                 else if(optionString[i] == '=')  { foundEquals = true;  }
 343                 if (foundEquals)       {   intputOption += optionString[i]; }
 344             }
 345             if(m->dirCheck(intputOption)){
 346                 setInputDirectory(intputOption);
 347                 m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
 348             }
 349         }
 350
 351         return 0;
 352         }
 353         catch(exception& e) {
 354                 m->errorOut(e, "CommandFactory", "getCommand");
 355                 exit(1);
 356         }
 357 }
 358 /***********************************************************/
 359
 360 /***********************************************************/
 361 //This function calls the appropriate command fucntions based on user input.
 362 Command* CommandFactory::getCommand(string commandName, string optionString){
 363         try {
 364
 365                 delete command;   //delete the old command
 366
 367         checkForRedirects(optionString);
 368
 369                 //user has opted to redirect output from dir where input files are located to some other place
 370                 if (outputDir != "") {
 371                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 372                         else { optionString += "outputdir=" + outputDir; }
 373                 }
 374
 375                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 376                 if (inputDir != "") {
 377                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 378                         else { optionString += "inputdir=" + inputDir; }
 379                 }
 380
 381                 if(commandName == "cluster")                            {       command = new ClusterCommand(optionString);                                     }
 382                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand(optionString);                         }
 383                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand(optionString);                           }
 384                 else if(commandName == "help")                                  {       command = new HelpCommand(optionString);                                        }
 385                 else if(commandName == "quit")                                  {       command = new QuitCommand(optionString);                                        }
 386                 else if(commandName == "collect.single")                {       command = new CollectCommand(optionString);                                     }
 387                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand(optionString);                       }
 388                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand(optionString);                            }
 389                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand(optionString);                      }
 390                 else if(commandName == "summary.single")                {       command = new SummaryCommand(optionString);                                     }
 391                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand(optionString);                       }
 392                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand(optionString);                     }
 393                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);           }
 394                 else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                                }
 395                 else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                                }
 396                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                               }
 397                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                               }
 398                 else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                                }
 399                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand(optionString);                                 }
 400                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand(optionString);                              }
 401                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand(optionString);                              }
 402                 else if(commandName == "venn")                                  {   command = new VennCommand(optionString);                                    }
 403                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand(optionString);                                  }
 404                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                               }
 405                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                               }
 406                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);                    }
 407                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                                }
 408                 else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                                   }
 409                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                          }
 410                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                          }
 411                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
 412                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
 413                 else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
 414                 else if(commandName == "shhh.flows")                    {       command = new ShhherCommand(optionString);                                      }
 415                 else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
 416                 else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
 417                 else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
 418                 else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                           }
 419                 else if(commandName == "system")                                {       command = new SystemCommand(optionString);                                      }
 420                 else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                          }
 421                 else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                        }
 422                 else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                        }
 423                 else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                            }
 424                 else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                        }
 425                 else if(commandName == "chimera.ccode")                 {       command = new ChimeraCcodeCommand(optionString);                        }
 426                 else if(commandName == "chimera.check")                 {       command = new ChimeraCheckCommand(optionString);                        }
 427                 else if(commandName == "chimera.slayer")                {       command = new ChimeraSlayerCommand(optionString);                       }
 428                 else if(commandName == "chimera.uchime")                {       command = new ChimeraUchimeCommand(optionString);                       }
 429                 else if(commandName == "chimera.pintail")               {       command = new ChimeraPintailCommand(optionString);                      }
 430                 else if(commandName == "chimera.bellerophon")   {       command = new ChimeraBellerophonCommand(optionString);          }
 431                 else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
 432                 else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                           }
 433                 else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                          }
 434                 else if(commandName == "pcoa")                                  {       command = new PCOACommand(optionString);                                        }
 435                 else if(commandName == "pca")                                   {       command = new PCACommand(optionString);                                         }
 436                 else if(commandName == "nmds")                                  {       command = new NMDSCommand(optionString);                                        }
 437                 else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
 438                 else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
 439                 else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
 440                 else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
 441                 else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
 442                 else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
 443                 else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
 444                 else if(commandName == "clearcut")                              {       command = new ClearcutCommand(optionString);                            }
 445                 else if(commandName == "catchall")                              {       command = new CatchAllCommand(optionString);                            }
 446                 else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
 447                 else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
 448                 else if(commandName == "classify.otu")                  {       command = new ClassifyOtuCommand(optionString);                         }
 449                 else if(commandName == "degap.seqs")                    {       command = new DegapSeqsCommand(optionString);                           }
 450                 else if(commandName == "get.relabund")                  {       command = new GetRelAbundCommand(optionString);                         }
 451                 else if(commandName == "sens.spec")                             {       command = new SensSpecCommand(optionString);                            }
 452                 else if(commandName == "seq.error")                             {       command = new SeqErrorCommand(optionString);                            }
 453                 else if(commandName == "sffinfo")                               {       command = new SffInfoCommand(optionString);                                     }
 454                 else if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
 455                 else if(commandName == "metastats")                             {       command = new MetaStatsCommand(optionString);                           }
 456                 else if(commandName == "split.groups")                  {       command = new SplitGroupCommand(optionString);                          }
 457                 else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
 458                 else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
 459                 else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
 460                 else if(commandName == "get.groups")                    {       command = new GetGroupsCommand(optionString);                           }
 461                 else if(commandName == "remove.groups")                 {       command = new RemoveGroupsCommand(optionString);                        }
 462                 else if(commandName == "get.otus")                              {       command = new GetOtusCommand(optionString);                                     }
 463                 else if(commandName == "remove.otus")                   {       command = new RemoveOtusCommand(optionString);                          }
 464                 else if(commandName == "fastq.info")                    {       command = new ParseFastaQCommand(optionString);                         }
 465                 else if(commandName == "pipeline.pds")                  {       command = new PipelineCommand(optionString);                            }
 466                 else if(commandName == "deunique.seqs")                 {       command = new DeUniqueSeqsCommand(optionString);                        }
 467                 else if(commandName == "pairwise.seqs")                 {       command = new PairwiseSeqsCommand(optionString);                        }
 468                 else if(commandName == "cluster.classic")               {       command = new ClusterDoturCommand(optionString);                        }
 469                 else if(commandName == "sub.sample")                    {       command = new SubSampleCommand(optionString);                           }
 470                 else if(commandName == "indicator")                             {       command = new IndicatorCommand(optionString);                           }
 471                 else if(commandName == "consensus.seqs")                {       command = new ConsensusSeqsCommand(optionString);                       }
 472                 else if(commandName == "corr.axes")                             {       command = new CorrAxesCommand(optionString);                            }
 473                 else if(commandName == "remove.rare")                   {       command = new RemoveRareCommand(optionString);                          }
 474                 else if(commandName == "merge.groups")                  {       command = new MergeGroupsCommand(optionString);                         }
 475                 else if(commandName == "amova")                                 {       command = new AmovaCommand(optionString);                                       }
 476                 else if(commandName == "homova")                                {       command = new HomovaCommand(optionString);                                      }
 477                 else if(commandName == "mantel")                                {       command = new MantelCommand(optionString);                                      }
 478                 else if(commandName == "make.fastq")                    {       command = new MakeFastQCommand(optionString);                           }
 479                 else if(commandName == "get.current")                   {       command = new GetCurrentCommand(optionString);                          }
 480                 else if(commandName == "set.current")                   {       command = new SetCurrentCommand(optionString);                          }
 481                 else if(commandName == "anosim")                                {       command = new AnosimCommand(optionString);                                      }
 482                 else if(commandName == "make.shared")                   {       command = new SharedCommand(optionString);                                      }
 483                 else if(commandName == "get.commandinfo")               {       command = new GetCommandInfoCommand(optionString);                      }
 484                 else if(commandName == "deunique.tree")                 {       command = new DeuniqueTreeCommand(optionString);                        }
 485                 else if(commandName == "count.seqs")                    {       command = new CountSeqsCommand(optionString);                           }
 486                 else if(commandName == "count.groups")                  {       command = new CountGroupsCommand(optionString);                         }
 487                 else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
 488                 else if(commandName == "summary.tax")                   {       command = new SummaryTaxCommand(optionString);                          }
 489                 else if(commandName == "summary.qual")                  {       command = new SummaryQualCommand(optionString);                         }
 490                 else if(commandName == "chimera.perseus")               {       command = new ChimeraPerseusCommand(optionString);                      }
 491                 else if(commandName == "shhh.seqs")                             {       command = new ShhhSeqsCommand(optionString);                            }
 492                 else if(commandName == "otu.association")               {       command = new OTUAssociationCommand(optionString);                      }
 493         else if(commandName == "sort.seqs")             {       command = new SortSeqsCommand(optionString);                }
 494         else if(commandName == "classify.tree")         {       command = new ClassifyTreeCommand(optionString);            }
 495         else if(commandName == "cooccurrence")          {       command = new CooccurrenceCommand(optionString);            }
 496         else if(commandName == "pcr.seqs")              {       command = new PcrSeqsCommand(optionString);                 }
 497         else if(commandName == "create.database")       {       command = new CreateDatabaseCommand(optionString);          }
 498         else if(commandName == "make.biom")             {       command = new MakeBiomCommand(optionString);                }
 499         else if(commandName == "get.coremicrobiome")    {       command = new GetCoreMicroBiomeCommand(optionString);       }
 500         else if(commandName == "list.otulabels")        {       command = new ListOtuLabelsCommand(optionString);           }
 501         else if(commandName == "get.otulabels")         {       command = new GetOtuLabelsCommand(optionString);            }
 502         else if(commandName == "remove.otulabels")      {       command = new RemoveOtuLabelsCommand(optionString);         }
 503         else if(commandName == "make.contigs")          {       command = new MakeContigsCommand(optionString);             }
 504         else if(commandName == "load.logfile")          {       command = new LoadLogfileCommand(optionString);             }
 505                 else                                                                                    {       command = new NoCommand(optionString);                                          }
 506
 507                 return command;
 508         }
 509         catch(exception& e) {
 510                 m->errorOut(e, "CommandFactory", "getCommand");
 511                 exit(1);
 512         }
 513 }
 514 /***********************************************************/
 515
 516 /***********************************************************/
 517 //This function calls the appropriate command fucntions based on user input.
 518 Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
 519         try {
 520                 delete pipecommand;   //delete the old command
 521
 522         checkForRedirects(optionString);
 523
 524                 //user has opted to redirect output from dir where input files are located to some other place
 525                 if (outputDir != "") {
 526                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 527                         else { optionString += "outputdir=" + outputDir; }
 528                 }
 529
 530                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 531                 if (inputDir != "") {
 532                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 533                         else { optionString += "inputdir=" + inputDir; }
 534                 }
 535
 536                 if(commandName == "cluster")                            {       pipecommand = new ClusterCommand(optionString);                                 }
 537                 else if(commandName == "unique.seqs")                   {       pipecommand = new DeconvoluteCommand(optionString);                             }
 538                 else if(commandName == "parsimony")                             {       pipecommand = new ParsimonyCommand(optionString);                               }
 539                 else if(commandName == "help")                                  {       pipecommand = new HelpCommand(optionString);                                    }
 540                 else if(commandName == "quit")                                  {       pipecommand = new QuitCommand(optionString);                                    }
 541                 else if(commandName == "collect.single")                {       pipecommand = new CollectCommand(optionString);                                 }
 542                 else if(commandName == "collect.shared")                {       pipecommand = new CollectSharedCommand(optionString);                   }
 543                 else if(commandName == "rarefaction.single")    {       pipecommand = new RareFactCommand(optionString);                                }
 544                 else if(commandName == "rarefaction.shared")    {       pipecommand = new RareFactSharedCommand(optionString);                  }
 545                 else if(commandName == "summary.single")                {       pipecommand = new SummaryCommand(optionString);                                 }
 546                 else if(commandName == "summary.shared")                {       pipecommand = new SummarySharedCommand(optionString);                   }
 547                 else if(commandName == "unifrac.weighted")              {       pipecommand = new UnifracWeightedCommand(optionString);                 }
 548                 else if(commandName == "unifrac.unweighted")    {       pipecommand = new UnifracUnweightedCommand(optionString);               }
 549                 else if(commandName == "get.group")             {   pipecommand = new GetgroupCommand(optionString);                            }
 550                 else if(commandName == "get.label")             {   pipecommand = new GetlabelCommand(optionString);                            }
 551                 else if(commandName == "get.sabund")            {   pipecommand = new GetSAbundCommand(optionString);                           }
 552                 else if(commandName == "get.rabund")            {   pipecommand = new GetRAbundCommand(optionString);                           }
 553                 else if(commandName == "libshuff")              {   pipecommand = new LibShuffCommand(optionString);                            }
 554                 else if(commandName == "heatmap.bin")                   {   pipecommand = new HeatMapCommand(optionString);                                     }
 555                 else if(commandName == "heatmap.sim")                   {   pipecommand = new HeatMapSimCommand(optionString);                          }
 556                 else if(commandName == "filter.seqs")                   {   pipecommand = new FilterSeqsCommand(optionString);                          }
 557                 else if(commandName == "venn")                                  {   pipecommand = new VennCommand(optionString);                                        }
 558                 else if(commandName == "bin.seqs")                              {   pipecommand = new BinSeqCommand(optionString);                                      }
 559                 else if(commandName == "get.oturep")                    {   pipecommand = new GetOTURepCommand(optionString);                           }
 560                 else if(commandName == "tree.shared")                   {   pipecommand = new TreeGroupCommand(optionString);                           }
 561                 else if(commandName == "dist.shared")                   {   pipecommand = new MatrixOutputCommand(optionString);                        }
 562                 else if(commandName == "dist.seqs")                             {   pipecommand = new DistanceCommand(optionString);                            }
 563                 else if(commandName == "align.seqs")                    {   pipecommand = new AlignCommand(optionString);                                       }
 564                 else if(commandName == "summary.seqs")                  {       pipecommand = new SeqSummaryCommand(optionString);                              }
 565                 else if(commandName == "screen.seqs")                   {       pipecommand = new ScreenSeqsCommand(optionString);                              }
 566                 else if(commandName == "reverse.seqs")                  {       pipecommand = new ReverseSeqsCommand(optionString);                             }
 567                 else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
 568                 else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
 569                 else if(commandName == "shhh.flows")                    {       pipecommand = new ShhherCommand(optionString);                                  }
 570                 else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
 571                 else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
 572                 else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
 573                 else if(commandName == "merge.files")                   {       pipecommand = new MergeFileCommand(optionString);                               }
 574                 else if(commandName == "system")                                {       pipecommand = new SystemCommand(optionString);                                  }
 575                 else if(commandName == "align.check")                   {       pipecommand = new AlignCheckCommand(optionString);                              }
 576                 else if(commandName == "get.sharedseqs")                {       pipecommand = new GetSharedOTUCommand(optionString);                    }
 577                 else if(commandName == "get.otulist")                   {       pipecommand = new GetListCountCommand(optionString);                    }
 578                 else if(commandName == "hcluster")                              {       pipecommand = new HClusterCommand(optionString);                                }
 579                 else if(commandName == "classify.seqs")                 {       pipecommand = new ClassifySeqsCommand(optionString);                    }
 580                 else if(commandName == "chimera.ccode")                 {       pipecommand = new ChimeraCcodeCommand(optionString);                    }
 581                 else if(commandName == "chimera.check")                 {       pipecommand = new ChimeraCheckCommand(optionString);                    }
 582                 else if(commandName == "chimera.uchime")                {       pipecommand = new ChimeraUchimeCommand(optionString);                   }
 583                 else if(commandName == "chimera.slayer")                {       pipecommand = new ChimeraSlayerCommand(optionString);                   }
 584                 else if(commandName == "chimera.pintail")               {       pipecommand = new ChimeraPintailCommand(optionString);                  }
 585                 else if(commandName == "chimera.bellerophon")   {       pipecommand = new ChimeraBellerophonCommand(optionString);              }
 586                 else if(commandName == "phylotype")                             {       pipecommand = new PhylotypeCommand(optionString);                               }
 587                 else if(commandName == "mgcluster")                             {       pipecommand = new MGClusterCommand(optionString);                               }
 588                 else if(commandName == "pre.cluster")                   {       pipecommand = new PreClusterCommand(optionString);                              }
 589                 else if(commandName == "pcoa")                                  {       pipecommand = new PCOACommand(optionString);                                    }
 590                 else if(commandName == "pca")                                   {       pipecommand = new PCACommand(optionString);                                             }
 591                 else if(commandName == "nmds")                                  {       pipecommand = new NMDSCommand(optionString);                                    }
 592                 else if(commandName == "otu.hierarchy")                 {       pipecommand = new OtuHierarchyCommand(optionString);                    }
 593                 else if(commandName == "set.dir")                               {       pipecommand = new SetDirectoryCommand(optionString);                    }
 594                 else if(commandName == "set.logfile")                   {       pipecommand = new SetLogFileCommand(optionString);                              }
 595                 else if(commandName == "parse.list")                    {       pipecommand = new ParseListCommand(optionString);                               }
 596                 else if(commandName == "phylo.diversity")               {       pipecommand = new PhyloDiversityCommand(optionString);                  }
 597                 else if(commandName == "make.group")                    {       pipecommand = new MakeGroupCommand(optionString);                               }
 598                 else if(commandName == "chop.seqs")                             {       pipecommand = new ChopSeqsCommand(optionString);                                }
 599                 else if(commandName == "clearcut")                              {       pipecommand = new ClearcutCommand(optionString);                                }
 600                 else if(commandName == "catchall")                              {       pipecommand = new CatchAllCommand(optionString);                                }
 601                 else if(commandName == "split.abund")                   {       pipecommand = new SplitAbundCommand(optionString);                              }
 602                 else if(commandName == "cluster.split")                 {       pipecommand = new ClusterSplitCommand(optionString);                    }
 603                 else if(commandName == "classify.otu")                  {       pipecommand = new ClassifyOtuCommand(optionString);                             }
 604                 else if(commandName == "degap.seqs")                    {       pipecommand = new DegapSeqsCommand(optionString);                               }
 605                 else if(commandName == "get.relabund")                  {       pipecommand = new GetRelAbundCommand(optionString);                             }
 606                 else if(commandName == "sens.spec")                             {       pipecommand = new SensSpecCommand(optionString);                                }
 607                 else if(commandName == "seq.error")                             {       pipecommand = new SeqErrorCommand(optionString);                                }
 608                 else if(commandName == "sffinfo")                               {       pipecommand = new SffInfoCommand(optionString);                                 }
 609                 else if(commandName == "normalize.shared")              {       pipecommand = new NormalizeSharedCommand(optionString);                 }
 610                 else if(commandName == "metastats")                             {       pipecommand = new MetaStatsCommand(optionString);                               }
 611                 else if(commandName == "split.groups")                  {       pipecommand = new SplitGroupCommand(optionString);                              }
 612                 else if(commandName == "cluster.fragments")             {       pipecommand = new ClusterFragmentsCommand(optionString);                }
 613                 else if(commandName == "get.lineage")                   {       pipecommand = new GetLineageCommand(optionString);                              }
 614                 else if(commandName == "get.groups")                    {       pipecommand = new GetGroupsCommand(optionString);                               }
 615                 else if(commandName == "remove.lineage")                {       pipecommand = new RemoveLineageCommand(optionString);                   }
 616                 else if(commandName == "remove.groups")                 {       pipecommand = new RemoveGroupsCommand(optionString);                    }
 617                 else if(commandName == "get.otus")                              {       pipecommand = new GetOtusCommand(optionString);                                 }
 618                 else if(commandName == "remove.otus")                   {       pipecommand = new RemoveOtusCommand(optionString);                              }
 619                 else if(commandName == "fastq.info")                    {       pipecommand = new ParseFastaQCommand(optionString);                             }
 620                 else if(commandName == "deunique.seqs")                 {       pipecommand = new DeUniqueSeqsCommand(optionString);                    }
 621                 else if(commandName == "pairwise.seqs")                 {       pipecommand = new PairwiseSeqsCommand(optionString);                    }
 622                 else if(commandName == "cluster.classic")               {       pipecommand = new ClusterDoturCommand(optionString);                    }
 623                 else if(commandName == "sub.sample")                    {       pipecommand = new SubSampleCommand(optionString);                               }
 624                 else if(commandName == "indicator")                             {       pipecommand = new IndicatorCommand(optionString);                               }
 625                 else if(commandName == "consensus.seqs")                {       pipecommand = new ConsensusSeqsCommand(optionString);                   }
 626                 else if(commandName == "corr.axes")                             {       pipecommand = new CorrAxesCommand(optionString);                                }
 627                 else if(commandName == "remove.rare")                   {       pipecommand = new RemoveRareCommand(optionString);                              }
 628                 else if(commandName == "merge.groups")                  {       pipecommand = new MergeGroupsCommand(optionString);                             }
 629                 else if(commandName == "amova")                                 {       pipecommand = new AmovaCommand(optionString);                                   }
 630                 else if(commandName == "homova")                                {       pipecommand = new HomovaCommand(optionString);                                  }
 631                 else if(commandName == "mantel")                                {       pipecommand = new MantelCommand(optionString);                                  }
 632                 else if(commandName == "anosim")                                {       pipecommand = new AnosimCommand(optionString);                                  }
 633                 else if(commandName == "make.fastq")                    {       pipecommand = new MakeFastQCommand(optionString);                               }
 634                 else if(commandName == "get.current")                   {       pipecommand = new GetCurrentCommand(optionString);                              }
 635                 else if(commandName == "set.current")                   {       pipecommand = new SetCurrentCommand(optionString);                              }
 636                 else if(commandName == "make.shared")                   {       pipecommand = new SharedCommand(optionString);                                  }
 637                 else if(commandName == "get.commandinfo")               {       pipecommand = new GetCommandInfoCommand(optionString);                  }
 638                 else if(commandName == "deunique.tree")                 {       pipecommand = new DeuniqueTreeCommand(optionString);                    }
 639                 else if(commandName == "count.seqs")                    {       pipecommand = new CountSeqsCommand(optionString);                               }
 640                 else if(commandName == "count.groups")                  {       pipecommand = new CountGroupsCommand(optionString);                             }
 641                 else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
 642                 else if(commandName == "summary.tax")                   {       pipecommand = new SummaryTaxCommand(optionString);                              }
 643                 else if(commandName == "summary.qual")                  {       pipecommand = new SummaryQualCommand(optionString);                             }
 644                 else if(commandName == "chimera.perseus")               {       pipecommand = new ChimeraPerseusCommand(optionString);                  }
 645                 else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhhSeqsCommand(optionString);                                }
 646                 else if(commandName == "otu.association")               {       pipecommand = new OTUAssociationCommand(optionString);                  }
 647         else if(commandName == "sort.seqs")             {       pipecommand = new SortSeqsCommand(optionString);                }
 648         else if(commandName == "classify.tree")         {       pipecommand = new ClassifyTreeCommand(optionString);            }
 649         else if(commandName == "cooccurrence")          {       pipecommand = new CooccurrenceCommand(optionString);            }
 650         else if(commandName == "pcr.seqs")              {       pipecommand = new PcrSeqsCommand(optionString);                 }
 651         else if(commandName == "create.database")       {       pipecommand = new CreateDatabaseCommand(optionString);          }
 652         else if(commandName == "make.biom")             {       pipecommand = new MakeBiomCommand(optionString);                }
 653         else if(commandName == "get.coremicrobiome")    {       pipecommand = new GetCoreMicroBiomeCommand(optionString);       }
 654         else if(commandName == "list.otulabels")        {       pipecommand = new ListOtuLabelsCommand(optionString);           }
 655         else if(commandName == "get.otulabels")         {       pipecommand = new GetOtuLabelsCommand(optionString);            }
 656         else if(commandName == "remove.otulabels")      {       pipecommand = new RemoveOtuLabelsCommand(optionString);         }
 657         else if(commandName == "make.contigs")          {       pipecommand = new MakeContigsCommand(optionString);             }
 658         else if(commandName == "load.logfile")          {       pipecommand = new LoadLogfileCommand(optionString);             }
 659                 else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 660
 661                 return pipecommand;
 662         }
 663         catch(exception& e) {
 664                 m->errorOut(e, "CommandFactory", "getCommand");
 665                 exit(1);
 666         }
 667 }
 668 /***********************************************************/
 669
 670 /***********************************************************/
 671 //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
 672 Command* CommandFactory::getCommand(string commandName){
 673         try {
 674                 delete shellcommand;   //delete the old command
 675
 676                 if(commandName == "cluster")                            {       shellcommand = new ClusterCommand();                            }
 677                 else if(commandName == "unique.seqs")                   {       shellcommand = new DeconvoluteCommand();                        }
 678                 else if(commandName == "parsimony")                             {       shellcommand = new ParsimonyCommand();                          }
 679                 else if(commandName == "help")                                  {       shellcommand = new HelpCommand();                                       }
 680                 else if(commandName == "quit")                                  {       shellcommand = new QuitCommand();                                       }
 681                 else if(commandName == "collect.single")                {       shellcommand = new CollectCommand();                            }
 682                 else if(commandName == "collect.shared")                {       shellcommand = new CollectSharedCommand();                      }
 683                 else if(commandName == "rarefaction.single")    {       shellcommand = new RareFactCommand();                           }
 684                 else if(commandName == "rarefaction.shared")    {       shellcommand = new RareFactSharedCommand();                     }
 685                 else if(commandName == "summary.single")                {       shellcommand = new SummaryCommand();                            }
 686                 else if(commandName == "summary.shared")                {       shellcommand = new SummarySharedCommand();                      }
 687                 else if(commandName == "unifrac.weighted")              {       shellcommand = new UnifracWeightedCommand();            }
 688                 else if(commandName == "unifrac.unweighted")    {       shellcommand = new UnifracUnweightedCommand();          }
 689                 else if(commandName == "get.group")             {   shellcommand = new GetgroupCommand();                               }
 690                 else if(commandName == "get.label")             {   shellcommand = new GetlabelCommand();                               }
 691                 else if(commandName == "get.sabund")            {   shellcommand = new GetSAbundCommand();                              }
 692                 else if(commandName == "get.rabund")            {   shellcommand = new GetRAbundCommand();                              }
 693                 else if(commandName == "libshuff")              {   shellcommand = new LibShuffCommand();                               }
 694                 else if(commandName == "heatmap.bin")                   {   shellcommand = new HeatMapCommand();                                }
 695                 else if(commandName == "heatmap.sim")                   {   shellcommand = new HeatMapSimCommand();                             }
 696                 else if(commandName == "filter.seqs")                   {   shellcommand = new FilterSeqsCommand();                             }
 697                 else if(commandName == "venn")                                  {   shellcommand = new VennCommand();                                   }
 698                 else if(commandName == "bin.seqs")                              {   shellcommand = new BinSeqCommand();                                 }
 699                 else if(commandName == "get.oturep")                    {   shellcommand = new GetOTURepCommand();                              }
 700                 else if(commandName == "tree.shared")                   {   shellcommand = new TreeGroupCommand();                              }
 701                 else if(commandName == "dist.shared")                   {   shellcommand = new MatrixOutputCommand();                   }
 702                 else if(commandName == "dist.seqs")                             {   shellcommand = new DistanceCommand();                               }
 703                 else if(commandName == "align.seqs")                    {   shellcommand = new AlignCommand();                                  }
 704                 else if(commandName == "summary.seqs")                  {       shellcommand = new SeqSummaryCommand();                         }
 705                 else if(commandName == "screen.seqs")                   {       shellcommand = new ScreenSeqsCommand();                         }
 706                 else if(commandName == "reverse.seqs")                  {       shellcommand = new ReverseSeqsCommand();                        }
 707                 else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
 708                 else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
 709                 else if(commandName == "shhh.flows")                    {       shellcommand = new ShhherCommand();                                     }
 710                 else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
 711                 else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
 712                 else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }
 713                 else if(commandName == "merge.files")                   {       shellcommand = new MergeFileCommand();                          }
 714                 else if(commandName == "system")                                {       shellcommand = new SystemCommand();                                     }
 715                 else if(commandName == "align.check")                   {       shellcommand = new AlignCheckCommand();                         }
 716                 else if(commandName == "get.sharedseqs")                {       shellcommand = new GetSharedOTUCommand();                       }
 717                 else if(commandName == "get.otulist")                   {       shellcommand = new GetListCountCommand();                       }
 718                 else if(commandName == "hcluster")                              {       shellcommand = new HClusterCommand();                           }
 719                 else if(commandName == "classify.seqs")                 {       shellcommand = new ClassifySeqsCommand();                       }
 720                 else if(commandName == "chimera.ccode")                 {       shellcommand = new ChimeraCcodeCommand();                       }
 721                 else if(commandName == "chimera.check")                 {       shellcommand = new ChimeraCheckCommand();                       }
 722                 else if(commandName == "chimera.slayer")                {       shellcommand = new ChimeraSlayerCommand();                      }
 723                 else if(commandName == "chimera.uchime")                {       shellcommand = new ChimeraUchimeCommand();                      }
 724                 else if(commandName == "chimera.pintail")               {       shellcommand = new ChimeraPintailCommand();                     }
 725                 else if(commandName == "chimera.bellerophon")   {       shellcommand = new ChimeraBellerophonCommand();         }
 726                 else if(commandName == "phylotype")                             {       shellcommand = new PhylotypeCommand();                          }
 727                 else if(commandName == "mgcluster")                             {       shellcommand = new MGClusterCommand();                          }
 728                 else if(commandName == "pre.cluster")                   {       shellcommand = new PreClusterCommand();                         }
 729                 else if(commandName == "pcoa")                                  {       shellcommand = new PCOACommand();                                       }
 730                 else if(commandName == "pca")                                   {       shellcommand = new PCACommand();                                        }
 731                 else if(commandName == "nmds")                                  {       shellcommand = new NMDSCommand();                                       }
 732                 else if(commandName == "otu.hierarchy")                 {       shellcommand = new OtuHierarchyCommand();                       }
 733                 else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
 734                 else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }
 735                 else if(commandName == "parse.list")                    {       shellcommand = new ParseListCommand();                          }
 736                 else if(commandName == "phylo.diversity")               {       shellcommand = new PhyloDiversityCommand();                     }
 737                 else if(commandName == "make.group")                    {       shellcommand = new MakeGroupCommand();                          }
 738                 else if(commandName == "chop.seqs")                             {       shellcommand = new ChopSeqsCommand();                           }
 739                 else if(commandName == "clearcut")                              {       shellcommand = new ClearcutCommand();                           }
 740                 else if(commandName == "catchall")                              {       shellcommand = new CatchAllCommand();                           }
 741                 else if(commandName == "split.abund")                   {       shellcommand = new SplitAbundCommand();                         }
 742                 else if(commandName == "cluster.split")                 {       shellcommand = new ClusterSplitCommand();                       }
 743                 else if(commandName == "classify.otu")                  {       shellcommand = new ClassifyOtuCommand();                        }
 744                 else if(commandName == "degap.seqs")                    {       shellcommand = new DegapSeqsCommand();                          }
 745                 else if(commandName == "get.relabund")                  {       shellcommand = new GetRelAbundCommand();                        }
 746                 else if(commandName == "sens.spec")                             {       shellcommand = new SensSpecCommand();                           }
 747                 else if(commandName == "seq.error")                             {       shellcommand = new SeqErrorCommand();                           }
 748                 else if(commandName == "sffinfo")                               {       shellcommand = new SffInfoCommand();                            }
 749                 else if(commandName == "normalize.shared")              {       shellcommand = new NormalizeSharedCommand();            }
 750                 else if(commandName == "metastats")                             {       shellcommand = new MetaStatsCommand();                          }
 751                 else if(commandName == "split.groups")                  {       shellcommand = new SplitGroupCommand();                         }
 752                 else if(commandName == "cluster.fragments")             {       shellcommand = new ClusterFragmentsCommand();           }
 753                 else if(commandName == "get.lineage")                   {       shellcommand = new GetLineageCommand();                         }
 754                 else if(commandName == "remove.lineage")                {       shellcommand = new RemoveLineageCommand();                      }
 755                 else if(commandName == "get.groups")                    {       shellcommand = new GetGroupsCommand();                          }
 756                 else if(commandName == "remove.groups")                 {       shellcommand = new RemoveGroupsCommand();                       }
 757                 else if(commandName == "get.otus")                              {       shellcommand = new GetOtusCommand();                            }
 758                 else if(commandName == "remove.otus")                   {       shellcommand = new RemoveOtusCommand();                         }
 759                 else if(commandName == "fastq.info")                    {       shellcommand = new ParseFastaQCommand();                        }
 760                 else if(commandName == "deunique.seqs")                 {       shellcommand = new DeUniqueSeqsCommand();                       }
 761                 else if(commandName == "pairwise.seqs")                 {       shellcommand = new PairwiseSeqsCommand();                       }
 762                 else if(commandName == "cluster.classic")               {       shellcommand = new ClusterDoturCommand();                       }
 763                 else if(commandName == "sub.sample")                    {       shellcommand = new SubSampleCommand();                          }
 764                 else if(commandName == "indicator")                             {       shellcommand = new IndicatorCommand();                          }
 765                 else if(commandName == "consensus.seqs")                {       shellcommand = new ConsensusSeqsCommand();                      }
 766                 else if(commandName == "corr.axes")                             {       shellcommand = new CorrAxesCommand();                           }
 767                 else if(commandName == "remove.rare")                   {       shellcommand = new RemoveRareCommand();                         }
 768                 else if(commandName == "merge.groups")                  {       shellcommand = new MergeGroupsCommand();                        }
 769                 else if(commandName == "amova")                                 {       shellcommand = new AmovaCommand();                                      }
 770                 else if(commandName == "homova")                                {       shellcommand = new HomovaCommand();                                     }
 771                 else if(commandName == "mantel")                                {       shellcommand = new MantelCommand();                                     }
 772                 else if(commandName == "anosim")                                {       shellcommand = new AnosimCommand();                                     }
 773                 else if(commandName == "make.fastq")                    {       shellcommand = new MakeFastQCommand();                          }
 774                 else if(commandName == "get.current")                   {       shellcommand = new GetCurrentCommand();                         }
 775                 else if(commandName == "set.current")                   {       shellcommand = new SetCurrentCommand();                         }
 776                 else if(commandName == "make.shared")                   {       shellcommand = new SharedCommand();                                     }
 777                 else if(commandName == "get.commandinfo")               {       shellcommand = new GetCommandInfoCommand();                     }
 778                 else if(commandName == "deunique.tree")                 {       shellcommand = new DeuniqueTreeCommand();                       }
 779                 else if(commandName == "count.seqs")                    {       shellcommand = new CountSeqsCommand();                          }
 780                 else if(commandName == "count.groups")                  {       shellcommand = new CountGroupsCommand();                        }
 781                 else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
 782                 else if(commandName == "summary.tax")                   {       shellcommand = new SummaryTaxCommand();                         }
 783                 else if(commandName == "summary.qual")                  {       shellcommand = new SummaryQualCommand();                        }
 784                 else if(commandName == "chimera.perseus")               {       shellcommand = new ChimeraPerseusCommand();                     }
 785                 else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhhSeqsCommand();                           }
 786                 else if(commandName == "otu.association")               {       shellcommand = new OTUAssociationCommand();                     }
 787         else if(commandName == "sort.seqs")             {       shellcommand = new SortSeqsCommand();               }
 788         else if(commandName == "classify.tree")         {       shellcommand = new ClassifyTreeCommand();           }
 789         else if(commandName == "cooccurrence")          {       shellcommand = new CooccurrenceCommand();           }
 790         else if(commandName == "pcr.seqs")              {       shellcommand = new PcrSeqsCommand();                }
 791         else if(commandName == "create.database")       {       shellcommand = new CreateDatabaseCommand();         }
 792         else if(commandName == "make.biom")             {       shellcommand = new MakeBiomCommand();               }
 793         else if(commandName == "get.coremicrobiome")    {       shellcommand = new GetCoreMicroBiomeCommand();      }
 794         else if(commandName == "list.otulabels")        {       shellcommand = new ListOtuLabelsCommand();          }
 795         else if(commandName == "get.otulabels")         {       shellcommand = new GetOtuLabelsCommand();           }
 796         else if(commandName == "remove.otulabels")      {       shellcommand = new RemoveOtuLabelsCommand();        }
 797         else if(commandName == "make.contigs")          {       shellcommand = new MakeContigsCommand();            }
 798         else if(commandName == "load.logfile")          {       shellcommand = new LoadLogfileCommand();            }
 799                 else                                                                                    {       shellcommand = new NoCommand();                                         }
 800
 801                 return shellcommand;
 802         }
 803         catch(exception& e) {
 804                 m->errorOut(e, "CommandFactory", "getCommand");
 805                 exit(1);
 806         }
 807 }
 808 /***********************************************************
 809 //This function is used to interrupt a command
 810 Command* CommandFactory::getCommand(){
 811         try {
 812                 delete command;   //delete the old command
 813
 814                 string s = "";
 815             command = new NoCommand(s);
 816
 817                 return command;
 818         }
 819         catch(exception& e) {
 820                 m->errorOut(e, "CommandFactory", "getCommand");
 821                 exit(1);
 822         }
 823 }
 824 ***********************************************************************/
 825 bool CommandFactory::isValidCommand(string command) {
 826         try {
 827
 828                 //is the command in the map
 829                 if ((commands.find(command)) != (commands.end())) {
 830                         return true;
 831                 }else{
 832                         m->mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
 833                         for (it = commands.begin(); it != commands.end(); it++) {
 834                                 m->mothurOut(it->first + ", ");
 835                         }
 836                         m->mothurOutEndLine();
 837                         return false;
 838                 }
 839
 840         }
 841         catch(exception& e) {
 842                 m->errorOut(e, "CommandFactory", "isValidCommand");
 843                 exit(1);
 844         }
 845 }
 846 /***********************************************************************/
 847 bool CommandFactory::isValidCommand(string command, string noError) {
 848         try {
 849
 850                 //is the command in the map
 851                 if ((commands.find(command)) != (commands.end())) {
 852                         return true;
 853                 }else{
 854                         return false;
 855                 }
 856
 857         }
 858         catch(exception& e) {
 859                 m->errorOut(e, "CommandFactory", "isValidCommand");
 860                 exit(1);
 861         }
 862 }
 863 /***********************************************************************/
 864 void CommandFactory::printCommands(ostream& out) {
 865         try {
 866                 out << "Valid commands are: ";
 867                 for (it = commands.begin(); it != commands.end(); it++) {
 868                         out << it->first << ",";
 869                 }
 870                 out << endl;
 871         }
 872         catch(exception& e) {
 873                 m->errorOut(e, "CommandFactory", "printCommands");
 874                 exit(1);
 875         }
 876 }
 877 /***********************************************************************/
 878
 879
 880
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