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 "readdistcommand.h"
  12 #include "readtreecommand.h"
  13 #include "readotucommand.h"
  14 #include "clustercommand.h"
  15 #include "collectcommand.h"
  16 #include "collectsharedcommand.h"
  17 #include "getgroupcommand.h"
  18 #include "getlabelcommand.h"
  19 #include "rarefactcommand.h"
  20 #include "summarycommand.h"
  21 #include "summarysharedcommand.h"
  22 #include "rarefactsharedcommand.h"
  23 #include "quitcommand.h"
  24 #include "helpcommand.h"
  25 #include "commandfactory.hpp"
  26 #include "deconvolutecommand.h"
  27 #include "parsimonycommand.h"
  28 #include "unifracunweightedcommand.h"
  29 #include "unifracweightedcommand.h"
  30 #include "libshuffcommand.h"
  31 #include "heatmapcommand.h"
  32 #include "heatmapsimcommand.h"
  33 #include "filterseqscommand.h"
  34 #include "venncommand.h"
  35 #include "nocommands.h"
  36 #include "binsequencecommand.h"
  37 #include "getoturepcommand.h"
  38 #include "treegroupscommand.h"
  39 #include "bootstrapsharedcommand.h"
  40 //#include "consensuscommand.h"
  41 #include "distancecommand.h"
  42 #include "aligncommand.h"
  43 #include "matrixoutputcommand.h"
  44 #include "getsabundcommand.h"
  45 #include "getrabundcommand.h"
  46 #include "seqsummarycommand.h"
  47 #include "screenseqscommand.h"
  48 #include "reversecommand.h"
  49 #include "trimseqscommand.h"
  50 #include "mergefilecommand.h"
  51 #include "listseqscommand.h"
  52 #include "getseqscommand.h"
  53 #include "removeseqscommand.h"
  54 #include "systemcommand.h"
  55 #include "secondarystructurecommand.h"
  56 #include "getsharedotucommand.h"
  57 #include "getlistcountcommand.h"
  58 #include "hclustercommand.h"
  59 #include "classifyseqscommand.h"
  60 #include "phylotypecommand.h"
  61 #include "mgclustercommand.h"
  62 #include "preclustercommand.h"
  63 #include "pcoacommand.h"
  64 #include "otuhierarchycommand.h"
  65 #include "setdircommand.h"
  66 #include "parselistscommand.h"
  67 #include "chimeraccodecommand.h"
  68 #include "chimeracheckcommand.h"
  69 #include "chimeraslayercommand.h"
  70 #include "chimerapintailcommand.h"
  71 #include "chimerabellerophoncommand.h"
  72 #include "chimerauchimecommand.h"
  73 #include "setlogfilecommand.h"
  74 #include "phylodiversitycommand.h"
  75 #include "makegroupcommand.h"
  76 #include "chopseqscommand.h"
  77 #include "clearcutcommand.h"
  78 #include "catchallcommand.h"
  79 #include "splitabundcommand.h"
  80 #include "clustersplitcommand.h"
  81 #include "classifyotucommand.h"
  82 #include "degapseqscommand.h"
  83 #include "getrelabundcommand.h"
  84 #include "sensspeccommand.h"
  85 #include "sffinfocommand.h"
  86 #include "seqerrorcommand.h"
  87 #include "normalizesharedcommand.h"
  88 #include "metastatscommand.h"
  89 #include "splitgroupscommand.h"
  90 #include "clusterfragmentscommand.h"
  91 #include "getlineagecommand.h"
  92 #include "removelineagecommand.h"
  93 #include "parsefastaqcommand.h"
  94 #include "pipelinepdscommand.h"
  95 #include "deuniqueseqscommand.h"
  96 #include "pairwiseseqscommand.h"
  97 #include "clusterdoturcommand.h"
  98 #include "subsamplecommand.h"
  99 #include "removegroupscommand.h"
 100 #include "getgroupscommand.h"
 101 #include "getotuscommand.h"
 102 #include "removeotuscommand.h"
 103 #include "indicatorcommand.h"
 104 #include "consensusseqscommand.h"
 105 #include "trimflowscommand.h"
 106 #include "corraxescommand.h"
 107 #include "shhhercommand.h"
 108 #include "pcacommand.h"
 109 #include "nmdscommand.h"
 110 #include "removerarecommand.h"
 111 #include "mergegroupscommand.h"
 112 #include "amovacommand.h"
 113 #include "homovacommand.h"
 114 #include "mantelcommand.h"
 115 #include "makefastqcommand.h"
 116 #include "anosimcommand.h"
 117 #include "getcurrentcommand.h"
 118 #include "setcurrentcommand.h"
 119 #include "sharedcommand.h"
 120 #include "getcommandinfocommand.h"
 121 #include "deuniquetreecommand.h"
 122 #include "countseqscommand.h"
 123 #include "countgroupscommand.h"
 124 #include "clearmemorycommand.h"
 125 #include "summarytaxcommand.h"
 126 #include "chimeraperseuscommand.h"
 127 #include "shhhseqscommand.h"
 128 #include "summaryqualcommand.h"
 129
 130 /*******************************************************/
 131
 132 /******************************************************/
 133 CommandFactory* CommandFactory::getInstance() {
 134         if( _uniqueInstance == 0) {
 135                 _uniqueInstance = new CommandFactory();
 136         }
 137         return _uniqueInstance;
 138 }
 139 /***********************************************************/
 140
 141 /***********************************************************/
 142 //note: This class is resposible for knowing which commands are mpiEnabled,
 143 //If a command is not enabled only process 0 will execute the command.
 144 //This avoids redundant outputs on pieces of code we have not paralellized.
 145 //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.
 146 //example:  commands["dist.seqs"] = "MPIEnabled";
 147
 148 CommandFactory::CommandFactory(){
 149         string s = "";
 150         m = MothurOut::getInstance();
 151
 152         command = new NoCommand(s);
 153         shellcommand = new NoCommand(s);
 154         pipecommand = new NoCommand(s);
 155
 156         outputDir = ""; inputDir = "";
 157         logFileName = "";
 158         append = false;
 159
 160         //initialize list of valid commands
 161         commands["read.dist"]                   = "read.dist";
 162         commands["read.otu"]                    = "read.otu";
 163         commands["read.tree"]                   = "read.tree";
 164         commands["make.shared"]                 = "make.shared";
 165         commands["bin.seqs"]                    = "bin.seqs";
 166         commands["get.oturep"]                  = "get.oturep";
 167         commands["cluster"]                             = "cluster";
 168         commands["unique.seqs"]                 = "unique.seqs";
 169         commands["dist.shared"]                 = "dist.shared";
 170         commands["collect.single"]              = "collect.single";
 171         commands["collect.shared"]              = "collect.shared";
 172         commands["rarefaction.single"]  = "rarefaction.single";
 173         commands["rarefaction.shared"]  = "rarefaction.shared";
 174         commands["summary.single"]              = "summary.single";
 175         commands["summary.shared"]              = "summary.shared";
 176         commands["parsimony"]                   = "parsimony";
 177         commands["unifrac.weighted"]    = "unifrac.weighted";
 178         commands["unifrac.unweighted"]  = "unifrac.unweighted";
 179         commands["libshuff"]                    = "libshuff";
 180         commands["tree.shared"]                 = "tree.shared";
 181         commands["heatmap.bin"]                 = "heatmap.bin";
 182         commands["heatmap.sim"]                 = "heatmap.sim";
 183         commands["venn"]                                = "venn";
 184         commands["get.group"]           = "get.group";
 185         commands["get.label"]           = "get.label";
 186         commands["get.sabund"]          = "get.sabund";
 187         commands["get.rabund"]          = "get.rabund";
 188         commands["bootstrap.shared"]    = "bootstrap.shared";
 189         //commands["consensus"]                 = "consensus";
 190         commands["help"]                                = "help";
 191         commands["reverse.seqs"]                = "reverse.seqs";
 192         commands["trim.seqs"]                   = "trim.seqs";
 193         commands["trim.flows"]                  = "trim.flows";
 194         commands["list.seqs"]                   = "list.seqs";
 195         commands["get.seqs"]                    = "get.seqs";
 196         commands["remove.seqs"]                 = "remove.seqs";
 197         commands["system"]                              = "system";
 198         commands["align.check"]                 = "align.check";
 199         commands["get.sharedseqs"]              = "get.sharedseqs";
 200         commands["get.otulist"]                 = "get.otulist";
 201         commands["hcluster"]                    = "hcluster";
 202         commands["phylotype"]                   = "phylotype";
 203         commands["mgcluster"]                   = "mgcluster";
 204         commands["pre.cluster"]                 = "pre.cluster";
 205         commands["pcoa"]                                = "pcoa";
 206         commands["otu.hierarchy"]               = "otu.hierarchy";
 207         commands["set.dir"]                             = "MPIEnabled";
 208         commands["merge.files"]                 = "merge.files";
 209         commands["parse.list"]                  = "parse.list";
 210         commands["set.logfile"]                 = "set.logfile";
 211         commands["phylo.diversity"]             = "phylo.diversity";
 212         commands["make.group"]                  = "make.group";
 213         commands["chop.seqs"]                   = "chop.seqs";
 214         commands["clearcut"]                    = "clearcut";
 215         commands["catchall"]                    = "catchall";
 216         commands["split.abund"]                 = "split.abund";
 217         commands["classify.otu"]                = "classify.otu";
 218         commands["degap.seqs"]                  = "degap.seqs";
 219         commands["get.relabund"]                = "get.relabund";
 220         commands["sffinfo"]                             = "sffinfo";
 221         commands["normalize.shared"]    = "normalize.shared";
 222         commands["metastats"]                   = "metastats";
 223         commands["split.groups"]                = "split.groups";
 224         commands["cluster.fragments"]   = "cluster.fragments";
 225         commands["get.lineage"]                 = "get.lineage";
 226         commands["remove.lineage"]              = "remove.lineage";
 227         commands["fastq.info"]                  = "fastq.info";
 228         commands["deunique.seqs"]               = "deunique.seqs";
 229         commands["cluster.classic"]             = "cluster.classic";
 230         commands["sub.sample"]                  = "sub.sample";
 231         commands["remove.groups"]               = "remove.groups";
 232         commands["get.groups"]                  = "get.groups";
 233         commands["get.otus"]                    = "get.otus";
 234         commands["remove.otus"]                 = "remove.otus";
 235         commands["indicator"]                   = "indicator";
 236         commands["consensus.seqs"]              = "consensus.seqs";
 237         commands["corr.axes"]                   = "corr.axes";
 238         commands["pca"]                                 = "pca";
 239         commands["nmds"]                                = "nmds";
 240         commands["remove.rare"]                 = "remove.rare";
 241         commands["amova"]                               = "amova";
 242         commands["homova"]                              = "homova";
 243         commands["mantel"]                              = "mantel";
 244         commands["anosim"]                              = "anosim";
 245         commands["make.fastq"]                  = "make.fastq";
 246         commands["merge.groups"]                = "merge.groups";
 247         commands["get.current"]                 = "MPIEnabled";
 248         commands["set.current"]                 = "MPIEnabled";
 249         commands["get.commandinfo"]             = "get.commandinfo";
 250         commands["deunique.tree"]               = "deunique.tree";
 251         commands["count.seqs"]                  = "count.seqs";
 252         commands["count.groups"]                = "count.groups";
 253         commands["clear.memory"]                = "clear.memory";
 254         commands["pairwise.seqs"]               = "MPIEnabled";
 255         commands["pipeline.pds"]                = "MPIEnabled";
 256         commands["classify.seqs"]               = "MPIEnabled";
 257         commands["dist.seqs"]                   = "MPIEnabled";
 258         commands["filter.seqs"]                 = "MPIEnabled";
 259         commands["align.seqs"]                  = "MPIEnabled";
 260         commands["chimera.ccode"]               = "MPIEnabled";
 261         commands["chimera.check"]               = "MPIEnabled";
 262         commands["chimera.slayer"]              = "MPIEnabled";
 263         commands["chimera.uchime"]              = "chimera.uchime";
 264         commands["chimera.perseus"]             = "chimera.perseus";
 265         commands["chimera.pintail"]             = "MPIEnabled";
 266         commands["chimera.bellerophon"] = "MPIEnabled";
 267         commands["screen.seqs"]                 = "MPIEnabled";
 268         commands["summary.seqs"]                = "MPIEnabled";
 269         commands["cluster.split"]               = "MPIEnabled";
 270         commands["shhh.flows"]                  = "MPIEnabled";
 271         commands["sens.spec"]                   = "sens.spec";
 272         commands["seq.error"]                   = "seq.error";
 273         commands["summary.tax"]                 = "summary.tax";
 274         commands["summary.qual"]                = "summary.qual";
 275         commands["shhh.seqs"]                   = "shhh.seqs";
 276         commands["quit"]                                = "MPIEnabled";
 277
 278 }
 279 /***********************************************************/
 280
 281 /***********************************************************/
 282 bool CommandFactory::MPIEnabled(string commandName) {
 283         bool mpi = false;
 284         it = commands.find(commandName);
 285         if (it != commands.end()) {
 286                 if (it->second == "MPIEnabled") { return true; }
 287         }
 288         return mpi;
 289 }
 290 /***********************************************************/
 291
 292 /***********************************************************/
 293 CommandFactory::~CommandFactory(){
 294         _uniqueInstance = 0;
 295         delete command;
 296         delete shellcommand;
 297         delete pipecommand;
 298 }
 299
 300 /***********************************************************/
 301
 302 /***********************************************************/
 303 //This function calls the appropriate command fucntions based on user input.
 304 Command* CommandFactory::getCommand(string commandName, string optionString){
 305         try {
 306                 delete command;   //delete the old command
 307
 308                 //user has opted to redirect output from dir where input files are located to some other place
 309                 if (outputDir != "") {
 310                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 311                         else { optionString += "outputdir=" + outputDir; }
 312                 }
 313
 314                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 315                 if (inputDir != "") {
 316                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 317                         else { optionString += "inputdir=" + inputDir; }
 318                 }
 319
 320                 if(commandName == "read.dist")                                  {       command = new ReadDistCommand(optionString);                            }
 321                 else if(commandName == "read.otu")                              {       command = new ReadOtuCommand(optionString);                                     }
 322                 else if(commandName == "read.tree")                             {       command = new ReadTreeCommand(optionString);                            }
 323                 else if(commandName == "cluster")                               {       command = new ClusterCommand(optionString);                                     }
 324                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand(optionString);                         }
 325                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand(optionString);                           }
 326                 else if(commandName == "help")                                  {       command = new HelpCommand(optionString);                                        }
 327                 else if(commandName == "quit")                                  {       command = new QuitCommand(optionString);                                        }
 328                 else if(commandName == "collect.single")                {       command = new CollectCommand(optionString);                                     }
 329                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand(optionString);                       }
 330                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand(optionString);                            }
 331                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand(optionString);                      }
 332                 else if(commandName == "summary.single")                {       command = new SummaryCommand(optionString);                                     }
 333                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand(optionString);                       }
 334                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand(optionString);                     }
 335                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);           }
 336                 else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                                }
 337                 else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                                }
 338                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                               }
 339                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                               }
 340                 else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                                }
 341                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand(optionString);                                 }
 342                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand(optionString);                              }
 343                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand(optionString);                              }
 344                 else if(commandName == "venn")                                  {   command = new VennCommand(optionString);                                    }
 345                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand(optionString);                                  }
 346                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                               }
 347                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                               }
 348                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);                    }
 349                 else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                              }
 350                 else if(commandName == "consensus")                             {   command = new ConcensusCommand(optionString);                               }
 351                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                                }
 352                 else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                                   }
 353                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                          }
 354                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                          }
 355                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
 356                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
 357                 else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
 358                 else if(commandName == "shhh.flows")                    {       command = new ShhherCommand(optionString);                                      }
 359                 else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
 360                 else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
 361                 else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
 362                 else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                           }
 363                 else if(commandName == "system")                                {       command = new SystemCommand(optionString);                                      }
 364                 else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                          }
 365                 else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                        }
 366                 else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                        }
 367                 else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                            }
 368                 else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                        }
 369                 else if(commandName == "chimera.ccode")                 {       command = new ChimeraCcodeCommand(optionString);                        }
 370                 else if(commandName == "chimera.check")                 {       command = new ChimeraCheckCommand(optionString);                        }
 371                 else if(commandName == "chimera.slayer")                {       command = new ChimeraSlayerCommand(optionString);                       }
 372                 else if(commandName == "chimera.uchime")                {       command = new ChimeraUchimeCommand(optionString);                       }
 373                 else if(commandName == "chimera.pintail")               {       command = new ChimeraPintailCommand(optionString);                      }
 374                 else if(commandName == "chimera.bellerophon")   {       command = new ChimeraBellerophonCommand(optionString);          }
 375                 else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
 376                 else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                           }
 377                 else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                          }
 378                 else if(commandName == "pcoa")                                  {       command = new PCOACommand(optionString);                                        }
 379                 else if(commandName == "pca")                                   {       command = new PCACommand(optionString);                                         }
 380                 else if(commandName == "nmds")                                  {       command = new NMDSCommand(optionString);                                        }
 381                 else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
 382                 else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
 383                 else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
 384                 else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
 385                 else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
 386                 else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
 387                 else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
 388                 else if(commandName == "clearcut")                              {       command = new ClearcutCommand(optionString);                            }
 389                 else if(commandName == "catchall")                              {       command = new CatchAllCommand(optionString);                            }
 390                 else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
 391                 else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
 392                 else if(commandName == "classify.otu")                  {       command = new ClassifyOtuCommand(optionString);                         }
 393                 else if(commandName == "degap.seqs")                    {       command = new DegapSeqsCommand(optionString);                           }
 394                 else if(commandName == "get.relabund")                  {       command = new GetRelAbundCommand(optionString);                         }
 395                 else if(commandName == "sens.spec")                             {       command = new SensSpecCommand(optionString);                            }
 396                 else if(commandName == "seq.error")                             {       command = new SeqErrorCommand(optionString);                            }
 397                 else if(commandName == "sffinfo")                               {       command = new SffInfoCommand(optionString);                                     }
 398                 else if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
 399                 else if(commandName == "metastats")                             {       command = new MetaStatsCommand(optionString);                           }
 400                 else if(commandName == "split.groups")                  {       command = new SplitGroupCommand(optionString);                          }
 401                 else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
 402                 else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
 403                 else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
 404                 else if(commandName == "get.groups")                    {       command = new GetGroupsCommand(optionString);                           }
 405                 else if(commandName == "remove.groups")                 {       command = new RemoveGroupsCommand(optionString);                        }
 406                 else if(commandName == "get.otus")                              {       command = new GetOtusCommand(optionString);                                     }
 407                 else if(commandName == "remove.otus")                   {       command = new RemoveOtusCommand(optionString);                          }
 408                 else if(commandName == "fastq.info")                    {       command = new ParseFastaQCommand(optionString);                         }
 409                 else if(commandName == "pipeline.pds")                  {       command = new PipelineCommand(optionString);                            }
 410                 else if(commandName == "deunique.seqs")                 {       command = new DeUniqueSeqsCommand(optionString);                        }
 411                 else if(commandName == "pairwise.seqs")                 {       command = new PairwiseSeqsCommand(optionString);                        }
 412                 else if(commandName == "cluster.classic")               {       command = new ClusterDoturCommand(optionString);                        }
 413                 else if(commandName == "sub.sample")                    {       command = new SubSampleCommand(optionString);                           }
 414                 else if(commandName == "indicator")                             {       command = new IndicatorCommand(optionString);                           }
 415                 else if(commandName == "consensus.seqs")                {       command = new ConsensusSeqsCommand(optionString);                       }
 416                 else if(commandName == "corr.axes")                             {       command = new CorrAxesCommand(optionString);                            }
 417                 else if(commandName == "remove.rare")                   {       command = new RemoveRareCommand(optionString);                          }
 418                 else if(commandName == "merge.groups")                  {       command = new MergeGroupsCommand(optionString);                         }
 419                 else if(commandName == "amova")                                 {       command = new AmovaCommand(optionString);                                       }
 420                 else if(commandName == "homova")                                {       command = new HomovaCommand(optionString);                                      }
 421                 else if(commandName == "mantel")                                {       command = new MantelCommand(optionString);                                      }
 422                 else if(commandName == "make.fastq")                    {       command = new MakeFastQCommand(optionString);                           }
 423                 else if(commandName == "get.current")                   {       command = new GetCurrentCommand(optionString);                          }
 424                 else if(commandName == "set.current")                   {       command = new SetCurrentCommand(optionString);                          }
 425                 else if(commandName == "anosim")                                {       command = new AnosimCommand(optionString);                                      }
 426                 else if(commandName == "make.shared")                   {       command = new SharedCommand(optionString);                                      }
 427                 else if(commandName == "get.commandinfo")               {       command = new GetCommandInfoCommand(optionString);                      }
 428                 else if(commandName == "deunique.tree")                 {       command = new DeuniqueTreeCommand(optionString);                        }
 429                 else if(commandName == "count.seqs")                    {       command = new CountSeqsCommand(optionString);                           }
 430                 else if(commandName == "count.groups")                  {       command = new CountGroupsCommand(optionString);                         }
 431                 else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
 432                 else if(commandName == "summary.tax")                   {       command = new SummaryTaxCommand(optionString);                          }
 433                 else if(commandName == "summary.qual")                  {       command = new SummaryQualCommand(optionString);                         }
 434                 else if(commandName == "chimera.perseus")               {       command = new ChimeraPerseusCommand(optionString);                      }
 435                 else if(commandName == "shhh.seqs")                             {       command = new ShhhSeqsCommand(optionString);                            }
 436                 else                                                                                    {       command = new NoCommand(optionString);                                          }
 437
 438                 return command;
 439         }
 440         catch(exception& e) {
 441                 m->errorOut(e, "CommandFactory", "getCommand");
 442                 exit(1);
 443         }
 444 }
 445 /***********************************************************/
 446
 447 /***********************************************************/
 448 //This function calls the appropriate command fucntions based on user input.
 449 Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
 450         try {
 451                 delete pipecommand;   //delete the old command
 452
 453                 //user has opted to redirect output from dir where input files are located to some other place
 454                 if (outputDir != "") {
 455                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 456                         else { optionString += "outputdir=" + outputDir; }
 457                 }
 458
 459                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 460                 if (inputDir != "") {
 461                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 462                         else { optionString += "inputdir=" + inputDir; }
 463                 }
 464
 465                 if(commandName == "read.dist")                                  {       pipecommand = new ReadDistCommand(optionString);                                }
 466                 else if(commandName == "read.otu")                              {       pipecommand = new ReadOtuCommand(optionString);                                 }
 467                 else if(commandName == "read.tree")                             {       pipecommand = new ReadTreeCommand(optionString);                                }
 468                 else if(commandName == "cluster")                               {       pipecommand = new ClusterCommand(optionString);                                 }
 469                 else if(commandName == "unique.seqs")                   {       pipecommand = new DeconvoluteCommand(optionString);                             }
 470                 else if(commandName == "parsimony")                             {       pipecommand = new ParsimonyCommand(optionString);                               }
 471                 else if(commandName == "help")                                  {       pipecommand = new HelpCommand(optionString);                                    }
 472                 else if(commandName == "quit")                                  {       pipecommand = new QuitCommand(optionString);                                    }
 473                 else if(commandName == "collect.single")                {       pipecommand = new CollectCommand(optionString);                                 }
 474                 else if(commandName == "collect.shared")                {       pipecommand = new CollectSharedCommand(optionString);                   }
 475                 else if(commandName == "rarefaction.single")    {       pipecommand = new RareFactCommand(optionString);                                }
 476                 else if(commandName == "rarefaction.shared")    {       pipecommand = new RareFactSharedCommand(optionString);                  }
 477                 else if(commandName == "summary.single")                {       pipecommand = new SummaryCommand(optionString);                                 }
 478                 else if(commandName == "summary.shared")                {       pipecommand = new SummarySharedCommand(optionString);                   }
 479                 else if(commandName == "unifrac.weighted")              {       pipecommand = new UnifracWeightedCommand(optionString);                 }
 480                 else if(commandName == "unifrac.unweighted")    {       pipecommand = new UnifracUnweightedCommand(optionString);               }
 481                 else if(commandName == "get.group")             {   pipecommand = new GetgroupCommand(optionString);                            }
 482                 else if(commandName == "get.label")             {   pipecommand = new GetlabelCommand(optionString);                            }
 483                 else if(commandName == "get.sabund")            {   pipecommand = new GetSAbundCommand(optionString);                           }
 484                 else if(commandName == "get.rabund")            {   pipecommand = new GetRAbundCommand(optionString);                           }
 485                 else if(commandName == "libshuff")              {   pipecommand = new LibShuffCommand(optionString);                            }
 486                 else if(commandName == "heatmap.bin")                   {   pipecommand = new HeatMapCommand(optionString);                                     }
 487                 else if(commandName == "heatmap.sim")                   {   pipecommand = new HeatMapSimCommand(optionString);                          }
 488                 else if(commandName == "filter.seqs")                   {   pipecommand = new FilterSeqsCommand(optionString);                          }
 489                 else if(commandName == "venn")                                  {   pipecommand = new VennCommand(optionString);                                        }
 490                 else if(commandName == "bin.seqs")                              {   pipecommand = new BinSeqCommand(optionString);                                      }
 491                 else if(commandName == "get.oturep")                    {   pipecommand = new GetOTURepCommand(optionString);                           }
 492                 else if(commandName == "tree.shared")                   {   pipecommand = new TreeGroupCommand(optionString);                           }
 493                 else if(commandName == "dist.shared")                   {   pipecommand = new MatrixOutputCommand(optionString);                        }
 494                 else if(commandName == "bootstrap.shared")              {   pipecommand = new BootSharedCommand(optionString);                          }
 495                 else if(commandName == "consensus")                             {   pipecommand = new ConcensusCommand(optionString);                           }
 496                 else if(commandName == "dist.seqs")                             {   pipecommand = new DistanceCommand(optionString);                            }
 497                 else if(commandName == "align.seqs")                    {   pipecommand = new AlignCommand(optionString);                                       }
 498                 else if(commandName == "summary.seqs")                  {       pipecommand = new SeqSummaryCommand(optionString);                              }
 499                 else if(commandName == "screen.seqs")                   {       pipecommand = new ScreenSeqsCommand(optionString);                              }
 500                 else if(commandName == "reverse.seqs")                  {       pipecommand = new ReverseSeqsCommand(optionString);                             }
 501                 else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
 502                 else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
 503                 else if(commandName == "shhh.flows")                    {       pipecommand = new ShhherCommand(optionString);                                  }
 504                 else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
 505                 else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
 506                 else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
 507                 else if(commandName == "merge.files")                   {       pipecommand = new MergeFileCommand(optionString);                               }
 508                 else if(commandName == "system")                                {       pipecommand = new SystemCommand(optionString);                                  }
 509                 else if(commandName == "align.check")                   {       pipecommand = new AlignCheckCommand(optionString);                              }
 510                 else if(commandName == "get.sharedseqs")                {       pipecommand = new GetSharedOTUCommand(optionString);                    }
 511                 else if(commandName == "get.otulist")                   {       pipecommand = new GetListCountCommand(optionString);                    }
 512                 else if(commandName == "hcluster")                              {       pipecommand = new HClusterCommand(optionString);                                }
 513                 else if(commandName == "classify.seqs")                 {       pipecommand = new ClassifySeqsCommand(optionString);                    }
 514                 else if(commandName == "chimera.ccode")                 {       pipecommand = new ChimeraCcodeCommand(optionString);                    }
 515                 else if(commandName == "chimera.check")                 {       pipecommand = new ChimeraCheckCommand(optionString);                    }
 516                 else if(commandName == "chimera.uchime")                {       pipecommand = new ChimeraUchimeCommand(optionString);                   }
 517                 else if(commandName == "chimera.slayer")                {       pipecommand = new ChimeraSlayerCommand(optionString);                   }
 518                 else if(commandName == "chimera.pintail")               {       pipecommand = new ChimeraPintailCommand(optionString);                  }
 519                 else if(commandName == "chimera.bellerophon")   {       pipecommand = new ChimeraBellerophonCommand(optionString);              }
 520                 else if(commandName == "phylotype")                             {       pipecommand = new PhylotypeCommand(optionString);                               }
 521                 else if(commandName == "mgcluster")                             {       pipecommand = new MGClusterCommand(optionString);                               }
 522                 else if(commandName == "pre.cluster")                   {       pipecommand = new PreClusterCommand(optionString);                              }
 523                 else if(commandName == "pcoa")                                  {       pipecommand = new PCOACommand(optionString);                                    }
 524                 else if(commandName == "pca")                                   {       pipecommand = new PCACommand(optionString);                                             }
 525                 else if(commandName == "nmds")                                  {       pipecommand = new NMDSCommand(optionString);                                    }
 526                 else if(commandName == "otu.hierarchy")                 {       pipecommand = new OtuHierarchyCommand(optionString);                    }
 527                 else if(commandName == "set.dir")                               {       pipecommand = new SetDirectoryCommand(optionString);                    }
 528                 else if(commandName == "set.logfile")                   {       pipecommand = new SetLogFileCommand(optionString);                              }
 529                 else if(commandName == "parse.list")                    {       pipecommand = new ParseListCommand(optionString);                               }
 530                 else if(commandName == "phylo.diversity")               {       pipecommand = new PhyloDiversityCommand(optionString);                  }
 531                 else if(commandName == "make.group")                    {       pipecommand = new MakeGroupCommand(optionString);                               }
 532                 else if(commandName == "chop.seqs")                             {       pipecommand = new ChopSeqsCommand(optionString);                                }
 533                 else if(commandName == "clearcut")                              {       pipecommand = new ClearcutCommand(optionString);                                }
 534                 else if(commandName == "catchall")                              {       pipecommand = new CatchAllCommand(optionString);                                }
 535                 else if(commandName == "split.abund")                   {       pipecommand = new SplitAbundCommand(optionString);                              }
 536                 else if(commandName == "cluster.split")                 {       pipecommand = new ClusterSplitCommand(optionString);                    }
 537                 else if(commandName == "classify.otu")                  {       pipecommand = new ClassifyOtuCommand(optionString);                             }
 538                 else if(commandName == "degap.seqs")                    {       pipecommand = new DegapSeqsCommand(optionString);                               }
 539                 else if(commandName == "get.relabund")                  {       pipecommand = new GetRelAbundCommand(optionString);                             }
 540                 else if(commandName == "sens.spec")                             {       pipecommand = new SensSpecCommand(optionString);                                }
 541                 else if(commandName == "seq.error")                             {       pipecommand = new SeqErrorCommand(optionString);                                }
 542                 else if(commandName == "sffinfo")                               {       pipecommand = new SffInfoCommand(optionString);                                 }
 543                 else if(commandName == "normalize.shared")              {       pipecommand = new NormalizeSharedCommand(optionString);                 }
 544                 else if(commandName == "metastats")                             {       pipecommand = new MetaStatsCommand(optionString);                               }
 545                 else if(commandName == "split.groups")                  {       pipecommand = new SplitGroupCommand(optionString);                              }
 546                 else if(commandName == "cluster.fragments")             {       pipecommand = new ClusterFragmentsCommand(optionString);                }
 547                 else if(commandName == "get.lineage")                   {       pipecommand = new GetLineageCommand(optionString);                              }
 548                 else if(commandName == "get.groups")                    {       pipecommand = new GetGroupsCommand(optionString);                               }
 549                 else if(commandName == "remove.lineage")                {       pipecommand = new RemoveLineageCommand(optionString);                   }
 550                 else if(commandName == "remove.groups")                 {       pipecommand = new RemoveGroupsCommand(optionString);                    }
 551                 else if(commandName == "get.otus")                              {       pipecommand = new GetOtusCommand(optionString);                                 }
 552                 else if(commandName == "remove.otus")                   {       pipecommand = new RemoveOtusCommand(optionString);                              }
 553                 else if(commandName == "fastq.info")                    {       pipecommand = new ParseFastaQCommand(optionString);                             }
 554                 else if(commandName == "deunique.seqs")                 {       pipecommand = new DeUniqueSeqsCommand(optionString);                    }
 555                 else if(commandName == "pairwise.seqs")                 {       pipecommand = new PairwiseSeqsCommand(optionString);                    }
 556                 else if(commandName == "cluster.classic")               {       pipecommand = new ClusterDoturCommand(optionString);                    }
 557                 else if(commandName == "sub.sample")                    {       pipecommand = new SubSampleCommand(optionString);                               }
 558                 else if(commandName == "indicator")                             {       pipecommand = new IndicatorCommand(optionString);                               }
 559                 else if(commandName == "consensus.seqs")                {       pipecommand = new ConsensusSeqsCommand(optionString);                   }
 560                 else if(commandName == "corr.axes")                             {       pipecommand = new CorrAxesCommand(optionString);                                }
 561                 else if(commandName == "remove.rare")                   {       pipecommand = new RemoveRareCommand(optionString);                              }
 562                 else if(commandName == "merge.groups")                  {       pipecommand = new MergeGroupsCommand(optionString);                             }
 563                 else if(commandName == "amova")                                 {       pipecommand = new AmovaCommand(optionString);                                   }
 564                 else if(commandName == "homova")                                {       pipecommand = new HomovaCommand(optionString);                                  }
 565                 else if(commandName == "mantel")                                {       pipecommand = new MantelCommand(optionString);                                  }
 566                 else if(commandName == "anosim")                                {       pipecommand = new AnosimCommand(optionString);                                  }
 567                 else if(commandName == "make.fastq")                    {       pipecommand = new MakeFastQCommand(optionString);                               }
 568                 else if(commandName == "get.current")                   {       pipecommand = new GetCurrentCommand(optionString);                              }
 569                 else if(commandName == "set.current")                   {       pipecommand = new SetCurrentCommand(optionString);                              }
 570                 else if(commandName == "make.shared")                   {       pipecommand = new SharedCommand(optionString);                                  }
 571                 else if(commandName == "get.commandinfo")               {       pipecommand = new GetCommandInfoCommand(optionString);                  }
 572                 else if(commandName == "deunique.tree")                 {       pipecommand = new DeuniqueTreeCommand(optionString);                    }
 573                 else if(commandName == "count.seqs")                    {       pipecommand = new CountSeqsCommand(optionString);                               }
 574                 else if(commandName == "count.groups")                  {       pipecommand = new CountGroupsCommand(optionString);                             }
 575                 else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
 576                 else if(commandName == "summary.tax")                   {       pipecommand = new SummaryTaxCommand(optionString);                              }
 577                 else if(commandName == "summary.qual")                  {       pipecommand = new SummaryQualCommand(optionString);                             }
 578                 else if(commandName == "chimera.perseus")               {       pipecommand = new ChimeraPerseusCommand(optionString);                  }
 579                 else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhhSeqsCommand(optionString);                                }
 580                 else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 581
 582                 return pipecommand;
 583         }
 584         catch(exception& e) {
 585                 m->errorOut(e, "CommandFactory", "getCommand");
 586                 exit(1);
 587         }
 588 }
 589 /***********************************************************/
 590
 591 /***********************************************************/
 592 //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
 593 Command* CommandFactory::getCommand(string commandName){
 594         try {
 595                 delete shellcommand;   //delete the old command
 596
 597                 if(commandName == "read.dist")                                  {       shellcommand = new ReadDistCommand();                           }
 598                 else if(commandName == "read.otu")                              {       shellcommand = new ReadOtuCommand();                            }
 599                 else if(commandName == "read.tree")                             {       shellcommand = new ReadTreeCommand();                           }
 600                 else if(commandName == "cluster")                               {       shellcommand = new ClusterCommand();                            }
 601                 else if(commandName == "unique.seqs")                   {       shellcommand = new DeconvoluteCommand();                        }
 602                 else if(commandName == "parsimony")                             {       shellcommand = new ParsimonyCommand();                          }
 603                 else if(commandName == "help")                                  {       shellcommand = new HelpCommand();                                       }
 604                 else if(commandName == "quit")                                  {       shellcommand = new QuitCommand();                                       }
 605                 else if(commandName == "collect.single")                {       shellcommand = new CollectCommand();                            }
 606                 else if(commandName == "collect.shared")                {       shellcommand = new CollectSharedCommand();                      }
 607                 else if(commandName == "rarefaction.single")    {       shellcommand = new RareFactCommand();                           }
 608                 else if(commandName == "rarefaction.shared")    {       shellcommand = new RareFactSharedCommand();                     }
 609                 else if(commandName == "summary.single")                {       shellcommand = new SummaryCommand();                            }
 610                 else if(commandName == "summary.shared")                {       shellcommand = new SummarySharedCommand();                      }
 611                 else if(commandName == "unifrac.weighted")              {       shellcommand = new UnifracWeightedCommand();            }
 612                 else if(commandName == "unifrac.unweighted")    {       shellcommand = new UnifracUnweightedCommand();          }
 613                 else if(commandName == "get.group")             {   shellcommand = new GetgroupCommand();                               }
 614                 else if(commandName == "get.label")             {   shellcommand = new GetlabelCommand();                               }
 615                 else if(commandName == "get.sabund")            {   shellcommand = new GetSAbundCommand();                              }
 616                 else if(commandName == "get.rabund")            {   shellcommand = new GetRAbundCommand();                              }
 617                 else if(commandName == "libshuff")              {   shellcommand = new LibShuffCommand();                               }
 618                 else if(commandName == "heatmap.bin")                   {   shellcommand = new HeatMapCommand();                                }
 619                 else if(commandName == "heatmap.sim")                   {   shellcommand = new HeatMapSimCommand();                             }
 620                 else if(commandName == "filter.seqs")                   {   shellcommand = new FilterSeqsCommand();                             }
 621                 else if(commandName == "venn")                                  {   shellcommand = new VennCommand();                                   }
 622                 else if(commandName == "bin.seqs")                              {   shellcommand = new BinSeqCommand();                                 }
 623                 else if(commandName == "get.oturep")                    {   shellcommand = new GetOTURepCommand();                              }
 624                 else if(commandName == "tree.shared")                   {   shellcommand = new TreeGroupCommand();                              }
 625                 else if(commandName == "dist.shared")                   {   shellcommand = new MatrixOutputCommand();                   }
 626                 else if(commandName == "bootstrap.shared")              {   shellcommand = new BootSharedCommand();                             }
 627                 else if(commandName == "consensus")                             {   shellcommand = new ConcensusCommand();                              }
 628                 else if(commandName == "dist.seqs")                             {   shellcommand = new DistanceCommand();                               }
 629                 else if(commandName == "align.seqs")                    {   shellcommand = new AlignCommand();                                  }
 630                 else if(commandName == "summary.seqs")                  {       shellcommand = new SeqSummaryCommand();                         }
 631                 else if(commandName == "screen.seqs")                   {       shellcommand = new ScreenSeqsCommand();                         }
 632                 else if(commandName == "reverse.seqs")                  {       shellcommand = new ReverseSeqsCommand();                        }
 633                 else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
 634                 else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
 635                 else if(commandName == "shhh.flows")                    {       shellcommand = new ShhherCommand();                                     }
 636                 else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
 637                 else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
 638                 else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }
 639                 else if(commandName == "merge.files")                   {       shellcommand = new MergeFileCommand();                          }
 640                 else if(commandName == "system")                                {       shellcommand = new SystemCommand();                                     }
 641                 else if(commandName == "align.check")                   {       shellcommand = new AlignCheckCommand();                         }
 642                 else if(commandName == "get.sharedseqs")                {       shellcommand = new GetSharedOTUCommand();                       }
 643                 else if(commandName == "get.otulist")                   {       shellcommand = new GetListCountCommand();                       }
 644                 else if(commandName == "hcluster")                              {       shellcommand = new HClusterCommand();                           }
 645                 else if(commandName == "classify.seqs")                 {       shellcommand = new ClassifySeqsCommand();                       }
 646                 else if(commandName == "chimera.ccode")                 {       shellcommand = new ChimeraCcodeCommand();                       }
 647                 else if(commandName == "chimera.check")                 {       shellcommand = new ChimeraCheckCommand();                       }
 648                 else if(commandName == "chimera.slayer")                {       shellcommand = new ChimeraSlayerCommand();                      }
 649                 else if(commandName == "chimera.uchime")                {       shellcommand = new ChimeraUchimeCommand();                      }
 650                 else if(commandName == "chimera.pintail")               {       shellcommand = new ChimeraPintailCommand();                     }
 651                 else if(commandName == "chimera.bellerophon")   {       shellcommand = new ChimeraBellerophonCommand();         }
 652                 else if(commandName == "phylotype")                             {       shellcommand = new PhylotypeCommand();                          }
 653                 else if(commandName == "mgcluster")                             {       shellcommand = new MGClusterCommand();                          }
 654                 else if(commandName == "pre.cluster")                   {       shellcommand = new PreClusterCommand();                         }
 655                 else if(commandName == "pcoa")                                  {       shellcommand = new PCOACommand();                                       }
 656                 else if(commandName == "pca")                                   {       shellcommand = new PCACommand();                                        }
 657                 else if(commandName == "nmds")                                  {       shellcommand = new NMDSCommand();                                       }
 658                 else if(commandName == "otu.hierarchy")                 {       shellcommand = new OtuHierarchyCommand();                       }
 659                 else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
 660                 else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }
 661                 else if(commandName == "parse.list")                    {       shellcommand = new ParseListCommand();                          }
 662                 else if(commandName == "phylo.diversity")               {       shellcommand = new PhyloDiversityCommand();                     }
 663                 else if(commandName == "make.group")                    {       shellcommand = new MakeGroupCommand();                          }
 664                 else if(commandName == "chop.seqs")                             {       shellcommand = new ChopSeqsCommand();                           }
 665                 else if(commandName == "clearcut")                              {       shellcommand = new ClearcutCommand();                           }
 666                 else if(commandName == "catchall")                              {       shellcommand = new CatchAllCommand();                           }
 667                 else if(commandName == "split.abund")                   {       shellcommand = new SplitAbundCommand();                         }
 668                 else if(commandName == "cluster.split")                 {       shellcommand = new ClusterSplitCommand();                       }
 669                 else if(commandName == "classify.otu")                  {       shellcommand = new ClassifyOtuCommand();                        }
 670                 else if(commandName == "degap.seqs")                    {       shellcommand = new DegapSeqsCommand();                          }
 671                 else if(commandName == "get.relabund")                  {       shellcommand = new GetRelAbundCommand();                        }
 672                 else if(commandName == "sens.spec")                             {       shellcommand = new SensSpecCommand();                           }
 673                 else if(commandName == "seq.error")                             {       shellcommand = new SeqErrorCommand();                           }
 674                 else if(commandName == "sffinfo")                               {       shellcommand = new SffInfoCommand();                            }
 675                 else if(commandName == "normalize.shared")              {       shellcommand = new NormalizeSharedCommand();            }
 676                 else if(commandName == "metastats")                             {       shellcommand = new MetaStatsCommand();                          }
 677                 else if(commandName == "split.groups")                  {       shellcommand = new SplitGroupCommand();                         }
 678                 else if(commandName == "cluster.fragments")             {       shellcommand = new ClusterFragmentsCommand();           }
 679                 else if(commandName == "get.lineage")                   {       shellcommand = new GetLineageCommand();                         }
 680                 else if(commandName == "remove.lineage")                {       shellcommand = new RemoveLineageCommand();                      }
 681                 else if(commandName == "get.groups")                    {       shellcommand = new GetGroupsCommand();                          }
 682                 else if(commandName == "remove.groups")                 {       shellcommand = new RemoveGroupsCommand();                       }
 683                 else if(commandName == "get.otus")                              {       shellcommand = new GetOtusCommand();                            }
 684                 else if(commandName == "remove.otus")                   {       shellcommand = new RemoveOtusCommand();                         }
 685                 else if(commandName == "fastq.info")                    {       shellcommand = new ParseFastaQCommand();                        }
 686                 else if(commandName == "deunique.seqs")                 {       shellcommand = new DeUniqueSeqsCommand();                       }
 687                 else if(commandName == "pairwise.seqs")                 {       shellcommand = new PairwiseSeqsCommand();                       }
 688                 else if(commandName == "cluster.classic")               {       shellcommand = new ClusterDoturCommand();                       }
 689                 else if(commandName == "sub.sample")                    {       shellcommand = new SubSampleCommand();                          }
 690                 else if(commandName == "indicator")                             {       shellcommand = new IndicatorCommand();                          }
 691                 else if(commandName == "consensus.seqs")                {       shellcommand = new ConsensusSeqsCommand();                      }
 692                 else if(commandName == "corr.axes")                             {       shellcommand = new CorrAxesCommand();                           }
 693                 else if(commandName == "remove.rare")                   {       shellcommand = new RemoveRareCommand();                         }
 694                 else if(commandName == "merge.groups")                  {       shellcommand = new MergeGroupsCommand();                        }
 695                 else if(commandName == "amova")                                 {       shellcommand = new AmovaCommand();                                      }
 696                 else if(commandName == "homova")                                {       shellcommand = new HomovaCommand();                                     }
 697                 else if(commandName == "mantel")                                {       shellcommand = new MantelCommand();                                     }
 698                 else if(commandName == "anosim")                                {       shellcommand = new AnosimCommand();                                     }
 699                 else if(commandName == "make.fastq")                    {       shellcommand = new MakeFastQCommand();                          }
 700                 else if(commandName == "get.current")                   {       shellcommand = new GetCurrentCommand();                         }
 701                 else if(commandName == "set.current")                   {       shellcommand = new SetCurrentCommand();                         }
 702                 else if(commandName == "make.shared")                   {       shellcommand = new SharedCommand();                                     }
 703                 else if(commandName == "get.commandinfo")               {       shellcommand = new GetCommandInfoCommand();                     }
 704                 else if(commandName == "deunique.tree")                 {       shellcommand = new DeuniqueTreeCommand();                       }
 705                 else if(commandName == "count.seqs")                    {       shellcommand = new CountSeqsCommand();                          }
 706                 else if(commandName == "count.groups")                  {       shellcommand = new CountGroupsCommand();                        }
 707                 else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
 708                 else if(commandName == "summary.tax")                   {       shellcommand = new SummaryTaxCommand();                         }
 709                 else if(commandName == "summary.qual")                  {       shellcommand = new SummaryQualCommand();                        }
 710                 else if(commandName == "chimera.perseus")               {       shellcommand = new ChimeraPerseusCommand();                     }
 711                 else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhhSeqsCommand();                           }
 712                 else                                                                                    {       shellcommand = new NoCommand();                                         }
 713
 714                 return shellcommand;
 715         }
 716         catch(exception& e) {
 717                 m->errorOut(e, "CommandFactory", "getCommand");
 718                 exit(1);
 719         }
 720 }
 721 /***********************************************************
 722 //This function is used to interrupt a command
 723 Command* CommandFactory::getCommand(){
 724         try {
 725                 delete command;   //delete the old command
 726
 727                 string s = "";
 728             command = new NoCommand(s);
 729
 730                 return command;
 731         }
 732         catch(exception& e) {
 733                 m->errorOut(e, "CommandFactory", "getCommand");
 734                 exit(1);
 735         }
 736 }
 737 /***********************************************************************/
 738 bool CommandFactory::isValidCommand(string command) {
 739         try {
 740
 741                 //is the command in the map
 742                 if ((commands.find(command)) != (commands.end())) {
 743                         return true;
 744                 }else{
 745                         m->mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
 746                         for (it = commands.begin(); it != commands.end(); it++) {
 747                                 m->mothurOut(it->first + ", ");
 748                         }
 749                         m->mothurOutEndLine();
 750                         return false;
 751                 }
 752
 753         }
 754         catch(exception& e) {
 755                 m->errorOut(e, "CommandFactory", "isValidCommand");
 756                 exit(1);
 757         }
 758 }
 759 /***********************************************************************/
 760 bool CommandFactory::isValidCommand(string command, string noError) {
 761         try {
 762
 763                 //is the command in the map
 764                 if ((commands.find(command)) != (commands.end())) {
 765                         return true;
 766                 }else{
 767                         return false;
 768                 }
 769
 770         }
 771         catch(exception& e) {
 772                 m->errorOut(e, "CommandFactory", "isValidCommand");
 773                 exit(1);
 774         }
 775 }
 776 /***********************************************************************/
 777 void CommandFactory::printCommands(ostream& out) {
 778         try {
 779                 out << "Valid commands are: ";
 780                 for (it = commands.begin(); it != commands.end(); it++) {
 781                         out << it->first << ",";
 782                 }
 783                 out << endl;
 784         }
 785         catch(exception& e) {
 786                 m->errorOut(e, "CommandFactory", "printCommands");
 787                 exit(1);
 788         }
 789 }
 790 /***********************************************************************/
 791
 792
 793
 794