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 "chimeraseqscommand.h"
  52 #include "listseqscommand.h"
  53 #include "getseqscommand.h"
  54 #include "removeseqscommand.h"
  55 #include "systemcommand.h"
  56 #include "secondarystructurecommand.h"
  57 #include "getsharedotucommand.h"
  58 #include "getlistcountcommand.h"
  59 #include "hclustercommand.h"
  60 #include "classifyseqscommand.h"
  61 #include "phylotypecommand.h"
  62 #include "mgclustercommand.h"
  63 #include "preclustercommand.h"
  64 #include "pcacommand.h"
  65 #include "otuhierarchycommand.h"
  66 #include "setdircommand.h"
  67 #include "parselistscommand.h"
  68 #include "parsesffcommand.h"
  69 #include "chimeraccodecommand.h"
  70 #include "chimeracheckcommand.h"
  71 #include "chimeraslayercommand.h"
  72 #include "chimerapintailcommand.h"
  73 #include "chimerabellerophoncommand.h"
  74 #include "setlogfilecommand.h"
  75 #include "phylodiversitycommand.h"
  76 #include "makegroupcommand.h"
  77 #include "chopseqscommand.h"
  78 #include "clearcutcommand.h"
  79 #include "catchallcommand.h"
  80 #include "splitabundcommand.h"
  81 #include "clustersplitcommand.h"
  82 #include "classifyotucommand.h"
  83 #include "degapseqscommand.h"
  84 #include "getrelabundcommand.h"
  85 #include "sensspeccommand.h"
  86 #include "sffinfocommand.h"
  87 #include "seqerrorcommand.h"
  88 #include "normalizesharedcommand.h"
  89 #include "metastatscommand.h"
  90 #include "splitgroupscommand.h"
  91 #include "clusterfragmentscommand.h"
  92 #include "getlineagecommand.h"
  93 #include "removelineagecommand.h"
  94 #include "parsefastaqcommand.h"
  95 #include "pipelinepdscommand.h"
  96 #include "deuniqueseqscommand.h"
  97 #include "pairwiseseqscommand.h"
  98 #include "clusterdoturcommand.h"
  99 #include "subsamplecommand.h"
 100
 101
 102 /*******************************************************/
 103
 104 /******************************************************/
 105 CommandFactory* CommandFactory::getInstance() {
 106         if( _uniqueInstance == 0) {
 107                 _uniqueInstance = new CommandFactory();
 108         }
 109         return _uniqueInstance;
 110 }
 111 /***********************************************************/
 112
 113 /***********************************************************/
 114 //note: This class is resposible for knowing which commands are mpiEnabled,
 115 //If a command is not enabled only process 0 will execute the command.
 116 //This avoids redundant outputs on pieces of code we have not paralellized.
 117 //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.
 118 //example:  commands["dist.seqs"] = "MPIEnabled";
 119
 120 CommandFactory::CommandFactory(){
 121         string s = "";
 122         m = MothurOut::getInstance();
 123
 124         command = new NoCommand(s);
 125         shellcommand = new NoCommand(s);
 126         pipecommand = new NoCommand(s);
 127
 128         outputDir = ""; inputDir = "";
 129         logFileName = "";
 130         append = false;
 131
 132         //initialize list of valid commands
 133         commands["read.dist"]                   = "read.dist";
 134         commands["read.otu"]                    = "read.otu";
 135         commands["read.tree"]                   = "read.tree";
 136         commands["bin.seqs"]                    = "bin.seqs";
 137         commands["get.oturep"]                  = "get.oturep";
 138         commands["cluster"]                             = "cluster";
 139         commands["unique.seqs"]                 = "unique.seqs";
 140         commands["dist.shared"]                 = "dist.shared";
 141         commands["collect.single"]              = "collect.single";
 142         commands["collect.shared"]              = "collect.shared";
 143         commands["rarefaction.single"]  = "rarefaction.single";
 144         commands["rarefaction.shared"]  = "rarefaction.shared";
 145         commands["summary.single"]              = "summary.single";
 146         commands["summary.shared"]              = "summary.shared";
 147         commands["parsimony"]                   = "parsimony";
 148         commands["unifrac.weighted"]    = "unifrac.weighted";
 149         commands["unifrac.unweighted"]  = "unifrac.unweighted";
 150         commands["libshuff"]                    = "libshuff";
 151         commands["tree.shared"]                 = "tree.shared";
 152         commands["heatmap.bin"]                 = "heatmap.bin";
 153         commands["heatmap.sim"]                 = "heatmap.sim";
 154         commands["venn"]                                = "venn";
 155         commands["get.group"]           = "get.group";
 156         commands["get.label"]           = "get.label";
 157         commands["get.sabund"]          = "get.sabund";
 158         commands["get.rabund"]          = "get.rabund";
 159         commands["bootstrap.shared"]    = "bootstrap.shared";
 160         //commands["consensus"]                 = "consensus";
 161         commands["help"]                                = "help";
 162         commands["reverse.seqs"]                = "reverse.seqs";
 163         commands["trim.seqs"]                   = "trim.seqs";
 164         commands["list.seqs"]                   = "list.seqs";
 165         commands["get.seqs"]                    = "get.seqs";
 166         commands["remove.seqs"]                 = "get.seqs";
 167         commands["system"]                              = "system";
 168         commands["align.check"]                 = "align.check";
 169         commands["get.sharedseqs"]              = "get.sharedseqs";
 170         commands["get.otulist"]                 = "get.otulist";
 171         commands["hcluster"]                    = "hcluster";
 172         commands["phylotype"]                   = "phylotype";
 173         commands["mgcluster"]                   = "mgcluster";
 174         commands["pre.cluster"]                 = "pre.cluster";
 175         commands["pcoa"]                                = "pcoa";
 176         commands["otu.hierarchy"]               = "otu.hierarchy";
 177         commands["set.dir"]                             = "set.dir";
 178         commands["merge.files"]                 = "merge.files";
 179         commands["parse.list"]                  = "parse.list";
 180         commands["parse.sff"]                   = "parse.sff";
 181         commands["set.logfile"]                 = "set.logfile";
 182         commands["phylo.diversity"]             = "phylo.diversity";
 183         commands["make.group"]                  = "make.group";
 184         commands["chop.seqs"]                   = "chop.seqs";
 185         commands["clearcut"]                    = "clearcut";
 186         commands["catchall"]                    = "catchall";
 187         commands["split.abund"]                 = "split.abund";
 188         commands["classify.otu"]                = "classify.otu";
 189         commands["degap.seqs"]                  = "degap.seqs";
 190         commands["get.relabund"]                = "get.relabund";
 191         commands["sffinfo"]                             = "sffinfo";
 192         commands["normalize.shared"]    = "normalize.shared";
 193         commands["metastats"]                   = "metastats";
 194         commands["split.groups"]                = "split.groups";
 195         commands["cluster.fragments"]   = "cluster.fragments";
 196         commands["get.lineage"]                 = "get.lineage";
 197         commands["remove.lineage"]              = "remove.lineage";
 198         commands["fastq.info"]                  = "fastq.info";
 199         commands["deunique.seqs"]               = "deunique.seqs";
 200         commands["cluster.classic"]             = "cluster.classic";
 201         commands["sub.sample"]                  = "sub.sample";
 202         commands["pairwise.seqs"]               = "MPIEnabled";
 203         commands["pipeline.pds"]                = "MPIEnabled";
 204         commands["classify.seqs"]               = "MPIEnabled";
 205         commands["dist.seqs"]                   = "MPIEnabled";
 206         commands["filter.seqs"]                 = "MPIEnabled";
 207         commands["align.seqs"]                  = "MPIEnabled";
 208         commands["chimera.seqs"]                = "chimera.seqs";
 209         commands["chimera.ccode"]               = "MPIEnabled";
 210         commands["chimera.check"]               = "MPIEnabled";
 211         commands["chimera.slayer"]              = "MPIEnabled";
 212         commands["chimera.pintail"]             = "MPIEnabled";
 213         commands["chimera.bellerophon"] = "MPIEnabled";
 214         commands["screen.seqs"]                 = "MPIEnabled";
 215         commands["summary.seqs"]                = "MPIEnabled";
 216         commands["cluster.split"]               = "MPIEnabled";
 217         commands["sens.spec"]                   = "sens.spec";
 218         commands["seq.error"]                   = "seq.error";
 219         commands["quit"]                                = "MPIEnabled";
 220
 221 }
 222 /***********************************************************/
 223
 224 /***********************************************************/
 225 bool CommandFactory::MPIEnabled(string commandName) {
 226         bool mpi = false;
 227         it = commands.find(commandName);
 228         if (it != commands.end()) {
 229                 if (it->second == "MPIEnabled") { return true; }
 230         }
 231         return mpi;
 232 }
 233 /***********************************************************/
 234
 235 /***********************************************************/
 236 CommandFactory::~CommandFactory(){
 237         _uniqueInstance = 0;
 238         delete command;
 239         delete shellcommand;
 240         delete pipecommand;
 241 }
 242
 243 /***********************************************************/
 244
 245 /***********************************************************/
 246 //This function calls the appropriate command fucntions based on user input.
 247 Command* CommandFactory::getCommand(string commandName, string optionString){
 248         try {
 249                 delete command;   //delete the old command
 250
 251                 //user has opted to redirect output from dir where input files are located to some other place
 252                 if (outputDir != "") {
 253                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 254                         else { optionString += "outputdir=" + outputDir; }
 255                 }
 256
 257                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 258                 if (inputDir != "") {
 259                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 260                         else { optionString += "inputdir=" + inputDir; }
 261                 }
 262
 263                 if(commandName == "read.dist")                                  {       command = new ReadDistCommand(optionString);                            }
 264                 else if(commandName == "read.otu")                              {       command = new ReadOtuCommand(optionString);                                     }
 265                 else if(commandName == "read.tree")                             {       command = new ReadTreeCommand(optionString);                            }
 266                 else if(commandName == "cluster")                               {       command = new ClusterCommand(optionString);                                     }
 267                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand(optionString);                         }
 268                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand(optionString);                           }
 269                 else if(commandName == "help")                                  {       command = new HelpCommand(optionString);                                        }
 270                 else if(commandName == "quit")                                  {       command = new QuitCommand(optionString);                                        }
 271                 else if(commandName == "collect.single")                {       command = new CollectCommand(optionString);                                     }
 272                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand(optionString);                       }
 273                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand(optionString);                            }
 274                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand(optionString);                      }
 275                 else if(commandName == "summary.single")                {       command = new SummaryCommand(optionString);                                     }
 276                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand(optionString);                       }
 277                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand(optionString);                     }
 278                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);           }
 279                 else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                                }
 280                 else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                                }
 281                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                               }
 282                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                               }
 283                 else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                                }
 284                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand(optionString);                                 }
 285                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand(optionString);                              }
 286                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand(optionString);                              }
 287                 else if(commandName == "venn")                                  {   command = new VennCommand(optionString);                                    }
 288                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand(optionString);                                  }
 289                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                               }
 290                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                               }
 291                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);                    }
 292                 else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                              }
 293                 else if(commandName == "consensus")                             {   command = new ConcensusCommand(optionString);                               }
 294                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                                }
 295                 else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                                   }
 296                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                          }
 297                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                          }
 298                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
 299                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
 300                 else if(commandName == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(optionString);                         }
 301                 else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
 302                 else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
 303                 else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
 304                 else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                           }
 305                 else if(commandName == "system")                                {       command = new SystemCommand(optionString);                                      }
 306                 else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                          }
 307                 else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                        }
 308                 else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                        }
 309                 else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                            }
 310                 else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                        }
 311                 else if(commandName == "chimera.ccode")                 {       command = new ChimeraCcodeCommand(optionString);                        }
 312                 else if(commandName == "chimera.check")                 {       command = new ChimeraCheckCommand(optionString);                        }
 313                 else if(commandName == "chimera.slayer")                {       command = new ChimeraSlayerCommand(optionString);                       }
 314                 else if(commandName == "chimera.pintail")               {       command = new ChimeraPintailCommand(optionString);                      }
 315                 else if(commandName == "chimera.bellerophon")   {       command = new ChimeraBellerophonCommand(optionString);          }
 316                 else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
 317                 else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                           }
 318                 else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                          }
 319                 else if(commandName == "pcoa")                                  {       command = new PCACommand(optionString);                                         }
 320                 else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
 321                 else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
 322                 else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
 323                 else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
 324                 else if(commandName == "parse.sff")                             {       command = new ParseSFFCommand(optionString);                            }
 325                 else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
 326                 else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
 327                 else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
 328                 else if(commandName == "clearcut")                              {       command = new ClearcutCommand(optionString);                            }
 329                 else if(commandName == "catchall")                              {       command = new CatchAllCommand(optionString);                            }
 330                 else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
 331                 else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
 332                 else if(commandName == "classify.otu")                  {       command = new ClassifyOtuCommand(optionString);                         }
 333                 else if(commandName == "degap.seqs")                    {       command = new DegapSeqsCommand(optionString);                           }
 334                 else if(commandName == "get.relabund")                  {       command = new GetRelAbundCommand(optionString);                         }
 335                 else if(commandName == "sens.spec")                             {       command = new SensSpecCommand(optionString);                            }
 336                 else if(commandName == "seq.error")                             {       command = new SeqErrorCommand(optionString);                            }
 337                 else if(commandName == "sffinfo")                               {       command = new SffInfoCommand(optionString);                                     }
 338                 else if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
 339                 else if(commandName == "metastats")                             {       command = new MetaStatsCommand(optionString);                           }
 340                 else if(commandName == "split.groups")                  {       command = new SplitGroupCommand(optionString);                          }
 341                 else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
 342                 else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
 343                 else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
 344                 else if(commandName == "fastq.info")                    {       command = new ParseFastaQCommand(optionString);                         }
 345                 else if(commandName == "pipeline.pds")                  {       command = new PipelineCommand(optionString);                            }
 346                 else if(commandName == "deunique.seqs")                 {       command = new DeUniqueSeqsCommand(optionString);                        }
 347                 else if(commandName == "pairwise.seqs")                 {       command = new PairwiseSeqsCommand(optionString);                        }
 348                 else if(commandName == "cluster.classic")               {       command = new ClusterDoturCommand(optionString);                        }
 349                 else if(commandName == "sub.sample")                    {       command = new SubSampleCommand(optionString);                           }
 350                 else                                                                                    {       command = new NoCommand(optionString);                                          }
 351
 352                 return command;
 353         }
 354         catch(exception& e) {
 355                 m->errorOut(e, "CommandFactory", "getCommand");
 356                 exit(1);
 357         }
 358 }
 359 /***********************************************************/
 360
 361 /***********************************************************/
 362 //This function calls the appropriate command fucntions based on user input.
 363 Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
 364         try {
 365                 delete pipecommand;   //delete the old command
 366
 367                 //user has opted to redirect output from dir where input files are located to some other place
 368                 if (outputDir != "") {
 369                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 370                         else { optionString += "outputdir=" + outputDir; }
 371                 }
 372
 373                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 374                 if (inputDir != "") {
 375                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 376                         else { optionString += "inputdir=" + inputDir; }
 377                 }
 378
 379                 if(commandName == "read.dist")                                  {       pipecommand = new ReadDistCommand(optionString);                                }
 380                 else if(commandName == "read.otu")                              {       pipecommand = new ReadOtuCommand(optionString);                                 }
 381                 else if(commandName == "read.tree")                             {       pipecommand = new ReadTreeCommand(optionString);                                }
 382                 else if(commandName == "cluster")                               {       pipecommand = new ClusterCommand(optionString);                                 }
 383                 else if(commandName == "unique.seqs")                   {       pipecommand = new DeconvoluteCommand(optionString);                             }
 384                 else if(commandName == "parsimony")                             {       pipecommand = new ParsimonyCommand(optionString);                               }
 385                 else if(commandName == "help")                                  {       pipecommand = new HelpCommand(optionString);                                    }
 386                 else if(commandName == "quit")                                  {       pipecommand = new QuitCommand(optionString);                                    }
 387                 else if(commandName == "collect.single")                {       pipecommand = new CollectCommand(optionString);                                 }
 388                 else if(commandName == "collect.shared")                {       pipecommand = new CollectSharedCommand(optionString);                   }
 389                 else if(commandName == "rarefaction.single")    {       pipecommand = new RareFactCommand(optionString);                                }
 390                 else if(commandName == "rarefaction.shared")    {       pipecommand = new RareFactSharedCommand(optionString);                  }
 391                 else if(commandName == "summary.single")                {       pipecommand = new SummaryCommand(optionString);                                 }
 392                 else if(commandName == "summary.shared")                {       pipecommand = new SummarySharedCommand(optionString);                   }
 393                 else if(commandName == "unifrac.weighted")              {       pipecommand = new UnifracWeightedCommand(optionString);                 }
 394                 else if(commandName == "unifrac.unweighted")    {       pipecommand = new UnifracUnweightedCommand(optionString);               }
 395                 else if(commandName == "get.group")             {   pipecommand = new GetgroupCommand(optionString);                            }
 396                 else if(commandName == "get.label")             {   pipecommand = new GetlabelCommand(optionString);                            }
 397                 else if(commandName == "get.sabund")            {   pipecommand = new GetSAbundCommand(optionString);                           }
 398                 else if(commandName == "get.rabund")            {   pipecommand = new GetRAbundCommand(optionString);                           }
 399                 else if(commandName == "libshuff")              {   pipecommand = new LibShuffCommand(optionString);                            }
 400                 else if(commandName == "heatmap.bin")                   {   pipecommand = new HeatMapCommand(optionString);                                     }
 401                 else if(commandName == "heatmap.sim")                   {   pipecommand = new HeatMapSimCommand(optionString);                          }
 402                 else if(commandName == "filter.seqs")                   {   pipecommand = new FilterSeqsCommand(optionString);                          }
 403                 else if(commandName == "venn")                                  {   pipecommand = new VennCommand(optionString);                                        }
 404                 else if(commandName == "bin.seqs")                              {   pipecommand = new BinSeqCommand(optionString);                                      }
 405                 else if(commandName == "get.oturep")                    {   pipecommand = new GetOTURepCommand(optionString);                           }
 406                 else if(commandName == "tree.shared")                   {   pipecommand = new TreeGroupCommand(optionString);                           }
 407                 else if(commandName == "dist.shared")                   {   pipecommand = new MatrixOutputCommand(optionString);                        }
 408                 else if(commandName == "bootstrap.shared")              {   pipecommand = new BootSharedCommand(optionString);                          }
 409                 else if(commandName == "consensus")                             {   pipecommand = new ConcensusCommand(optionString);                           }
 410                 else if(commandName == "dist.seqs")                             {   pipecommand = new DistanceCommand(optionString);                            }
 411                 else if(commandName == "align.seqs")                    {   pipecommand = new AlignCommand(optionString);                                       }
 412                 else if(commandName == "summary.seqs")                  {       pipecommand = new SeqSummaryCommand(optionString);                              }
 413                 else if(commandName == "screen.seqs")                   {       pipecommand = new ScreenSeqsCommand(optionString);                              }
 414                 else if(commandName == "reverse.seqs")                  {       pipecommand = new ReverseSeqsCommand(optionString);                             }
 415                 else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
 416                 else if(commandName == "chimera.seqs")                  {       pipecommand = new ChimeraSeqsCommand(optionString);                             }
 417                 else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
 418                 else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
 419                 else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
 420                 else if(commandName == "merge.files")                   {       pipecommand = new MergeFileCommand(optionString);                               }
 421                 else if(commandName == "system")                                {       pipecommand = new SystemCommand(optionString);                                  }
 422                 else if(commandName == "align.check")                   {       pipecommand = new AlignCheckCommand(optionString);                              }
 423                 else if(commandName == "get.sharedseqs")                {       pipecommand = new GetSharedOTUCommand(optionString);                    }
 424                 else if(commandName == "get.otulist")                   {       pipecommand = new GetListCountCommand(optionString);                    }
 425                 else if(commandName == "hcluster")                              {       pipecommand = new HClusterCommand(optionString);                                }
 426                 else if(commandName == "classify.seqs")                 {       pipecommand = new ClassifySeqsCommand(optionString);                    }
 427                 else if(commandName == "chimera.ccode")                 {       pipecommand = new ChimeraCcodeCommand(optionString);                    }
 428                 else if(commandName == "chimera.check")                 {       pipecommand = new ChimeraCheckCommand(optionString);                    }
 429                 else if(commandName == "chimera.slayer")                {       pipecommand = new ChimeraSlayerCommand(optionString);                   }
 430                 else if(commandName == "chimera.pintail")               {       pipecommand = new ChimeraPintailCommand(optionString);                  }
 431                 else if(commandName == "chimera.bellerophon")   {       pipecommand = new ChimeraBellerophonCommand(optionString);              }
 432                 else if(commandName == "phylotype")                             {       pipecommand = new PhylotypeCommand(optionString);                               }
 433                 else if(commandName == "mgcluster")                             {       pipecommand = new MGClusterCommand(optionString);                               }
 434                 else if(commandName == "pre.cluster")                   {       pipecommand = new PreClusterCommand(optionString);                              }
 435                 else if(commandName == "pcoa")                                  {       pipecommand = new PCACommand(optionString);                                             }
 436                 else if(commandName == "otu.hierarchy")                 {       pipecommand = new OtuHierarchyCommand(optionString);                    }
 437                 else if(commandName == "set.dir")                               {       pipecommand = new SetDirectoryCommand(optionString);                    }
 438                 else if(commandName == "set.logfile")                   {       pipecommand = new SetLogFileCommand(optionString);                              }
 439                 else if(commandName == "parse.list")                    {       pipecommand = new ParseListCommand(optionString);                               }
 440                 else if(commandName == "parse.sff")                             {       pipecommand = new ParseSFFCommand(optionString);                                }
 441                 else if(commandName == "phylo.diversity")               {       pipecommand = new PhyloDiversityCommand(optionString);                  }
 442                 else if(commandName == "make.group")                    {       pipecommand = new MakeGroupCommand(optionString);                               }
 443                 else if(commandName == "chop.seqs")                             {       pipecommand = new ChopSeqsCommand(optionString);                                }
 444                 else if(commandName == "clearcut")                              {       pipecommand = new ClearcutCommand(optionString);                                }
 445                 else if(commandName == "catchall")                              {       pipecommand = new CatchAllCommand(optionString);                                }
 446                 else if(commandName == "split.abund")                   {       pipecommand = new SplitAbundCommand(optionString);                              }
 447                 else if(commandName == "cluster.split")                 {       pipecommand = new ClusterSplitCommand(optionString);                    }
 448                 else if(commandName == "classify.otu")                  {       pipecommand = new ClassifyOtuCommand(optionString);                             }
 449                 else if(commandName == "degap.seqs")                    {       pipecommand = new DegapSeqsCommand(optionString);                               }
 450                 else if(commandName == "get.relabund")                  {       pipecommand = new GetRelAbundCommand(optionString);                             }
 451                 else if(commandName == "sens.spec")                             {       pipecommand = new SensSpecCommand(optionString);                                }
 452                 else if(commandName == "seq.error")                             {       pipecommand = new SeqErrorCommand(optionString);                                }
 453                 else if(commandName == "sffinfo")                               {       pipecommand = new SffInfoCommand(optionString);                                 }
 454                 else if(commandName == "normalize.shared")              {       pipecommand = new NormalizeSharedCommand(optionString);                 }
 455                 else if(commandName == "metastats")                             {       pipecommand = new MetaStatsCommand(optionString);                               }
 456                 else if(commandName == "split.groups")                  {       pipecommand = new SplitGroupCommand(optionString);                              }
 457                 else if(commandName == "cluster.fragments")             {       pipecommand = new ClusterFragmentsCommand(optionString);                }
 458                 else if(commandName == "get.lineage")                   {       pipecommand = new GetLineageCommand(optionString);                              }
 459                 else if(commandName == "remove.lineage")                {       pipecommand = new RemoveLineageCommand(optionString);                   }
 460                 else if(commandName == "fastq.info")                    {       pipecommand = new ParseFastaQCommand(optionString);                             }
 461                 else if(commandName == "deunique.seqs")                 {       pipecommand = new DeUniqueSeqsCommand(optionString);                    }
 462                 else if(commandName == "pairwise.seqs")                 {       pipecommand = new PairwiseSeqsCommand(optionString);                    }
 463                 else if(commandName == "cluster.classic")               {       pipecommand = new ClusterDoturCommand(optionString);                    }
 464                 else if(commandName == "sub.sample")                    {       pipecommand = new SubSampleCommand(optionString);                               }
 465                 else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 466
 467                 return pipecommand;
 468         }
 469         catch(exception& e) {
 470                 m->errorOut(e, "CommandFactory", "getCommand");
 471                 exit(1);
 472         }
 473 }
 474 /***********************************************************/
 475
 476 /***********************************************************/
 477 //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
 478 Command* CommandFactory::getCommand(string commandName){
 479         try {
 480                 delete shellcommand;   //delete the old command
 481
 482                 if(commandName == "read.dist")                                  {       shellcommand = new ReadDistCommand();                           }
 483                 else if(commandName == "read.otu")                              {       shellcommand = new ReadOtuCommand();                            }
 484                 else if(commandName == "read.tree")                             {       shellcommand = new ReadTreeCommand();                           }
 485                 else if(commandName == "cluster")                               {       shellcommand = new ClusterCommand();                            }
 486                 else if(commandName == "unique.seqs")                   {       shellcommand = new DeconvoluteCommand();                        }
 487                 else if(commandName == "parsimony")                             {       shellcommand = new ParsimonyCommand();                          }
 488                 else if(commandName == "help")                                  {       shellcommand = new HelpCommand();                                       }
 489                 else if(commandName == "quit")                                  {       shellcommand = new QuitCommand();                                       }
 490                 else if(commandName == "collect.single")                {       shellcommand = new CollectCommand();                            }
 491                 else if(commandName == "collect.shared")                {       shellcommand = new CollectSharedCommand();                      }
 492                 else if(commandName == "rarefaction.single")    {       shellcommand = new RareFactCommand();                           }
 493                 else if(commandName == "rarefaction.shared")    {       shellcommand = new RareFactSharedCommand();                     }
 494                 else if(commandName == "summary.single")                {       shellcommand = new SummaryCommand();                            }
 495                 else if(commandName == "summary.shared")                {       shellcommand = new SummarySharedCommand();                      }
 496                 else if(commandName == "unifrac.weighted")              {       shellcommand = new UnifracWeightedCommand();            }
 497                 else if(commandName == "unifrac.unweighted")    {       shellcommand = new UnifracUnweightedCommand();          }
 498                 else if(commandName == "get.group")             {   shellcommand = new GetgroupCommand();                               }
 499                 else if(commandName == "get.label")             {   shellcommand = new GetlabelCommand();                               }
 500                 else if(commandName == "get.sabund")            {   shellcommand = new GetSAbundCommand();                              }
 501                 else if(commandName == "get.rabund")            {   shellcommand = new GetRAbundCommand();                              }
 502                 else if(commandName == "libshuff")              {   shellcommand = new LibShuffCommand();                               }
 503                 else if(commandName == "heatmap.bin")                   {   shellcommand = new HeatMapCommand();                                }
 504                 else if(commandName == "heatmap.sim")                   {   shellcommand = new HeatMapSimCommand();                             }
 505                 else if(commandName == "filter.seqs")                   {   shellcommand = new FilterSeqsCommand();                             }
 506                 else if(commandName == "venn")                                  {   shellcommand = new VennCommand();                                   }
 507                 else if(commandName == "bin.seqs")                              {   shellcommand = new BinSeqCommand();                                 }
 508                 else if(commandName == "get.oturep")                    {   shellcommand = new GetOTURepCommand();                              }
 509                 else if(commandName == "tree.shared")                   {   shellcommand = new TreeGroupCommand();                              }
 510                 else if(commandName == "dist.shared")                   {   shellcommand = new MatrixOutputCommand();                   }
 511                 else if(commandName == "bootstrap.shared")              {   shellcommand = new BootSharedCommand();                             }
 512                 else if(commandName == "consensus")                             {   shellcommand = new ConcensusCommand();                              }
 513                 else if(commandName == "dist.seqs")                             {   shellcommand = new DistanceCommand();                               }
 514                 else if(commandName == "align.seqs")                    {   shellcommand = new AlignCommand();                                  }
 515                 else if(commandName == "summary.seqs")                  {       shellcommand = new SeqSummaryCommand();                         }
 516                 else if(commandName == "screen.seqs")                   {       shellcommand = new ScreenSeqsCommand();                         }
 517                 else if(commandName == "reverse.seqs")                  {       shellcommand = new ReverseSeqsCommand();                        }
 518                 else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
 519                 else if(commandName == "chimera.seqs")                  {       shellcommand = new ChimeraSeqsCommand();                        }
 520                 else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
 521                 else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
 522                 else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }
 523                 else if(commandName == "merge.files")                   {       shellcommand = new MergeFileCommand();                          }
 524                 else if(commandName == "system")                                {       shellcommand = new SystemCommand();                                     }
 525                 else if(commandName == "align.check")                   {       shellcommand = new AlignCheckCommand();                         }
 526                 else if(commandName == "get.sharedseqs")                {       shellcommand = new GetSharedOTUCommand();                       }
 527                 else if(commandName == "get.otulist")                   {       shellcommand = new GetListCountCommand();                       }
 528                 else if(commandName == "hcluster")                              {       shellcommand = new HClusterCommand();                           }
 529                 else if(commandName == "classify.seqs")                 {       shellcommand = new ClassifySeqsCommand();                       }
 530                 else if(commandName == "chimera.ccode")                 {       shellcommand = new ChimeraCcodeCommand();                       }
 531                 else if(commandName == "chimera.check")                 {       shellcommand = new ChimeraCheckCommand();                       }
 532                 else if(commandName == "chimera.slayer")                {       shellcommand = new ChimeraSlayerCommand();                      }
 533                 else if(commandName == "chimera.pintail")               {       shellcommand = new ChimeraPintailCommand();                     }
 534                 else if(commandName == "chimera.bellerophon")   {       shellcommand = new ChimeraBellerophonCommand();         }
 535                 else if(commandName == "phylotype")                             {       shellcommand = new PhylotypeCommand();                          }
 536                 else if(commandName == "mgcluster")                             {       shellcommand = new MGClusterCommand();                          }
 537                 else if(commandName == "pre.cluster")                   {       shellcommand = new PreClusterCommand();                         }
 538                 else if(commandName == "pcoa")                                  {       shellcommand = new PCACommand();                                        }
 539                 else if(commandName == "otu.hierarchy")                 {       shellcommand = new OtuHierarchyCommand();                       }
 540                 else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
 541                 else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }
 542                 else if(commandName == "parse.list")                    {       shellcommand = new ParseListCommand();                          }
 543                 else if(commandName == "parse.sff")                             {       shellcommand = new ParseSFFCommand();                           }
 544                 else if(commandName == "phylo.diversity")               {       shellcommand = new PhyloDiversityCommand();                     }
 545                 else if(commandName == "make.group")                    {       shellcommand = new MakeGroupCommand();                          }
 546                 else if(commandName == "chop.seqs")                             {       shellcommand = new ChopSeqsCommand();                           }
 547                 else if(commandName == "clearcut")                              {       shellcommand = new ClearcutCommand();                           }
 548                 else if(commandName == "catchall")                              {       shellcommand = new CatchAllCommand();                           }
 549                 else if(commandName == "split.abund")                   {       shellcommand = new SplitAbundCommand();                         }
 550                 else if(commandName == "cluster.split")                 {       shellcommand = new ClusterSplitCommand();                       }
 551                 else if(commandName == "classify.otu")                  {       shellcommand = new ClassifyOtuCommand();                        }
 552                 else if(commandName == "degap.seqs")                    {       shellcommand = new DegapSeqsCommand();                          }
 553                 else if(commandName == "get.relabund")                  {       shellcommand = new GetRelAbundCommand();                        }
 554                 else if(commandName == "sens.spec")                             {       shellcommand = new SensSpecCommand();                           }
 555                 else if(commandName == "seq.error")                             {       shellcommand = new SeqErrorCommand();                           }
 556                 else if(commandName == "sffinfo")                               {       shellcommand = new SffInfoCommand();                            }
 557                 else if(commandName == "normalize.shared")              {       shellcommand = new NormalizeSharedCommand();            }
 558                 else if(commandName == "metastats")                             {       shellcommand = new MetaStatsCommand();                          }
 559                 else if(commandName == "split.groups")                  {       shellcommand = new SplitGroupCommand();                         }
 560                 else if(commandName == "cluster.fragments")             {       shellcommand = new ClusterFragmentsCommand();           }
 561                 else if(commandName == "get.lineage")                   {       shellcommand = new GetLineageCommand();                         }
 562                 else if(commandName == "remove.lineage")                {       shellcommand = new RemoveLineageCommand();                      }
 563                 else if(commandName == "fastq.info")                    {       shellcommand = new ParseFastaQCommand();                        }
 564                 else if(commandName == "deunique.seqs")                 {       shellcommand = new DeUniqueSeqsCommand();                       }
 565                 else if(commandName == "pairwise.seqs")                 {       shellcommand = new PairwiseSeqsCommand();                       }
 566                 else if(commandName == "cluster.classic")               {       shellcommand = new ClusterDoturCommand();                       }
 567                 else if(commandName == "sub.sample")                    {       shellcommand = new SubSampleCommand();                          }
 568                 else                                                                                    {       shellcommand = new NoCommand();                                         }
 569
 570                 return shellcommand;
 571         }
 572         catch(exception& e) {
 573                 m->errorOut(e, "CommandFactory", "getCommand");
 574                 exit(1);
 575         }
 576 }
 577 /***********************************************************
 578 //This function is used to interrupt a command
 579 Command* CommandFactory::getCommand(){
 580         try {
 581                 delete command;   //delete the old command
 582
 583                 string s = "";
 584             command = new NoCommand(s);
 585
 586                 return command;
 587         }
 588         catch(exception& e) {
 589                 m->errorOut(e, "CommandFactory", "getCommand");
 590                 exit(1);
 591         }
 592 }
 593 /***********************************************************************/
 594 bool CommandFactory::isValidCommand(string command) {
 595         try {
 596
 597                 //is the command in the map
 598                 if ((commands.find(command)) != (commands.end())) {
 599                         return true;
 600                 }else{
 601                         m->mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
 602                         for (it = commands.begin(); it != commands.end(); it++) {
 603                                 m->mothurOut(it->first + ", ");
 604                         }
 605                         m->mothurOutEndLine();
 606                         return false;
 607                 }
 608
 609         }
 610         catch(exception& e) {
 611                 m->errorOut(e, "CommandFactory", "isValidCommand");
 612                 exit(1);
 613         }
 614 }
 615 /***********************************************************************/
 616 bool CommandFactory::isValidCommand(string command, string noError) {
 617         try {
 618
 619                 //is the command in the map
 620                 if ((commands.find(command)) != (commands.end())) {
 621                         return true;
 622                 }else{
 623                         return false;
 624                 }
 625
 626         }
 627         catch(exception& e) {
 628                 m->errorOut(e, "CommandFactory", "isValidCommand");
 629                 exit(1);
 630         }
 631 }
 632 /***********************************************************************/
 633 void CommandFactory::printCommands(ostream& out) {
 634         try {
 635                 out << "Valid commands are: ";
 636                 for (it = commands.begin(); it != commands.end(); it++) {
 637                         out << it->first << ",";
 638                 }
 639                 out << endl;
 640         }
 641         catch(exception& e) {
 642                 m->errorOut(e, "CommandFactory", "printCommands");
 643                 exit(1);
 644         }
 645 }
 646 /***********************************************************************/
 647
 648
 649
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