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
  96 /*******************************************************/
  97
  98 /******************************************************/
  99 CommandFactory* CommandFactory::getInstance() {
 100         if( _uniqueInstance == 0) {
 101                 _uniqueInstance = new CommandFactory();
 102         }
 103         return _uniqueInstance;
 104 }
 105 /***********************************************************/
 106
 107 /***********************************************************/
 108 //note: This class is resposible for knowing which commands are mpiEnabled,
 109 //If a command is not enabled only process 0 will execute the command.
 110 //This avoids redundant outputs on pieces of code we have not paralellized.
 111 //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.
 112 //example:  commands["dist.seqs"] = "MPIEnabled";
 113
 114 CommandFactory::CommandFactory(){
 115         string s = "";
 116         m = MothurOut::getInstance();
 117
 118         command = new NoCommand(s);
 119
 120         outputDir = ""; inputDir = "";
 121         logFileName = "";
 122         append = false;
 123
 124         //initialize list of valid commands
 125         commands["read.dist"]                   = "read.dist";
 126         commands["read.otu"]                    = "read.otu";
 127         commands["read.tree"]                   = "read.tree";
 128         commands["bin.seqs"]                    = "bin.seqs";
 129         commands["get.oturep"]                  = "get.oturep";
 130         commands["cluster"]                             = "cluster";
 131         commands["unique.seqs"]                 = "unique.seqs";
 132         commands["dist.shared"]                 = "dist.shared";
 133         commands["collect.single"]              = "collect.single";
 134         commands["collect.shared"]              = "collect.shared";
 135         commands["rarefaction.single"]  = "rarefaction.single";
 136         commands["rarefaction.shared"]  = "rarefaction.shared";
 137         commands["summary.single"]              = "summary.single";
 138         commands["summary.shared"]              = "summary.shared";
 139         commands["parsimony"]                   = "parsimony";
 140         commands["unifrac.weighted"]    = "unifrac.weighted";
 141         commands["unifrac.unweighted"]  = "unifrac.unweighted";
 142         commands["libshuff"]                    = "libshuff";
 143         commands["tree.shared"]                 = "tree.shared";
 144         commands["heatmap.bin"]                 = "heatmap.bin";
 145         commands["heatmap.sim"]                 = "heatmap.sim";
 146         commands["venn"]                                = "venn";
 147         commands["get.group"]           = "get.group";
 148         commands["get.label"]           = "get.label";
 149         commands["get.sabund"]          = "get.sabund";
 150         commands["get.rabund"]          = "get.rabund";
 151         commands["bootstrap.shared"]    = "bootstrap.shared";
 152         //commands["consensus"]                 = "consensus";
 153         commands["help"]                                = "help";
 154         commands["reverse.seqs"]                = "reverse.seqs";
 155         commands["trim.seqs"]                   = "trim.seqs";
 156         commands["list.seqs"]                   = "list.seqs";
 157         commands["get.seqs"]                    = "get.seqs";
 158         commands["remove.seqs"]                 = "get.seqs";
 159         commands["system"]                              = "system";
 160         commands["align.check"]                 = "align.check";
 161         commands["get.sharedseqs"]              = "get.sharedseqs";
 162         commands["get.otulist"]                 = "get.otulist";
 163         commands["hcluster"]                    = "hcluster";
 164         commands["phylotype"]                   = "phylotype";
 165         commands["mgcluster"]                   = "mgcluster";
 166         commands["pre.cluster"]                 = "pre.cluster";
 167         commands["pcoa"]                                = "pcoa";
 168         commands["otu.hierarchy"]               = "otu.hierarchy";
 169         commands["set.dir"]                             = "set.dir";
 170         commands["merge.files"]                 = "merge.files";
 171         commands["parse.list"]                  = "parse.list";
 172         commands["parse.sff"]                   = "parse.sff";
 173         commands["set.logfile"]                 = "set.logfile";
 174         commands["phylo.diversity"]             = "phylo.diversity";
 175         commands["make.group"]                  = "make.group";
 176         commands["chop.seqs"]                   = "chop.seqs";
 177         commands["clearcut"]                    = "clearcut";
 178         commands["catchall"]                    = "catchall";
 179         commands["split.abund"]                 = "split.abund";
 180         commands["classify.otu"]                = "classify.otu";
 181         commands["degap.seqs"]                  = "degap.seqs";
 182         commands["get.relabund"]                = "get.relabund";
 183         commands["sffinfo"]                             = "sffinfo";
 184         commands["normalize.shared"]    = "normalize.shared";
 185         commands["metastats"]                   = "metastats";
 186         commands["split.groups"]                = "split.groups";
 187         commands["cluster.fragments"]   = "cluster.fragments";
 188         commands["get.lineage"]                 = "get.lineage";
 189         commands["remove.lineage"]              = "remove.lineage";
 190         commands["parse.fastaq"]                = "parse.fastaq";
 191         commands["classify.seqs"]               = "MPIEnabled";
 192         commands["dist.seqs"]                   = "MPIEnabled";
 193         commands["filter.seqs"]                 = "MPIEnabled";
 194         commands["align.seqs"]                  = "MPIEnabled";
 195         commands["chimera.seqs"]                = "chimera.seqs";
 196         commands["chimera.ccode"]               = "MPIEnabled";
 197         commands["chimera.check"]               = "MPIEnabled";
 198         commands["chimera.slayer"]              = "MPIEnabled";
 199         commands["chimera.pintail"]             = "MPIEnabled";
 200         commands["chimera.bellerophon"] = "MPIEnabled";
 201         commands["screen.seqs"]                 = "MPIEnabled";
 202         commands["summary.seqs"]                = "MPIEnabled";
 203         commands["cluster.split"]               = "MPIEnabled";
 204         commands["sens.spec"]                   = "sens.spec";
 205         commands["seq.error"]                   = "seq.error";
 206         commands["quit"]                                = "MPIEnabled";
 207
 208 }
 209 /***********************************************************/
 210
 211 /***********************************************************/
 212 bool CommandFactory::MPIEnabled(string commandName) {
 213         bool mpi = false;
 214         it = commands.find(commandName);
 215         if (it != commands.end()) {
 216                 if (it->second == "MPIEnabled") { return true; }
 217         }
 218         return mpi;
 219 }
 220 /***********************************************************/
 221
 222 /***********************************************************/
 223 CommandFactory::~CommandFactory(){
 224         _uniqueInstance = 0;
 225         delete command;
 226 }
 227
 228 /***********************************************************/
 229
 230 /***********************************************************/
 231 //This function calls the appropriate command fucntions based on user input.
 232 Command* CommandFactory::getCommand(string commandName, string optionString){
 233         try {
 234                 delete command;   //delete the old command
 235
 236                 //user has opted to redirect output from dir where input files are located to some other place
 237                 if (outputDir != "") {
 238                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 239                         else { optionString += "outputdir=" + outputDir; }
 240                 }
 241
 242                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 243                 if (inputDir != "") {
 244                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 245                         else { optionString += "inputdir=" + inputDir; }
 246                 }
 247
 248                 if(commandName == "read.dist")                                  {       command = new ReadDistCommand(optionString);                            }
 249                 else if(commandName == "read.otu")                              {       command = new ReadOtuCommand(optionString);                                     }
 250                 else if(commandName == "read.tree")                             {       command = new ReadTreeCommand(optionString);                            }
 251                 else if(commandName == "cluster")                               {       command = new ClusterCommand(optionString);                                     }
 252                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand(optionString);                         }
 253                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand(optionString);                           }
 254                 else if(commandName == "help")                                  {       command = new HelpCommand(optionString);                                        }
 255                 else if(commandName == "quit")                                  {       command = new QuitCommand(optionString);                                        }
 256                 else if(commandName == "collect.single")                {       command = new CollectCommand(optionString);                                     }
 257                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand(optionString);                       }
 258                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand(optionString);                            }
 259                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand(optionString);                      }
 260                 else if(commandName == "summary.single")                {       command = new SummaryCommand(optionString);                                     }
 261                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand(optionString);                       }
 262                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand(optionString);                     }
 263                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);           }
 264                 else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                                }
 265                 else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                                }
 266                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                               }
 267                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                               }
 268                 else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                                }
 269                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand(optionString);                                 }
 270                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand(optionString);                              }
 271                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand(optionString);                              }
 272                 else if(commandName == "venn")                                  {   command = new VennCommand(optionString);                                    }
 273                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand(optionString);                                  }
 274                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                               }
 275                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                               }
 276                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);                    }
 277                 else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                              }
 278                 else if(commandName == "consensus")                             {   command = new ConcensusCommand(optionString);                               }
 279                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                                }
 280                 else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                                   }
 281                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                          }
 282                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                          }
 283                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
 284                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
 285                 else if(commandName == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(optionString);                         }
 286                 else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
 287                 else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
 288                 else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
 289                 else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                           }
 290                 else if(commandName == "system")                                {       command = new SystemCommand(optionString);                                      }
 291                 else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                          }
 292                 else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                        }
 293                 else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                        }
 294                 else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                            }
 295                 else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                        }
 296                 else if(commandName == "chimera.ccode")                 {       command = new ChimeraCcodeCommand(optionString);                        }
 297                 else if(commandName == "chimera.check")                 {       command = new ChimeraCheckCommand(optionString);                        }
 298                 else if(commandName == "chimera.slayer")                {       command = new ChimeraSlayerCommand(optionString);                       }
 299                 else if(commandName == "chimera.pintail")               {       command = new ChimeraPintailCommand(optionString);                      }
 300                 else if(commandName == "chimera.bellerophon")   {       command = new ChimeraBellerophonCommand(optionString);          }
 301                 else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
 302                 else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                           }
 303                 else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                          }
 304                 else if(commandName == "pcoa")                                  {       command = new PCACommand(optionString);                                         }
 305                 else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
 306                 else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
 307                 else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
 308                 else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
 309                 else if(commandName == "parse.sff")                             {       command = new ParseSFFCommand(optionString);                            }
 310                 else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
 311                 else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
 312                 else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
 313                 else if(commandName == "clearcut")                              {       command = new ClearcutCommand(optionString);                            }
 314                 else if(commandName == "catchall")                              {       command = new CatchAllCommand(optionString);                            }
 315                 else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
 316                 else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
 317                 else if(commandName == "classify.otu")                  {       command = new ClassifyOtuCommand(optionString);                         }
 318                 else if(commandName == "degap.seqs")                    {       command = new DegapSeqsCommand(optionString);                           }
 319                 else if(commandName == "get.relabund")                  {       command = new GetRelAbundCommand(optionString);                         }
 320                 else if(commandName == "sens.spec")                             {       command = new SensSpecCommand(optionString);                            }
 321                 else if(commandName == "seq.error")                             {       command = new SeqErrorCommand(optionString);                            }
 322                 else if(commandName == "sffinfo")                               {       command = new SffInfoCommand(optionString);                                     }
 323                 else if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
 324                 else if(commandName == "metastats")                             {       command = new MetaStatsCommand(optionString);                           }
 325                 else if(commandName == "split.groups")                  {       command = new SplitGroupCommand(optionString);                          }
 326                 else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
 327                 else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
 328                 else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
 329                 else if(commandName == "parse.fastaq")                  {       command = new ParseFastaQCommand(optionString);                         }
 330                 else                                                                                    {       command = new NoCommand(optionString);                                          }
 331
 332                 return command;
 333         }
 334         catch(exception& e) {
 335                 m->errorOut(e, "CommandFactory", "getCommand");
 336                 exit(1);
 337         }
 338 }
 339 /***********************************************************/
 340 //This function is used to interrupt a command
 341 Command* CommandFactory::getCommand(){
 342         try {
 343                 delete command;   //delete the old command
 344
 345                 string s = "";
 346             command = new NoCommand(s);
 347
 348                 return command;
 349         }
 350         catch(exception& e) {
 351                 m->errorOut(e, "CommandFactory", "getCommand");
 352                 exit(1);
 353         }
 354 }
 355 /***********************************************************************/
 356 bool CommandFactory::isValidCommand(string command) {
 357         try {
 358
 359                 //is the command in the map
 360                 if ((commands.find(command)) != (commands.end())) {
 361                         return true;
 362                 }else{
 363                         m->mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
 364                         for (it = commands.begin(); it != commands.end(); it++) {
 365                                 m->mothurOut(it->first + ", ");
 366                         }
 367                         m->mothurOutEndLine();
 368                         return false;
 369                 }
 370
 371         }
 372         catch(exception& e) {
 373                 m->errorOut(e, "CommandFactory", "isValidCommand");
 374                 exit(1);
 375         }
 376 }
 377
 378 /***********************************************************************/
 379 void CommandFactory::printCommands(ostream& out) {
 380         try {
 381                 out << "Valid commands are: ";
 382                 for (it = commands.begin(); it != commands.end(); it++) {
 383                         out << it->first << ",";
 384                 }
 385                 out << endl;
 386         }
 387         catch(exception& e) {
 388                 m->errorOut(e, "CommandFactory", "printCommands");
 389                 exit(1);
 390         }
 391 }
 392 /***********************************************************************/
 393
 394
 395
 396