setcurrentcommand.cpp

   1 /*
   2  *  setcurrentcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/16/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "setcurrentcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> SetCurrentCommand::setParameters(){
  14         try {
  15
  16                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  17                 CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pflow);
  18         CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pbiom);
  19                 CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
  20                 CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
  21                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
  22                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  23                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  24                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
  25                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptaxonomy);
  26                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
  27                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
  28                 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
  29                 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
  30                 CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
  31                 CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(porder);
  32                 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptree);
  33                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
  34                 CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
  35                 CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prelabund);
  36                 CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
  37                 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
  38                 CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
  39                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  40                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  41
  42                 vector<string> myArray;
  43                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  44                 return myArray;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "SetCurrentCommand", "setParameters");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 string SetCurrentCommand::getHelpString(){
  53         try {
  54                 string helpString = "";
  55                 helpString += "The set.current command allows you to set the current files saved by mothur.\n";
  56                 helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom and taxonomy.\n";
  57                 helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
  58                 helpString += "The set.current command should be in the following format: \n";
  59                 helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
  60                 return helpString;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "SetCurrentCommand", "getHelpString");
  64                 exit(1);
  65         }
  66 }
  67
  68
  69 //**********************************************************************************************************************
  70 SetCurrentCommand::SetCurrentCommand(){
  71         try {
  72                 abort = true; calledHelp = true;
  73                 setParameters();
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81 SetCurrentCommand::SetCurrentCommand(string option)  {
  82         try {
  83                 abort = false; calledHelp = false;
  84
  85                 //allow user to run help
  86                 if(option == "help") { help(); abort = true; calledHelp = true; }
  87                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  88
  89                 else {
  90                         //valid paramters for this command
  91                         vector<string> myArray = setParameters();
  92
  93                         OptionParser parser(option);
  94                         map<string,string> parameters = parser.getParameters();
  95
  96                         ValidParameters validParameter;
  97                         map<string,string>::iterator it;
  98                         //check to make sure all parameters are valid for command
  99                         for (it = parameters.begin(); it != parameters.end(); it++) {
 100                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 101                         }
 102
 103
 104                         //if the user changes the input directory command factory will send this info to us in the output parameter
 105                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 106                         if (inputDir == "not found"){   inputDir = "";          }
 107                         else {
 108                                 string path;
 109                                 it = parameters.find("phylip");
 110                                 //user has given a template file
 111                                 if(it != parameters.end()){
 112                                         path = m->hasPath(it->second);
 113                                         //if the user has not given a path then, add inputdir. else leave path alone.
 114                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 115                                 }
 116
 117                                 it = parameters.find("column");
 118                                 //user has given a template file
 119                                 if(it != parameters.end()){
 120                                         path = m->hasPath(it->second);
 121                                         //if the user has not given a path then, add inputdir. else leave path alone.
 122                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 123                                 }
 124
 125                                 it = parameters.find("fasta");
 126                                 //user has given a template file
 127                                 if(it != parameters.end()){
 128                                         path = m->hasPath(it->second);
 129                                         //if the user has not given a path then, add inputdir. else leave path alone.
 130                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 131                                 }
 132
 133                                 it = parameters.find("list");
 134                                 //user has given a template file
 135                                 if(it != parameters.end()){
 136                                         path = m->hasPath(it->second);
 137                                         //if the user has not given a path then, add inputdir. else leave path alone.
 138                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 139                                 }
 140
 141                                 it = parameters.find("rabund");
 142                                 //user has given a template file
 143                                 if(it != parameters.end()){
 144                                         path = m->hasPath(it->second);
 145                                         //if the user has not given a path then, add inputdir. else leave path alone.
 146                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 147                                 }
 148
 149                                 it = parameters.find("sabund");
 150                                 //user has given a template file
 151                                 if(it != parameters.end()){
 152                                         path = m->hasPath(it->second);
 153                                         //if the user has not given a path then, add inputdir. else leave path alone.
 154                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 155                                 }
 156
 157                                 it = parameters.find("name");
 158                                 //user has given a template file
 159                                 if(it != parameters.end()){
 160                                         path = m->hasPath(it->second);
 161                                         //if the user has not given a path then, add inputdir. else leave path alone.
 162                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 163                                 }
 164
 165                                 it = parameters.find("group");
 166                                 //user has given a template file
 167                                 if(it != parameters.end()){
 168                                         path = m->hasPath(it->second);
 169                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 171                                 }
 172
 173                                 it = parameters.find("design");
 174                                 //user has given a template file
 175                                 if(it != parameters.end()){
 176                                         path = m->hasPath(it->second);
 177                                         //if the user has not given a path then, add inputdir. else leave path alone.
 178                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 179                                 }
 180
 181                                 it = parameters.find("order");
 182                                 //user has given a template file
 183                                 if(it != parameters.end()){
 184                                         path = m->hasPath(it->second);
 185                                         //if the user has not given a path then, add inputdir. else leave path alone.
 186                                         if (path == "") {       parameters["order"] = inputDir + it->second;            }
 187                                 }
 188
 189                                 it = parameters.find("tree");
 190                                 //user has given a template file
 191                                 if(it != parameters.end()){
 192                                         path = m->hasPath(it->second);
 193                                         //if the user has not given a path then, add inputdir. else leave path alone.
 194                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 195                                 }
 196
 197                                 it = parameters.find("shared");
 198                                 //user has given a template file
 199                                 if(it != parameters.end()){
 200                                         path = m->hasPath(it->second);
 201                                         //if the user has not given a path then, add inputdir. else leave path alone.
 202                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 203                                 }
 204
 205                                 it = parameters.find("ordergroup");
 206                                 //user has given a template file
 207                                 if(it != parameters.end()){
 208                                         path = m->hasPath(it->second);
 209                                         //if the user has not given a path then, add inputdir. else leave path alone.
 210                                         if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
 211                                 }
 212
 213                                 it = parameters.find("relabund");
 214                                 //user has given a template file
 215                                 if(it != parameters.end()){
 216                                         path = m->hasPath(it->second);
 217                                         //if the user has not given a path then, add inputdir. else leave path alone.
 218                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 219                                 }
 220
 221                                 it = parameters.find("fasta");
 222                                 //user has given a template file
 223                                 if(it != parameters.end()){
 224                                         path = m->hasPath(it->second);
 225                                         //if the user has not given a path then, add inputdir. else leave path alone.
 226                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 227                                 }
 228
 229                                 it = parameters.find("qfile");
 230                                 //user has given a template file
 231                                 if(it != parameters.end()){
 232                                         path = m->hasPath(it->second);
 233                                         //if the user has not given a path then, add inputdir. else leave path alone.
 234                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 235                                 }
 236
 237                                 it = parameters.find("sff");
 238                                 //user has given a template file
 239                                 if(it != parameters.end()){
 240                                         path = m->hasPath(it->second);
 241                                         //if the user has not given a path then, add inputdir. else leave path alone.
 242                                         if (path == "") {       parameters["sff"] = inputDir + it->second;              }
 243                                 }
 244
 245                                 it = parameters.find("oligos");
 246                                 //user has given a template file
 247                                 if(it != parameters.end()){
 248                                         path = m->hasPath(it->second);
 249                                         //if the user has not given a path then, add inputdir. else leave path alone.
 250                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 251                                 }
 252
 253                                 it = parameters.find("accnos");
 254                                 //user has given a template file
 255                                 if(it != parameters.end()){
 256                                         path = m->hasPath(it->second);
 257                                         //if the user has not given a path then, add inputdir. else leave path alone.
 258                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 259                                 }
 260
 261                                 it = parameters.find("taxonomy");
 262                                 //user has given a template file
 263                                 if(it != parameters.end()){
 264                                         path = m->hasPath(it->second);
 265                                         //if the user has not given a path then, add inputdir. else leave path alone.
 266                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 267                                 }
 268
 269                                 it = parameters.find("flow");
 270                                 //user has given a template file
 271                                 if(it != parameters.end()){
 272                                         path = m->hasPath(it->second);
 273                                         //if the user has not given a path then, add inputdir. else leave path alone.
 274                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 275                                 }
 276
 277                 it = parameters.find("biom");
 278                                 //user has given a template file
 279                                 if(it != parameters.end()){
 280                                         path = m->hasPath(it->second);
 281                                         //if the user has not given a path then, add inputdir. else leave path alone.
 282                                         if (path == "") {       parameters["biom"] = inputDir + it->second;             }
 283                                 }
 284                         }
 285
 286                         //check for parameters
 287                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 288                         if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
 289                         else if (phylipfile == "not found") {  phylipfile = "";  }
 290                         if (phylipfile != "") { m->setPhylipFile(phylipfile); }
 291
 292                         columnfile = validParameter.validFile(parameters, "column", true);
 293                         if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
 294                         else if (columnfile == "not found") {  columnfile = "";  }
 295                         if (columnfile != "") { m->setColumnFile(columnfile); }
 296
 297                         listfile = validParameter.validFile(parameters, "list", true);
 298                         if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
 299                         else if (listfile == "not found") {  listfile = "";  }
 300                         if (listfile != "") { m->setListFile(listfile); }
 301
 302                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 303                         if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
 304                         else if (rabundfile == "not found") {  rabundfile = "";  }
 305                         if (rabundfile != "") { m->setRabundFile(rabundfile); }
 306
 307                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 308                         if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
 309                         else if (sabundfile == "not found") {  sabundfile = "";  }
 310                         if (sabundfile != "") { m->setSabundFile(sabundfile); }
 311
 312                         namefile = validParameter.validFile(parameters, "name", true);
 313                         if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
 314                         else if (namefile == "not found") {  namefile = "";  }
 315                         if (namefile != "") { m->setNameFile(namefile); }
 316
 317                         groupfile = validParameter.validFile(parameters, "group", true);
 318                         if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
 319                         else if (groupfile == "not found") {  groupfile = "";  }
 320                         if (groupfile != "") { m->setGroupFile(groupfile); }
 321
 322                         designfile = validParameter.validFile(parameters, "design", true);
 323                         if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
 324                         else if (designfile == "not found") {  designfile = "";  }
 325                         if (designfile != "") { m->setDesignFile(designfile); }
 326
 327                         orderfile = validParameter.validFile(parameters, "order", true);
 328                         if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
 329                         else if (orderfile == "not found") {  orderfile = "";  }
 330                         if (orderfile != "") { m->setOrderFile(orderfile); }
 331
 332                         treefile = validParameter.validFile(parameters, "tree", true);
 333                         if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
 334                         else if (treefile == "not found") {  treefile = "";  }
 335                         if (treefile != "") { m->setTreeFile(treefile); }
 336
 337                         sharedfile = validParameter.validFile(parameters, "shared", true);
 338                         if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
 339                         else if (sharedfile == "not found") {  sharedfile = "";  }
 340                         if (sharedfile != "") { m->setSharedFile(sharedfile); }
 341
 342                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 343                         if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
 344                         else if (ordergroupfile == "not found") {  ordergroupfile = "";  }
 345                         if (ordergroupfile != "") { m->setOrderGroupFile(ordergroupfile); }
 346
 347                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 348                         if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
 349                         else if (relabundfile == "not found") {  relabundfile = "";  }
 350                         if (relabundfile != "") { m->setRelAbundFile(relabundfile); }
 351
 352                         fastafile = validParameter.validFile(parameters, "fasta", true);
 353                         if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
 354                         else if (fastafile == "not found") {  fastafile = "";  }
 355                         if (fastafile != "") { m->setFastaFile(fastafile); }
 356
 357                         qualfile = validParameter.validFile(parameters, "qfile", true);
 358                         if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
 359                         else if (qualfile == "not found") {  qualfile = "";  }
 360                         if (qualfile != "") { m->setQualFile(qualfile); }
 361
 362                         sfffile = validParameter.validFile(parameters, "sff", true);
 363                         if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
 364                         else if (sfffile == "not found") {  sfffile = "";  }
 365                         if (sfffile != "") { m->setSFFFile(sfffile); }
 366
 367                         oligosfile = validParameter.validFile(parameters, "oligos", true);
 368                         if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
 369                         else if (oligosfile == "not found") {  oligosfile = "";  }
 370                         if (oligosfile != "") { m->setOligosFile(oligosfile); }
 371
 372                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 373                         if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
 374                         else if (accnosfile == "not found") {  accnosfile = "";  }
 375                         if (accnosfile != "") { m->setAccnosFile(accnosfile); }
 376
 377                         taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
 378                         if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
 379                         else if (taxonomyfile == "not found") {  taxonomyfile = "";  }
 380                         if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
 381
 382                         flowfile = validParameter.validFile(parameters, "flow", true);
 383                         if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
 384                         else if (flowfile == "not found") {  flowfile = "";  }
 385                         if (flowfile != "") { m->setFlowFile(flowfile); }
 386
 387             biomfile = validParameter.validFile(parameters, "biom", true);
 388                         if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine(); biomfile = ""; }
 389                         else if (biomfile == "not found") {  biomfile = "";  }
 390                         if (biomfile != "") { m->setBiomFile(biomfile); }
 391
 392                         processors = validParameter.validFile(parameters, "processors", false);
 393                         if (processors == "not found") {  processors = "1";  }
 394                         if (processors != "") { m->setProcessors(processors); }
 395
 396                         clearTypes = validParameter.validFile(parameters, "clear", false);
 397                         if (clearTypes == "not found") { clearTypes = ""; }
 398                         else { m->splitAtDash(clearTypes, types);       }
 399                 }
 400
 401         }
 402         catch(exception& e) {
 403                 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
 404                 exit(1);
 405         }
 406 }
 407 //**********************************************************************************************************************
 408
 409 int SetCurrentCommand::execute(){
 410         try {
 411
 412                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 413
 414                 //user wants to clear a type
 415                 if (types.size() != 0) {
 416                         for (int i = 0; i < types.size(); i++) {
 417
 418                                 if (m->control_pressed) { break; }
 419
 420                                 //look for file types
 421                                 if (types[i] == "fasta") {
 422                                         m->setFastaFile("");
 423                                 }else if (types[i] == "qfile") {
 424                                         m->setQualFile("");
 425                                 }else if (types[i] == "phylip") {
 426                                         m->setPhylipFile("");
 427                                 }else if (types[i] == "column") {
 428                                         m->setColumnFile("");
 429                                 }else if (types[i] == "list") {
 430                                         m->setListFile("");
 431                                 }else if (types[i] == "rabund") {
 432                                         m->setRabundFile("");
 433                                 }else if (types[i] == "sabund") {
 434                                         m->setSabundFile("");
 435                                 }else if (types[i] == "name") {
 436                                         m->setNameFile("");
 437                                 }else if (types[i] == "group") {
 438                                         m->setGroupFile("");
 439                                 }else if (types[i] == "order") {
 440                                         m->setOrderFile("");
 441                                 }else if (types[i] == "ordergroup") {
 442                                         m->setOrderGroupFile("");
 443                                 }else if (types[i] == "tree") {
 444                                         m->setTreeFile("");
 445                                 }else if (types[i] == "shared") {
 446                                         m->setSharedFile("");
 447                                 }else if (types[i] == "relabund") {
 448                                         m->setRelAbundFile("");
 449                                 }else if (types[i] == "design") {
 450                                         m->setDesignFile("");
 451                                 }else if (types[i] == "sff") {
 452                                         m->setSFFFile("");
 453                                 }else if (types[i] == "oligos") {
 454                                         m->setOligosFile("");
 455                                 }else if (types[i] == "accnos") {
 456                                         m->setAccnosFile("");
 457                                 }else if (types[i] == "taxonomy") {
 458                                         m->setTaxonomyFile("");
 459                                 }else if (types[i] == "flow") {
 460                                         m->setFlowFile("");
 461                 }else if (types[i] == "biom") {
 462                                         m->setBiomFile("");
 463                                 }else if (types[i] == "processors") {
 464                                         m->setProcessors("1");
 465                                 }else if (types[i] == "all") {
 466                                         m->clearCurrentFiles();
 467                                 }else {
 468                                         m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
 469                                 }
 470                         }
 471                 }
 472
 473                 m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
 474                 m->printCurrentFiles();
 475
 476                 return 0;
 477         }
 478
 479         catch(exception& e) {
 480                 m->errorOut(e, "SetCurrentCommand", "execute");
 481                 exit(1);
 482         }
 483 }
 484
 485 //**********************************************************************************************************************
 486
 487
 488