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,true); 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 pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount);
  36                 CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund);
  37                 CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff);
  38                 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
  39                 CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
  40                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  41                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  42
  43                 vector<string> myArray;
  44                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  45                 return myArray;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "SetCurrentCommand", "setParameters");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 string SetCurrentCommand::getHelpString(){
  54         try {
  55                 string helpString = "";
  56                 helpString += "The set.current command allows you to set the current files saved by mothur.\n";
  57                 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, count and taxonomy.\n";
  58                 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";
  59                 helpString += "The set.current command should be in the following format: \n";
  60                 helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
  61                 return helpString;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "SetCurrentCommand", "getHelpString");
  65                 exit(1);
  66         }
  67 }
  68
  69
  70 //**********************************************************************************************************************
  71 SetCurrentCommand::SetCurrentCommand(){
  72         try {
  73                 abort = true; calledHelp = true;
  74                 setParameters();
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82 SetCurrentCommand::SetCurrentCommand(string option)  {
  83         try {
  84                 abort = false; calledHelp = false;
  85
  86                 //allow user to run help
  87                 if(option == "help") { help(); abort = true; calledHelp = true; }
  88                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  89
  90                 else {
  91                         //valid paramters for this command
  92                         vector<string> myArray = setParameters();
  93
  94                         OptionParser parser(option);
  95                         map<string,string> parameters = parser.getParameters();
  96
  97                         ValidParameters validParameter;
  98                         map<string,string>::iterator it;
  99                         //check to make sure all parameters are valid for command
 100                         for (it = parameters.begin(); it != parameters.end(); it++) {
 101                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 102                         }
 103
 104
 105                         //if the user changes the input directory command factory will send this info to us in the output parameter
 106                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 107                         if (inputDir == "not found"){   inputDir = "";          }
 108                         else {
 109                                 string path;
 110                                 it = parameters.find("phylip");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 116                                 }
 117
 118                                 it = parameters.find("column");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 124                                 }
 125
 126                                 it = parameters.find("fasta");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 132                                 }
 133
 134                                 it = parameters.find("list");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 140                                 }
 141
 142                                 it = parameters.find("rabund");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 148                                 }
 149
 150                                 it = parameters.find("sabund");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 156                                 }
 157
 158                                 it = parameters.find("name");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 164                                 }
 165
 166                                 it = parameters.find("group");
 167                                 //user has given a template file
 168                                 if(it != parameters.end()){
 169                                         path = m->hasPath(it->second);
 170                                         //if the user has not given a path then, add inputdir. else leave path alone.
 171                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 172                                 }
 173
 174                                 it = parameters.find("design");
 175                                 //user has given a template file
 176                                 if(it != parameters.end()){
 177                                         path = m->hasPath(it->second);
 178                                         //if the user has not given a path then, add inputdir. else leave path alone.
 179                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 180                                 }
 181
 182                                 it = parameters.find("order");
 183                                 //user has given a template file
 184                                 if(it != parameters.end()){
 185                                         path = m->hasPath(it->second);
 186                                         //if the user has not given a path then, add inputdir. else leave path alone.
 187                                         if (path == "") {       parameters["order"] = inputDir + it->second;            }
 188                                 }
 189
 190                                 it = parameters.find("tree");
 191                                 //user has given a template file
 192                                 if(it != parameters.end()){
 193                                         path = m->hasPath(it->second);
 194                                         //if the user has not given a path then, add inputdir. else leave path alone.
 195                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 196                                 }
 197
 198                                 it = parameters.find("shared");
 199                                 //user has given a template file
 200                                 if(it != parameters.end()){
 201                                         path = m->hasPath(it->second);
 202                                         //if the user has not given a path then, add inputdir. else leave path alone.
 203                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 204                                 }
 205
 206                                 it = parameters.find("ordergroup");
 207                                 //user has given a template file
 208                                 if(it != parameters.end()){
 209                                         path = m->hasPath(it->second);
 210                                         //if the user has not given a path then, add inputdir. else leave path alone.
 211                                         if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
 212                                 }
 213
 214                 it = parameters.find("count");
 215                                 //user has given a template file
 216                                 if(it != parameters.end()){
 217                                         path = m->hasPath(it->second);
 218                                         //if the user has not given a path then, add inputdir. else leave path alone.
 219                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 220                                 }
 221
 222                                 it = parameters.find("relabund");
 223                                 //user has given a template file
 224                                 if(it != parameters.end()){
 225                                         path = m->hasPath(it->second);
 226                                         //if the user has not given a path then, add inputdir. else leave path alone.
 227                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 228                                 }
 229
 230                                 it = parameters.find("fasta");
 231                                 //user has given a template file
 232                                 if(it != parameters.end()){
 233                                         path = m->hasPath(it->second);
 234                                         //if the user has not given a path then, add inputdir. else leave path alone.
 235                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 236                                 }
 237
 238                                 it = parameters.find("qfile");
 239                                 //user has given a template file
 240                                 if(it != parameters.end()){
 241                                         path = m->hasPath(it->second);
 242                                         //if the user has not given a path then, add inputdir. else leave path alone.
 243                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 244                                 }
 245
 246                                 it = parameters.find("sff");
 247                                 //user has given a template file
 248                                 if(it != parameters.end()){
 249                                         path = m->hasPath(it->second);
 250                                         //if the user has not given a path then, add inputdir. else leave path alone.
 251                                         if (path == "") {       parameters["sff"] = inputDir + it->second;              }
 252                                 }
 253
 254                                 it = parameters.find("oligos");
 255                                 //user has given a template file
 256                                 if(it != parameters.end()){
 257                                         path = m->hasPath(it->second);
 258                                         //if the user has not given a path then, add inputdir. else leave path alone.
 259                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 260                                 }
 261
 262                                 it = parameters.find("accnos");
 263                                 //user has given a template file
 264                                 if(it != parameters.end()){
 265                                         path = m->hasPath(it->second);
 266                                         //if the user has not given a path then, add inputdir. else leave path alone.
 267                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 268                                 }
 269
 270                                 it = parameters.find("taxonomy");
 271                                 //user has given a template file
 272                                 if(it != parameters.end()){
 273                                         path = m->hasPath(it->second);
 274                                         //if the user has not given a path then, add inputdir. else leave path alone.
 275                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 276                                 }
 277
 278                                 it = parameters.find("flow");
 279                                 //user has given a template file
 280                                 if(it != parameters.end()){
 281                                         path = m->hasPath(it->second);
 282                                         //if the user has not given a path then, add inputdir. else leave path alone.
 283                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 284                                 }
 285
 286                 it = parameters.find("biom");
 287                                 //user has given a template file
 288                                 if(it != parameters.end()){
 289                                         path = m->hasPath(it->second);
 290                                         //if the user has not given a path then, add inputdir. else leave path alone.
 291                                         if (path == "") {       parameters["biom"] = inputDir + it->second;             }
 292                                 }
 293                         }
 294
 295                         //check for parameters
 296                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 297                         if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
 298                         else if (phylipfile == "not found") {  phylipfile = "";  }
 299                         if (phylipfile != "") { m->setPhylipFile(phylipfile); }
 300
 301                         columnfile = validParameter.validFile(parameters, "column", true);
 302                         if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
 303                         else if (columnfile == "not found") {  columnfile = "";  }
 304                         if (columnfile != "") { m->setColumnFile(columnfile); }
 305
 306                         listfile = validParameter.validFile(parameters, "list", true);
 307                         if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
 308                         else if (listfile == "not found") {  listfile = "";  }
 309                         if (listfile != "") { m->setListFile(listfile); }
 310
 311                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 312                         if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
 313                         else if (rabundfile == "not found") {  rabundfile = "";  }
 314                         if (rabundfile != "") { m->setRabundFile(rabundfile); }
 315
 316                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 317                         if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
 318                         else if (sabundfile == "not found") {  sabundfile = "";  }
 319                         if (sabundfile != "") { m->setSabundFile(sabundfile); }
 320
 321                         namefile = validParameter.validFile(parameters, "name", true);
 322                         if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
 323                         else if (namefile == "not found") {  namefile = "";  }
 324                         if (namefile != "") { m->setNameFile(namefile); }
 325
 326                         groupfile = validParameter.validFile(parameters, "group", true);
 327                         if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
 328                         else if (groupfile == "not found") {  groupfile = "";  }
 329                         if (groupfile != "") { m->setGroupFile(groupfile); }
 330
 331             countfile = validParameter.validFile(parameters, "count", true);
 332                         if (countfile == "not open") { m->mothurOut("Ignoring: " + parameters["count"]); m->mothurOutEndLine(); countfile = ""; }
 333                         else if (countfile == "not found") {  countfile = "";  }
 334                         if (countfile != "") { m->setCountTableFile(countfile); }
 335
 336                         designfile = validParameter.validFile(parameters, "design", true);
 337                         if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
 338                         else if (designfile == "not found") {  designfile = "";  }
 339                         if (designfile != "") { m->setDesignFile(designfile); }
 340
 341                         orderfile = validParameter.validFile(parameters, "order", true);
 342                         if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
 343                         else if (orderfile == "not found") {  orderfile = "";  }
 344                         if (orderfile != "") { m->setOrderFile(orderfile); }
 345
 346                         treefile = validParameter.validFile(parameters, "tree", true);
 347                         if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
 348                         else if (treefile == "not found") {  treefile = "";  }
 349                         if (treefile != "") { m->setTreeFile(treefile); }
 350
 351                         sharedfile = validParameter.validFile(parameters, "shared", true);
 352                         if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
 353                         else if (sharedfile == "not found") {  sharedfile = "";  }
 354                         if (sharedfile != "") { m->setSharedFile(sharedfile); }
 355
 356                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 357                         if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
 358                         else if (ordergroupfile == "not found") {  ordergroupfile = "";  }
 359                         if (ordergroupfile != "") { m->setOrderGroupFile(ordergroupfile); }
 360
 361                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 362                         if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
 363                         else if (relabundfile == "not found") {  relabundfile = "";  }
 364                         if (relabundfile != "") { m->setRelAbundFile(relabundfile); }
 365
 366                         fastafile = validParameter.validFile(parameters, "fasta", true);
 367                         if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
 368                         else if (fastafile == "not found") {  fastafile = "";  }
 369                         if (fastafile != "") { m->setFastaFile(fastafile); }
 370
 371                         qualfile = validParameter.validFile(parameters, "qfile", true);
 372                         if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
 373                         else if (qualfile == "not found") {  qualfile = "";  }
 374                         if (qualfile != "") { m->setQualFile(qualfile); }
 375
 376                         sfffile = validParameter.validFile(parameters, "sff", true);
 377                         if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
 378                         else if (sfffile == "not found") {  sfffile = "";  }
 379                         if (sfffile != "") { m->setSFFFile(sfffile); }
 380
 381                         oligosfile = validParameter.validFile(parameters, "oligos", true);
 382                         if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
 383                         else if (oligosfile == "not found") {  oligosfile = "";  }
 384                         if (oligosfile != "") { m->setOligosFile(oligosfile); }
 385
 386                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 387                         if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
 388                         else if (accnosfile == "not found") {  accnosfile = "";  }
 389                         if (accnosfile != "") { m->setAccnosFile(accnosfile); }
 390
 391                         taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
 392                         if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
 393                         else if (taxonomyfile == "not found") {  taxonomyfile = "";  }
 394                         if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
 395
 396                         flowfile = validParameter.validFile(parameters, "flow", true);
 397                         if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
 398                         else if (flowfile == "not found") {  flowfile = "";  }
 399                         if (flowfile != "") { m->setFlowFile(flowfile); }
 400
 401             biomfile = validParameter.validFile(parameters, "biom", true);
 402                         if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine(); biomfile = ""; }
 403                         else if (biomfile == "not found") {  biomfile = "";  }
 404                         if (biomfile != "") { m->setBiomFile(biomfile); }
 405
 406                         processors = validParameter.validFile(parameters, "processors", false);
 407                         if (processors == "not found") {  processors = "1";  }
 408                         if (processors != "") { m->setProcessors(processors); }
 409
 410                         clearTypes = validParameter.validFile(parameters, "clear", false);
 411                         if (clearTypes == "not found") { clearTypes = ""; }
 412                         else { m->splitAtDash(clearTypes, types);       }
 413                 }
 414
 415         }
 416         catch(exception& e) {
 417                 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
 418                 exit(1);
 419         }
 420 }
 421 //**********************************************************************************************************************
 422
 423 int SetCurrentCommand::execute(){
 424         try {
 425
 426                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 427
 428                 //user wants to clear a type
 429                 if (types.size() != 0) {
 430                         for (int i = 0; i < types.size(); i++) {
 431
 432                                 if (m->control_pressed) { break; }
 433
 434                                 //look for file types
 435                                 if (types[i] == "fasta") {
 436                                         m->setFastaFile("");
 437                                 }else if (types[i] == "qfile") {
 438                                         m->setQualFile("");
 439                                 }else if (types[i] == "phylip") {
 440                                         m->setPhylipFile("");
 441                                 }else if (types[i] == "column") {
 442                                         m->setColumnFile("");
 443                                 }else if (types[i] == "list") {
 444                                         m->setListFile("");
 445                                 }else if (types[i] == "rabund") {
 446                                         m->setRabundFile("");
 447                                 }else if (types[i] == "sabund") {
 448                                         m->setSabundFile("");
 449                                 }else if (types[i] == "name") {
 450                                         m->setNameFile("");
 451                                 }else if (types[i] == "group") {
 452                                         m->setGroupFile("");
 453                                 }else if (types[i] == "order") {
 454                                         m->setOrderFile("");
 455                                 }else if (types[i] == "ordergroup") {
 456                                         m->setOrderGroupFile("");
 457                                 }else if (types[i] == "tree") {
 458                                         m->setTreeFile("");
 459                                 }else if (types[i] == "shared") {
 460                                         m->setSharedFile("");
 461                                 }else if (types[i] == "relabund") {
 462                                         m->setRelAbundFile("");
 463                                 }else if (types[i] == "design") {
 464                                         m->setDesignFile("");
 465                                 }else if (types[i] == "sff") {
 466                                         m->setSFFFile("");
 467                                 }else if (types[i] == "oligos") {
 468                                         m->setOligosFile("");
 469                                 }else if (types[i] == "accnos") {
 470                                         m->setAccnosFile("");
 471                                 }else if (types[i] == "taxonomy") {
 472                                         m->setTaxonomyFile("");
 473                                 }else if (types[i] == "flow") {
 474                                         m->setFlowFile("");
 475                 }else if (types[i] == "biom") {
 476                                         m->setBiomFile("");
 477                 }else if (types[i] == "count") {
 478                                         m->setCountTableFile("");
 479                                 }else if (types[i] == "processors") {
 480                                         m->setProcessors("1");
 481                                 }else if (types[i] == "all") {
 482                                         m->clearCurrentFiles();
 483                                 }else {
 484                                         m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
 485                                 }
 486                         }
 487                 }
 488
 489                 m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
 490                 m->printCurrentFiles();
 491
 492                 return 0;
 493         }
 494
 495         catch(exception& e) {
 496                 m->errorOut(e, "SetCurrentCommand", "execute");
 497                 exit(1);
 498         }
 499 }
 500
 501 //**********************************************************************************************************************
 502
 503
 504