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 psummary("summary", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psummary);
  22                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfasta);
  23                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
  24                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
  25                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist);
  26                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy);
  27                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile);
  28                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
  29                 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund);
  30                 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psabund);
  31                 CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
  32                 CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(porder);
  33                 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptree);
  34                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pshared);
  35                 CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pordergroup);
  36         CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount);
  37                 CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund);
  38                 CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff);
  39                 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
  40                 CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
  41                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  42                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  43
  44                 vector<string> myArray;
  45                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  46                 return myArray;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "SetCurrentCommand", "setParameters");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 string SetCurrentCommand::getHelpString(){
  55         try {
  56                 string helpString = "";
  57                 helpString += "The set.current command allows you to set the current files saved by mothur.\n";
  58                 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, summary and taxonomy.\n";
  59                 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";
  60                 helpString += "The set.current command should be in the following format: \n";
  61                 helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
  62                 return helpString;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "SetCurrentCommand", "getHelpString");
  66                 exit(1);
  67         }
  68 }
  69
  70
  71 //**********************************************************************************************************************
  72 SetCurrentCommand::SetCurrentCommand(){
  73         try {
  74                 abort = true; calledHelp = true;
  75                 setParameters();
  76         }
  77         catch(exception& e) {
  78                 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
  79                 exit(1);
  80         }
  81 }
  82 //**********************************************************************************************************************
  83 SetCurrentCommand::SetCurrentCommand(string option)  {
  84         try {
  85                 abort = false; calledHelp = false;
  86
  87                 //allow user to run help
  88                 if(option == "help") { help(); abort = true; calledHelp = true; }
  89                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  90
  91                 else {
  92                         //valid paramters for this command
  93                         vector<string> myArray = setParameters();
  94
  95                         OptionParser parser(option);
  96                         map<string,string> parameters = parser.getParameters();
  97
  98                         ValidParameters validParameter;
  99                         map<string,string>::iterator it;
 100                         //check to make sure all parameters are valid for command
 101                         for (it = parameters.begin(); it != parameters.end(); it++) {
 102                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 103                         }
 104
 105
 106                         //if the user changes the input directory command factory will send this info to us in the output parameter
 107                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 108                         if (inputDir == "not found"){   inputDir = "";          }
 109                         else {
 110                                 string path;
 111                                 it = parameters.find("phylip");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 117                                 }
 118
 119                                 it = parameters.find("column");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 125                                 }
 126
 127                                 it = parameters.find("fasta");
 128                                 //user has given a template file
 129                                 if(it != parameters.end()){
 130                                         path = m->hasPath(it->second);
 131                                         //if the user has not given a path then, add inputdir. else leave path alone.
 132                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 133                                 }
 134
 135                                 it = parameters.find("list");
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 141                                 }
 142
 143                                 it = parameters.find("rabund");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 149                                 }
 150
 151                                 it = parameters.find("sabund");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 157                                 }
 158
 159                                 it = parameters.find("name");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 165                                 }
 166
 167                                 it = parameters.find("group");
 168                                 //user has given a template file
 169                                 if(it != parameters.end()){
 170                                         path = m->hasPath(it->second);
 171                                         //if the user has not given a path then, add inputdir. else leave path alone.
 172                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 173                                 }
 174
 175                                 it = parameters.find("design");
 176                                 //user has given a template file
 177                                 if(it != parameters.end()){
 178                                         path = m->hasPath(it->second);
 179                                         //if the user has not given a path then, add inputdir. else leave path alone.
 180                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 181                                 }
 182
 183                                 it = parameters.find("order");
 184                                 //user has given a template file
 185                                 if(it != parameters.end()){
 186                                         path = m->hasPath(it->second);
 187                                         //if the user has not given a path then, add inputdir. else leave path alone.
 188                                         if (path == "") {       parameters["order"] = inputDir + it->second;            }
 189                                 }
 190
 191                                 it = parameters.find("tree");
 192                                 //user has given a template file
 193                                 if(it != parameters.end()){
 194                                         path = m->hasPath(it->second);
 195                                         //if the user has not given a path then, add inputdir. else leave path alone.
 196                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 197                                 }
 198
 199                                 it = parameters.find("shared");
 200                                 //user has given a template file
 201                                 if(it != parameters.end()){
 202                                         path = m->hasPath(it->second);
 203                                         //if the user has not given a path then, add inputdir. else leave path alone.
 204                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 205                                 }
 206
 207                                 it = parameters.find("ordergroup");
 208                                 //user has given a template file
 209                                 if(it != parameters.end()){
 210                                         path = m->hasPath(it->second);
 211                                         //if the user has not given a path then, add inputdir. else leave path alone.
 212                                         if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
 213                                 }
 214
 215                 it = parameters.find("count");
 216                                 //user has given a template file
 217                                 if(it != parameters.end()){
 218                                         path = m->hasPath(it->second);
 219                                         //if the user has not given a path then, add inputdir. else leave path alone.
 220                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 221                                 }
 222
 223                                 it = parameters.find("relabund");
 224                                 //user has given a template file
 225                                 if(it != parameters.end()){
 226                                         path = m->hasPath(it->second);
 227                                         //if the user has not given a path then, add inputdir. else leave path alone.
 228                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 229                                 }
 230
 231                                 it = parameters.find("fasta");
 232                                 //user has given a template file
 233                                 if(it != parameters.end()){
 234                                         path = m->hasPath(it->second);
 235                                         //if the user has not given a path then, add inputdir. else leave path alone.
 236                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 237                                 }
 238
 239                                 it = parameters.find("qfile");
 240                                 //user has given a template file
 241                                 if(it != parameters.end()){
 242                                         path = m->hasPath(it->second);
 243                                         //if the user has not given a path then, add inputdir. else leave path alone.
 244                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 245                                 }
 246
 247                                 it = parameters.find("sff");
 248                                 //user has given a template file
 249                                 if(it != parameters.end()){
 250                                         path = m->hasPath(it->second);
 251                                         //if the user has not given a path then, add inputdir. else leave path alone.
 252                                         if (path == "") {       parameters["sff"] = inputDir + it->second;              }
 253                                 }
 254
 255                                 it = parameters.find("oligos");
 256                                 //user has given a template file
 257                                 if(it != parameters.end()){
 258                                         path = m->hasPath(it->second);
 259                                         //if the user has not given a path then, add inputdir. else leave path alone.
 260                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 261                                 }
 262
 263                                 it = parameters.find("accnos");
 264                                 //user has given a template file
 265                                 if(it != parameters.end()){
 266                                         path = m->hasPath(it->second);
 267                                         //if the user has not given a path then, add inputdir. else leave path alone.
 268                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 269                                 }
 270
 271                                 it = parameters.find("taxonomy");
 272                                 //user has given a template file
 273                                 if(it != parameters.end()){
 274                                         path = m->hasPath(it->second);
 275                                         //if the user has not given a path then, add inputdir. else leave path alone.
 276                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 277                                 }
 278
 279                                 it = parameters.find("flow");
 280                                 //user has given a template file
 281                                 if(it != parameters.end()){
 282                                         path = m->hasPath(it->second);
 283                                         //if the user has not given a path then, add inputdir. else leave path alone.
 284                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 285                                 }
 286
 287                 it = parameters.find("biom");
 288                                 //user has given a template file
 289                                 if(it != parameters.end()){
 290                                         path = m->hasPath(it->second);
 291                                         //if the user has not given a path then, add inputdir. else leave path alone.
 292                                         if (path == "") {       parameters["biom"] = inputDir + it->second;             }
 293                                 }
 294
 295                 it = parameters.find("summary");
 296                                 //user has given a template file
 297                                 if(it != parameters.end()){
 298                                         path = m->hasPath(it->second);
 299                                         //if the user has not given a path then, add inputdir. else leave path alone.
 300                                         if (path == "") {       parameters["summary"] = inputDir + it->second;          }
 301                                 }
 302                         }
 303
 304                         //check for parameters
 305                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 306                         if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
 307                         else if (phylipfile == "not found") {  phylipfile = "";  }
 308                         if (phylipfile != "") { m->setPhylipFile(phylipfile); }
 309
 310                         columnfile = validParameter.validFile(parameters, "column", true);
 311                         if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
 312                         else if (columnfile == "not found") {  columnfile = "";  }
 313                         if (columnfile != "") { m->setColumnFile(columnfile); }
 314
 315                         listfile = validParameter.validFile(parameters, "list", true);
 316                         if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
 317                         else if (listfile == "not found") {  listfile = "";  }
 318                         if (listfile != "") { m->setListFile(listfile); }
 319
 320                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 321                         if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
 322                         else if (rabundfile == "not found") {  rabundfile = "";  }
 323                         if (rabundfile != "") { m->setRabundFile(rabundfile); }
 324
 325                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 326                         if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
 327                         else if (sabundfile == "not found") {  sabundfile = "";  }
 328                         if (sabundfile != "") { m->setSabundFile(sabundfile); }
 329
 330                         namefile = validParameter.validFile(parameters, "name", true);
 331                         if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
 332                         else if (namefile == "not found") {  namefile = "";  }
 333                         if (namefile != "") { m->setNameFile(namefile); }
 334
 335                         groupfile = validParameter.validFile(parameters, "group", true);
 336                         if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
 337                         else if (groupfile == "not found") {  groupfile = "";  }
 338                         if (groupfile != "") { m->setGroupFile(groupfile); }
 339
 340             countfile = validParameter.validFile(parameters, "count", true);
 341                         if (countfile == "not open") { m->mothurOut("Ignoring: " + parameters["count"]); m->mothurOutEndLine(); countfile = ""; }
 342                         else if (countfile == "not found") {  countfile = "";  }
 343                         if (countfile != "") { m->setCountTableFile(countfile); }
 344
 345                         designfile = validParameter.validFile(parameters, "design", true);
 346                         if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
 347                         else if (designfile == "not found") {  designfile = "";  }
 348                         if (designfile != "") { m->setDesignFile(designfile); }
 349
 350                         orderfile = validParameter.validFile(parameters, "order", true);
 351                         if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
 352                         else if (orderfile == "not found") {  orderfile = "";  }
 353                         if (orderfile != "") { m->setOrderFile(orderfile); }
 354
 355                         treefile = validParameter.validFile(parameters, "tree", true);
 356                         if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
 357                         else if (treefile == "not found") {  treefile = "";  }
 358                         if (treefile != "") { m->setTreeFile(treefile); }
 359
 360                         sharedfile = validParameter.validFile(parameters, "shared", true);
 361                         if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
 362                         else if (sharedfile == "not found") {  sharedfile = "";  }
 363                         if (sharedfile != "") { m->setSharedFile(sharedfile); }
 364
 365                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 366                         if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
 367                         else if (ordergroupfile == "not found") {  ordergroupfile = "";  }
 368                         if (ordergroupfile != "") { m->setOrderGroupFile(ordergroupfile); }
 369
 370                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 371                         if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
 372                         else if (relabundfile == "not found") {  relabundfile = "";  }
 373                         if (relabundfile != "") { m->setRelAbundFile(relabundfile); }
 374
 375                         fastafile = validParameter.validFile(parameters, "fasta", true);
 376                         if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
 377                         else if (fastafile == "not found") {  fastafile = "";  }
 378                         if (fastafile != "") { m->setFastaFile(fastafile); }
 379
 380                         qualfile = validParameter.validFile(parameters, "qfile", true);
 381                         if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
 382                         else if (qualfile == "not found") {  qualfile = "";  }
 383                         if (qualfile != "") { m->setQualFile(qualfile); }
 384
 385                         sfffile = validParameter.validFile(parameters, "sff", true);
 386                         if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
 387                         else if (sfffile == "not found") {  sfffile = "";  }
 388                         if (sfffile != "") { m->setSFFFile(sfffile); }
 389
 390                         oligosfile = validParameter.validFile(parameters, "oligos", true);
 391                         if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
 392                         else if (oligosfile == "not found") {  oligosfile = "";  }
 393                         if (oligosfile != "") { m->setOligosFile(oligosfile); }
 394
 395                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 396                         if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
 397                         else if (accnosfile == "not found") {  accnosfile = "";  }
 398                         if (accnosfile != "") { m->setAccnosFile(accnosfile); }
 399
 400                         taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
 401                         if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
 402                         else if (taxonomyfile == "not found") {  taxonomyfile = "";  }
 403                         if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
 404
 405                         flowfile = validParameter.validFile(parameters, "flow", true);
 406                         if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
 407                         else if (flowfile == "not found") {  flowfile = "";  }
 408                         if (flowfile != "") { m->setFlowFile(flowfile); }
 409
 410             biomfile = validParameter.validFile(parameters, "biom", true);
 411                         if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine(); biomfile = ""; }
 412                         else if (biomfile == "not found") {  biomfile = "";  }
 413                         if (biomfile != "") { m->setBiomFile(biomfile); }
 414
 415             summaryfile = validParameter.validFile(parameters, "summary", true);
 416                         if (summaryfile == "not open") { m->mothurOut("Ignoring: " + parameters["summary"]); m->mothurOutEndLine(); summaryfile = ""; }
 417                         else if (summaryfile == "not found") {  summaryfile = "";  }
 418                         if (summaryfile != "") { m->setSummaryFile(summaryfile); }
 419
 420
 421                         processors = validParameter.validFile(parameters, "processors", false);
 422                         if (processors == "not found") {  processors = "1";  }
 423                         if (processors != "") { m->setProcessors(processors); }
 424
 425                         clearTypes = validParameter.validFile(parameters, "clear", false);
 426                         if (clearTypes == "not found") { clearTypes = ""; }
 427                         else { m->splitAtDash(clearTypes, types);       }
 428                 }
 429
 430         }
 431         catch(exception& e) {
 432                 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
 433                 exit(1);
 434         }
 435 }
 436 //**********************************************************************************************************************
 437
 438 int SetCurrentCommand::execute(){
 439         try {
 440
 441                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 442
 443                 //user wants to clear a type
 444                 if (types.size() != 0) {
 445                         for (int i = 0; i < types.size(); i++) {
 446
 447                                 if (m->control_pressed) { break; }
 448
 449                                 //look for file types
 450                                 if (types[i] == "fasta") {
 451                                         m->setFastaFile("");
 452                                 }else if (types[i] == "qfile") {
 453                                         m->setQualFile("");
 454                                 }else if (types[i] == "phylip") {
 455                                         m->setPhylipFile("");
 456                                 }else if (types[i] == "column") {
 457                                         m->setColumnFile("");
 458                                 }else if (types[i] == "list") {
 459                                         m->setListFile("");
 460                                 }else if (types[i] == "rabund") {
 461                                         m->setRabundFile("");
 462                                 }else if (types[i] == "sabund") {
 463                                         m->setSabundFile("");
 464                                 }else if (types[i] == "name") {
 465                                         m->setNameFile("");
 466                                 }else if (types[i] == "group") {
 467                                         m->setGroupFile("");
 468                                 }else if (types[i] == "order") {
 469                                         m->setOrderFile("");
 470                                 }else if (types[i] == "ordergroup") {
 471                                         m->setOrderGroupFile("");
 472                                 }else if (types[i] == "tree") {
 473                                         m->setTreeFile("");
 474                                 }else if (types[i] == "shared") {
 475                                         m->setSharedFile("");
 476                                 }else if (types[i] == "relabund") {
 477                                         m->setRelAbundFile("");
 478                                 }else if (types[i] == "design") {
 479                                         m->setDesignFile("");
 480                                 }else if (types[i] == "sff") {
 481                                         m->setSFFFile("");
 482                                 }else if (types[i] == "oligos") {
 483                                         m->setOligosFile("");
 484                                 }else if (types[i] == "accnos") {
 485                                         m->setAccnosFile("");
 486                                 }else if (types[i] == "taxonomy") {
 487                                         m->setTaxonomyFile("");
 488                                 }else if (types[i] == "flow") {
 489                                         m->setFlowFile("");
 490                 }else if (types[i] == "biom") {
 491                                         m->setBiomFile("");
 492                 }else if (types[i] == "count") {
 493                                         m->setCountTableFile("");
 494                 }else if (types[i] == "summary") {
 495                                         m->setSummaryFile("");
 496                                 }else if (types[i] == "processors") {
 497                                         m->setProcessors("1");
 498                                 }else if (types[i] == "all") {
 499                                         m->clearCurrentFiles();
 500                                 }else {
 501                                         m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
 502                                 }
 503                         }
 504                 }
 505
 506                 m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
 507                 m->printCurrentFiles();
 508
 509                 return 0;
 510         }
 511
 512         catch(exception& e) {
 513                 m->errorOut(e, "SetCurrentCommand", "execute");
 514                 exit(1);
 515         }
 516 }
 517
 518 //**********************************************************************************************************************
 519
 520
 521