getgroupscommand.cpp

   1 /*
   2  *  getgroupscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/10/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getgroupscommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13 #include "sharedutilities.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> GetGroupsCommand::setParameters(){
  17         try {
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
  19                 CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
  21                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
  22                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
  23                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
  24                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  25                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  26                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  27
  28                 vector<string> myArray;
  29                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  30                 return myArray;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "GetGroupsCommand", "setParameters");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 string GetGroupsCommand::getHelpString(){
  39         try {
  40                 string helpString = "";
  41                 helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy.\n";
  42                 helpString += "It outputs a file containing the sequences in the those specified groups.\n";
  43                 helpString += "The get.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is required, unless you have a current group file.\n";
  44                 helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
  45                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like.  You can separate group names with dashes.\n";
  46                 helpString += "The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
  47                 helpString += "Example get.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n";
  48                 helpString += "or get.groups(groups=pasture, fasta=amazon.fasta, group=amazon.groups).\n";
  49                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "GetGroupsCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 GetGroupsCommand::GetGroupsCommand(){
  59         try {
  60                 abort = true; calledHelp = true;
  61                 setParameters();
  62                 vector<string> tempOutNames;
  63                 outputTypes["fasta"] = tempOutNames;
  64                 outputTypes["taxonomy"] = tempOutNames;
  65                 outputTypes["name"] = tempOutNames;
  66                 outputTypes["group"] = tempOutNames;
  67                 outputTypes["list"] = tempOutNames;
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75 GetGroupsCommand::GetGroupsCommand(string option)  {
  76         try {
  77                 abort = false; calledHelp = false;
  78
  79                 //allow user to run help
  80                 if(option == "help") { help(); abort = true; calledHelp = true; }
  81
  82                 else {
  83                         vector<string> myArray = setParameters();
  84
  85                         OptionParser parser(option);
  86                         map<string,string> parameters = parser.getParameters();
  87
  88                         ValidParameters validParameter;
  89                         map<string,string>::iterator it;
  90
  91                         //check to make sure all parameters are valid for command
  92                         for (it = parameters.begin(); it != parameters.end(); it++) {
  93                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  94                         }
  95
  96                         //initialize outputTypes
  97                         vector<string> tempOutNames;
  98                         outputTypes["fasta"] = tempOutNames;
  99                         outputTypes["taxonomy"] = tempOutNames;
 100                         outputTypes["name"] = tempOutNames;
 101                         outputTypes["group"] = tempOutNames;
 102                         outputTypes["list"] = tempOutNames;
 103
 104
 105                         //if the user changes the output directory command factory will send this info to us in the output parameter
 106                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 107
 108                         //if the user changes the input directory command factory will send this info to us in the output parameter
 109                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 110                         if (inputDir == "not found"){   inputDir = "";          }
 111                         else {
 112                                 string path;
 113                                 it = parameters.find("fasta");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 119                                 }
 120
 121                                 it = parameters.find("accnos");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 127                                 }
 128
 129                                 it = parameters.find("list");
 130                                 //user has given a template file
 131                                 if(it != parameters.end()){
 132                                         path = m->hasPath(it->second);
 133                                         //if the user has not given a path then, add inputdir. else leave path alone.
 134                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 135                                 }
 136
 137                                 it = parameters.find("name");
 138                                 //user has given a template file
 139                                 if(it != parameters.end()){
 140                                         path = m->hasPath(it->second);
 141                                         //if the user has not given a path then, add inputdir. else leave path alone.
 142                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 143                                 }
 144
 145                                 it = parameters.find("group");
 146                                 //user has given a template file
 147                                 if(it != parameters.end()){
 148                                         path = m->hasPath(it->second);
 149                                         //if the user has not given a path then, add inputdir. else leave path alone.
 150                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 151                                 }
 152
 153                                 it = parameters.find("taxonomy");
 154                                 //user has given a template file
 155                                 if(it != parameters.end()){
 156                                         path = m->hasPath(it->second);
 157                                         //if the user has not given a path then, add inputdir. else leave path alone.
 158                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 159                                 }
 160                         }
 161
 162
 163                         //check for required parameters
 164                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 165                         if (accnosfile == "not open") { abort = true; }
 166                         else if (accnosfile == "not found") {  accnosfile = ""; }
 167
 168                         fastafile = validParameter.validFile(parameters, "fasta", true);
 169                         if (fastafile == "not open") { abort = true; }
 170                         else if (fastafile == "not found") {  fastafile = "";  }
 171
 172                         namefile = validParameter.validFile(parameters, "name", true);
 173                         if (namefile == "not open") { abort = true; }
 174                         else if (namefile == "not found") {  namefile = "";  }
 175
 176                         groupfile = validParameter.validFile(parameters, "group", true);
 177                         if (groupfile == "not open") { abort = true; }
 178                         else if (groupfile == "not found") {
 179                                 //if there is a current group file, use it
 180                                 groupfile = m->getGroupFile();
 181                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 182                                 else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
 183                         }
 184
 185                         listfile = validParameter.validFile(parameters, "list", true);
 186                         if (listfile == "not open") { abort = true; }
 187                         else if (listfile == "not found") {  listfile = "";  }
 188
 189                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 190                         if (taxfile == "not open") { abort = true; }
 191                         else if (taxfile == "not found") {  taxfile = "";  }
 192
 193                         groups = validParameter.validFile(parameters, "groups", false);
 194                         if (groups == "not found") { groups = "all"; }
 195                         m->splitAtDash(groups, Groups);
 196
 197
 198                         if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
 199
 200                         if ((fastafile == "") && (namefile == "") && (groupfile == "")  && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group or list."); m->mothurOutEndLine(); abort = true; }
 201                 }
 202
 203         }
 204         catch(exception& e) {
 205                 m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
 206                 exit(1);
 207         }
 208 }
 209 //**********************************************************************************************************************
 210
 211 int GetGroupsCommand::execute(){
 212         try {
 213
 214                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 215
 216                 groupMap = new GroupMap(groupfile);
 217                 groupMap->readMap();
 218
 219                 //get groups you want to remove
 220                 if (accnosfile != "") { readAccnos(); }
 221
 222                 //make sure groups are valid
 223                 //takes care of user setting groupNames that are invalid or setting groups=all
 224                 SharedUtil* util = new SharedUtil();
 225                 util->setGroups(Groups, groupMap->namesOfGroups);
 226                 delete util;
 227
 228                 //fill names with names of sequences that are from the groups we want to remove
 229                 fillNames();
 230
 231                 if (m->control_pressed) { delete groupMap; return 0; }
 232
 233                 //read through the correct file and output lines you want to keep
 234                 if (namefile != "")                     {               readName();             }
 235                 if (fastafile != "")            {               readFasta();    }
 236                 if (groupfile != "")            {               readGroup();    }
 237                 if (listfile != "")                     {               readList();             }
 238                 if (taxfile != "")                      {               readTax();              }
 239
 240                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 241
 242                 m->mothurOut("Selected " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
 243                 for (int i = 0; i < Groups.size(); i++) {       m->mothurOut(Groups[i]); m->mothurOut(" contains " + toString(groupMap->getNumSeqs(Groups[i])) + " sequences."); m->mothurOutEndLine(); }
 244                 m->mothurOutEndLine();
 245
 246
 247
 248                 if (outputNames.size() != 0) {
 249                         m->mothurOutEndLine();
 250                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 251                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 252                         m->mothurOutEndLine();
 253
 254                         //set fasta file as new current fastafile
 255                         string current = "";
 256                         itTypes = outputTypes.find("fasta");
 257                         if (itTypes != outputTypes.end()) {
 258                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 259                         }
 260
 261                         itTypes = outputTypes.find("name");
 262                         if (itTypes != outputTypes.end()) {
 263                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 264                         }
 265
 266                         itTypes = outputTypes.find("group");
 267                         if (itTypes != outputTypes.end()) {
 268                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 269                         }
 270
 271                         itTypes = outputTypes.find("list");
 272                         if (itTypes != outputTypes.end()) {
 273                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 274                         }
 275
 276                         itTypes = outputTypes.find("taxonomy");
 277                         if (itTypes != outputTypes.end()) {
 278                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 279                         }
 280                 }
 281
 282                 return 0;
 283         }
 284
 285         catch(exception& e) {
 286                 m->errorOut(e, "GetGroupsCommand", "execute");
 287                 exit(1);
 288         }
 289 }
 290
 291 //**********************************************************************************************************************
 292 int GetGroupsCommand::readFasta(){
 293         try {
 294                 string thisOutputDir = outputDir;
 295                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 296                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 297
 298                 ofstream out;
 299                 m->openOutputFile(outputFileName, out);
 300
 301                 ifstream in;
 302                 m->openInputFile(fastafile, in);
 303                 string name;
 304
 305                 bool wroteSomething = false;
 306
 307                 while(!in.eof()){
 308                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 309
 310                         Sequence currSeq(in);
 311                         name = currSeq.getName();
 312
 313                         if (name != "") {
 314                                 //if this name is in the accnos file
 315                                 if (names.count(name) != 0) {
 316                                         wroteSomething = true;
 317
 318                                         currSeq.printSequence(out);
 319                                 }
 320                         }
 321                         m->gobble(in);
 322                 }
 323                 in.close();
 324                 out.close();
 325
 326                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 327                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 328
 329                 return 0;
 330
 331         }
 332         catch(exception& e) {
 333                 m->errorOut(e, "GetGroupsCommand", "readFasta");
 334                 exit(1);
 335         }
 336 }
 337
 338 //**********************************************************************************************************************
 339 int GetGroupsCommand::readList(){
 340         try {
 341                 string thisOutputDir = outputDir;
 342                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 343                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 344
 345                 ofstream out;
 346                 m->openOutputFile(outputFileName, out);
 347
 348                 ifstream in;
 349                 m->openInputFile(listfile, in);
 350
 351                 bool wroteSomething = false;
 352
 353                 while(!in.eof()){
 354                         //read in list vector
 355                         ListVector list(in);
 356
 357                         //make a new list vector
 358                         ListVector newList;
 359                         newList.setLabel(list.getLabel());
 360
 361                         //for each bin
 362                         for (int i = 0; i < list.getNumBins(); i++) {
 363                                 if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 364
 365                                 //parse out names that are in accnos file
 366                                 string binnames = list.get(i);
 367
 368                                 string newNames = "";
 369                                 while (binnames.find_first_of(',') != -1) {
 370                                         string name = binnames.substr(0,binnames.find_first_of(','));
 371                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 372
 373                                         //if that name is in the .accnos file, add it
 374                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 375                                 }
 376
 377                                 //get last name
 378                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 379
 380                                 //if there are names in this bin add to new list
 381                                 if (newNames != "") {
 382                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 383                                         newList.push_back(newNames);
 384                                 }
 385                         }
 386
 387                         //print new listvector
 388                         if (newList.getNumBins() != 0) {
 389                                 wroteSomething = true;
 390                                 newList.print(out);
 391                         }
 392
 393                         m->gobble(in);
 394                 }
 395                 in.close();
 396                 out.close();
 397
 398                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 399                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 400
 401                 return 0;
 402
 403         }
 404         catch(exception& e) {
 405                 m->errorOut(e, "GetGroupsCommand", "readList");
 406                 exit(1);
 407         }
 408 }
 409 //**********************************************************************************************************************
 410 int GetGroupsCommand::readName(){
 411         try {
 412                 string thisOutputDir = outputDir;
 413                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 414                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 415
 416                 ofstream out;
 417                 m->openOutputFile(outputFileName, out);
 418
 419                 ifstream in;
 420                 m->openInputFile(namefile, in);
 421                 string name, firstCol, secondCol;
 422
 423                 bool wroteSomething = false;
 424
 425                 while(!in.eof()){
 426                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 427
 428                         in >> firstCol;         m->gobble(in);
 429                         in >> secondCol;
 430
 431                         vector<string> parsedNames;
 432                         m->splitAtComma(secondCol, parsedNames);
 433
 434                         vector<string> validSecond;  validSecond.clear();
 435                         for (int i = 0; i < parsedNames.size(); i++) {
 436                                 if (names.count(parsedNames[i]) != 0) {
 437                                         validSecond.push_back(parsedNames[i]);
 438                                 }
 439                         }
 440
 441                         //if the name in the first column is in the set then print it and any other names in second column also in set
 442                         if (names.count(firstCol) != 0) {
 443
 444                                 wroteSomething = true;
 445
 446                                 out << firstCol << '\t';
 447
 448                                 //you know you have at least one valid second since first column is valid
 449                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 450                                 out << validSecond[validSecond.size()-1] << endl;
 451
 452                                 //make first name in set you come to first column and then add the remaining names to second column
 453                         }else {
 454
 455                                 //you want part of this row
 456                                 if (validSecond.size() != 0) {
 457
 458                                         wroteSomething = true;
 459
 460                                         out << validSecond[0] << '\t';
 461
 462                                         //you know you have at least one valid second since first column is valid
 463                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 464                                         out << validSecond[validSecond.size()-1] << endl;
 465                                 }
 466                         }
 467
 468                         m->gobble(in);
 469                 }
 470                 in.close();
 471                 out.close();
 472
 473                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 474                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 475
 476                 return 0;
 477         }
 478         catch(exception& e) {
 479                 m->errorOut(e, "GetGroupsCommand", "readName");
 480                 exit(1);
 481         }
 482 }
 483
 484 //**********************************************************************************************************************
 485 int GetGroupsCommand::readGroup(){
 486         try {
 487                 string thisOutputDir = outputDir;
 488                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 489                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 490
 491                 ofstream out;
 492                 m->openOutputFile(outputFileName, out);
 493
 494                 ifstream in;
 495                 m->openInputFile(groupfile, in);
 496                 string name, group;
 497
 498                 bool wroteSomething = false;
 499
 500                 while(!in.eof()){
 501                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 502
 503                         in >> name;                             //read from first column
 504                         in >> group;                    //read from second column
 505
 506                         //if this name is in the accnos file
 507                         if (names.count(name) != 0) {
 508                                 wroteSomething = true;
 509                                 out << name << '\t' << group << endl;
 510                         }
 511
 512                         m->gobble(in);
 513                 }
 514                 in.close();
 515                 out.close();
 516
 517                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 518                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 519
 520                 return 0;
 521         }
 522         catch(exception& e) {
 523                 m->errorOut(e, "GetGroupsCommand", "readGroup");
 524                 exit(1);
 525         }
 526 }
 527 //**********************************************************************************************************************
 528 int GetGroupsCommand::readTax(){
 529         try {
 530                 string thisOutputDir = outputDir;
 531                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 532                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 533                 ofstream out;
 534                 m->openOutputFile(outputFileName, out);
 535
 536                 ifstream in;
 537                 m->openInputFile(taxfile, in);
 538                 string name, tax;
 539
 540                 bool wroteSomething = false;
 541
 542                 while(!in.eof()){
 543                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 544
 545                         in >> name;                             //read from first column
 546                         in >> tax;                      //read from second column
 547
 548                         //if this name is in the accnos file
 549                         if (names.count(name) != 0) {
 550                                 wroteSomething = true;
 551                                 out << name << '\t' << tax << endl;
 552                         }
 553
 554                         m->gobble(in);
 555                 }
 556                 in.close();
 557                 out.close();
 558
 559                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 560                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 561
 562                 return 0;
 563         }
 564         catch(exception& e) {
 565                 m->errorOut(e, "GetGroupsCommand", "readTax");
 566                 exit(1);
 567         }
 568 }
 569 //**********************************************************************************************************************
 570 void GetGroupsCommand::readAccnos(){
 571         try {
 572                 Groups.clear();
 573
 574                 ifstream in;
 575                 m->openInputFile(accnosfile, in);
 576                 string name;
 577
 578                 while(!in.eof()){
 579                         in >> name;
 580
 581                         Groups.push_back(name);
 582
 583                         m->gobble(in);
 584                 }
 585                 in.close();
 586
 587         }
 588         catch(exception& e) {
 589                 m->errorOut(e, "GetGroupsCommand", "readAccnos");
 590                 exit(1);
 591         }
 592 }
 593 //**********************************************************************************************************************
 594 int GetGroupsCommand::fillNames(){
 595         try {
 596                 vector<string> seqs = groupMap->getNamesSeqs();
 597
 598                 for (int i = 0; i < seqs.size(); i++) {
 599
 600                         if (m->control_pressed) { return 0; }
 601
 602                         string group = groupMap->getGroup(seqs[i]);
 603
 604                         if (m->inUsersGroups(group, Groups)) {
 605                                 names.insert(seqs[i]);
 606                         }
 607                 }
 608
 609                 return 0;
 610         }
 611         catch(exception& e) {
 612                 m->errorOut(e, "GetGroupsCommand", "fillNames");
 613                 exit(1);
 614         }
 615 }
 616
 617 //**********************************************************************************************************************
 618
 619