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