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::getValidParameters(){
  17         try {
  18                 string Array[] =  {"fasta","name", "group", "accnos", "groups","list","taxonomy","outputdir","inputdir" };
  19                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  20                 return myArray;
  21         }
  22         catch(exception& e) {
  23                 m->errorOut(e, "GetGroupsCommand", "getValidParameters");
  24                 exit(1);
  25         }
  26 }
  27 //**********************************************************************************************************************
  28 GetGroupsCommand::GetGroupsCommand(){
  29         try {
  30                 abort = true; calledHelp = true;
  31                 vector<string> tempOutNames;
  32                 outputTypes["fasta"] = tempOutNames;
  33                 outputTypes["taxonomy"] = tempOutNames;
  34                 outputTypes["name"] = tempOutNames;
  35                 outputTypes["group"] = tempOutNames;
  36                 outputTypes["list"] = tempOutNames;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 vector<string> GetGroupsCommand::getRequiredParameters(){
  45         try {
  46                 string Array[] =  {"group"};
  47                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  48                 return myArray;
  49         }
  50         catch(exception& e) {
  51                 m->errorOut(e, "GetGroupsCommand", "getRequiredParameters");
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56 vector<string> GetGroupsCommand::getRequiredFiles(){
  57         try {
  58                 vector<string> myArray;
  59                 return myArray;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "GetGroupsCommand", "getRequiredFiles");
  63                 exit(1);
  64         }
  65 }
  66 //**********************************************************************************************************************
  67 GetGroupsCommand::GetGroupsCommand(string option)  {
  68         try {
  69                 abort = false; calledHelp = false;
  70
  71                 //allow user to run help
  72                 if(option == "help") { help(); abort = true; calledHelp = true; }
  73
  74                 else {
  75                         //valid paramters for this command
  76                         string Array[] =  {"fasta","name", "group", "accnos", "groups", "list","taxonomy","outputdir","inputdir" };
  77                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  78
  79                         OptionParser parser(option);
  80                         map<string,string> parameters = parser.getParameters();
  81
  82                         ValidParameters validParameter;
  83                         map<string,string>::iterator it;
  84
  85                         //check to make sure all parameters are valid for command
  86                         for (it = parameters.begin(); it != parameters.end(); it++) {
  87                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  88                         }
  89
  90                         //initialize outputTypes
  91                         vector<string> tempOutNames;
  92                         outputTypes["fasta"] = tempOutNames;
  93                         outputTypes["taxonomy"] = tempOutNames;
  94                         outputTypes["name"] = tempOutNames;
  95                         outputTypes["group"] = tempOutNames;
  96                         outputTypes["list"] = tempOutNames;
  97
  98
  99                         //if the user changes the output directory command factory will send this info to us in the output parameter
 100                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 101
 102                         //if the user changes the input directory command factory will send this info to us in the output parameter
 103                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 104                         if (inputDir == "not found"){   inputDir = "";          }
 105                         else {
 106                                 string path;
 107                                 it = parameters.find("fasta");
 108                                 //user has given a template file
 109                                 if(it != parameters.end()){
 110                                         path = m->hasPath(it->second);
 111                                         //if the user has not given a path then, add inputdir. else leave path alone.
 112                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 113                                 }
 114
 115                                 it = parameters.find("accnos");
 116                                 //user has given a template file
 117                                 if(it != parameters.end()){
 118                                         path = m->hasPath(it->second);
 119                                         //if the user has not given a path then, add inputdir. else leave path alone.
 120                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 121                                 }
 122
 123                                 it = parameters.find("list");
 124                                 //user has given a template file
 125                                 if(it != parameters.end()){
 126                                         path = m->hasPath(it->second);
 127                                         //if the user has not given a path then, add inputdir. else leave path alone.
 128                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 129                                 }
 130
 131                                 it = parameters.find("name");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 137                                 }
 138
 139                                 it = parameters.find("group");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 145                                 }
 146
 147                                 it = parameters.find("taxonomy");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 153                                 }
 154                         }
 155
 156
 157                         //check for required parameters
 158                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 159                         if (accnosfile == "not open") { abort = true; }
 160                         else if (accnosfile == "not found") {  accnosfile = ""; }
 161
 162                         fastafile = validParameter.validFile(parameters, "fasta", true);
 163                         if (fastafile == "not open") { abort = true; }
 164                         else if (fastafile == "not found") {  fastafile = "";  }
 165
 166                         namefile = validParameter.validFile(parameters, "name", true);
 167                         if (namefile == "not open") { abort = true; }
 168                         else if (namefile == "not found") {  namefile = "";  }
 169
 170                         groupfile = validParameter.validFile(parameters, "group", true);
 171                         if (groupfile == "not open") { abort = true; }
 172                         else if (groupfile == "not found") {  groupfile = "";  m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); abort = true; }
 173
 174                         listfile = validParameter.validFile(parameters, "list", true);
 175                         if (listfile == "not open") { abort = true; }
 176                         else if (listfile == "not found") {  listfile = "";  }
 177
 178                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 179                         if (taxfile == "not open") { abort = true; }
 180                         else if (taxfile == "not found") {  taxfile = "";  }
 181
 182                         groups = validParameter.validFile(parameters, "groups", false);
 183                         if (groups == "not found") { groups = ""; }
 184                         else {
 185                                 m->splitAtDash(groups, Groups);
 186                         }
 187
 188                         if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
 189
 190                         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; }
 191                 }
 192
 193         }
 194         catch(exception& e) {
 195                 m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
 196                 exit(1);
 197         }
 198 }
 199 //**********************************************************************************************************************
 200
 201 void GetGroupsCommand::help(){
 202         try {
 203                 m->mothurOut("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");
 204                 m->mothurOut("It outputs a file containing the sequences in the those specified groups.\n");
 205                 m->mothurOut("The get.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is required.\n");
 206                 m->mothurOut("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");
 207                 m->mothurOut("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");
 208                 m->mothurOut("The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
 209                 m->mothurOut("Example get.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
 210                 m->mothurOut("or get.groups(groups=pasture, fasta=amazon.fasta, group=amazon.groups).\n");
 211                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 212         }
 213         catch(exception& e) {
 214                 m->errorOut(e, "GetGroupsCommand", "help");
 215                 exit(1);
 216         }
 217 }
 218
 219 //**********************************************************************************************************************
 220
 221 int GetGroupsCommand::execute(){
 222         try {
 223
 224                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 225
 226                 groupMap = new GroupMap(groupfile);
 227                 groupMap->readMap();
 228
 229                 //get groups you want to remove
 230                 if (accnosfile != "") { readAccnos(); }
 231
 232                 //make sure groups are valid
 233                 //takes care of user setting groupNames that are invalid or setting groups=all
 234                 SharedUtil* util = new SharedUtil();
 235                 util->setGroups(Groups, groupMap->namesOfGroups);
 236                 delete util;
 237
 238                 //fill names with names of sequences that are from the groups we want to remove
 239                 fillNames();
 240
 241                 if (m->control_pressed) { delete groupMap; return 0; }
 242
 243                 //read through the correct file and output lines you want to keep
 244                 if (namefile != "")                     {               readName();             }
 245                 if (fastafile != "")            {               readFasta();    }
 246                 if (groupfile != "")            {               readGroup();    }
 247                 if (listfile != "")                     {               readList();             }
 248                 if (taxfile != "")                      {               readTax();              }
 249
 250                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 251
 252                 m->mothurOut("Selected " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
 253                 for (int i = 0; i < Groups.size(); i++) {       m->mothurOut(Groups[i]); m->mothurOut(" contains " + toString(groupMap->getNumSeqs(Groups[i])) + " sequences."); m->mothurOutEndLine(); }
 254                 m->mothurOutEndLine();
 255
 256
 257
 258                 if (outputNames.size() != 0) {
 259                         m->mothurOutEndLine();
 260                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 261                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 262                         m->mothurOutEndLine();
 263
 264                         //set fasta file as new current fastafile
 265                         string current = "";
 266                         itTypes = outputTypes.find("fasta");
 267                         if (itTypes != outputTypes.end()) {
 268                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 269                         }
 270
 271                         itTypes = outputTypes.find("name");
 272                         if (itTypes != outputTypes.end()) {
 273                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 274                         }
 275
 276                         itTypes = outputTypes.find("group");
 277                         if (itTypes != outputTypes.end()) {
 278                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 279                         }
 280
 281                         itTypes = outputTypes.find("list");
 282                         if (itTypes != outputTypes.end()) {
 283                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 284                         }
 285
 286                         itTypes = outputTypes.find("taxonomy");
 287                         if (itTypes != outputTypes.end()) {
 288                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 289                         }
 290                 }
 291
 292                 return 0;
 293         }
 294
 295         catch(exception& e) {
 296                 m->errorOut(e, "GetGroupsCommand", "execute");
 297                 exit(1);
 298         }
 299 }
 300
 301 //**********************************************************************************************************************
 302 int GetGroupsCommand::readFasta(){
 303         try {
 304                 string thisOutputDir = outputDir;
 305                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 306                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 307
 308                 ofstream out;
 309                 m->openOutputFile(outputFileName, out);
 310
 311                 ifstream in;
 312                 m->openInputFile(fastafile, in);
 313                 string name;
 314
 315                 bool wroteSomething = false;
 316
 317                 while(!in.eof()){
 318                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 319
 320                         Sequence currSeq(in);
 321                         name = currSeq.getName();
 322
 323                         if (name != "") {
 324                                 //if this name is in the accnos file
 325                                 if (names.count(name) != 0) {
 326                                         wroteSomething = true;
 327
 328                                         currSeq.printSequence(out);
 329                                 }
 330                         }
 331                         m->gobble(in);
 332                 }
 333                 in.close();
 334                 out.close();
 335
 336                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 337                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 338
 339                 return 0;
 340
 341         }
 342         catch(exception& e) {
 343                 m->errorOut(e, "GetGroupsCommand", "readFasta");
 344                 exit(1);
 345         }
 346 }
 347
 348 //**********************************************************************************************************************
 349 int GetGroupsCommand::readList(){
 350         try {
 351                 string thisOutputDir = outputDir;
 352                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 353                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 354
 355                 ofstream out;
 356                 m->openOutputFile(outputFileName, out);
 357
 358                 ifstream in;
 359                 m->openInputFile(listfile, in);
 360
 361                 bool wroteSomething = false;
 362
 363                 while(!in.eof()){
 364                         //read in list vector
 365                         ListVector list(in);
 366
 367                         //make a new list vector
 368                         ListVector newList;
 369                         newList.setLabel(list.getLabel());
 370
 371                         //for each bin
 372                         for (int i = 0; i < list.getNumBins(); i++) {
 373                                 if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 374
 375                                 //parse out names that are in accnos file
 376                                 string binnames = list.get(i);
 377
 378                                 string newNames = "";
 379                                 while (binnames.find_first_of(',') != -1) {
 380                                         string name = binnames.substr(0,binnames.find_first_of(','));
 381                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 382
 383                                         //if that name is in the .accnos file, add it
 384                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 385                                 }
 386
 387                                 //get last name
 388                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 389
 390                                 //if there are names in this bin add to new list
 391                                 if (newNames != "") {
 392                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 393                                         newList.push_back(newNames);
 394                                 }
 395                         }
 396
 397                         //print new listvector
 398                         if (newList.getNumBins() != 0) {
 399                                 wroteSomething = true;
 400                                 newList.print(out);
 401                         }
 402
 403                         m->gobble(in);
 404                 }
 405                 in.close();
 406                 out.close();
 407
 408                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 409                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 410
 411                 return 0;
 412
 413         }
 414         catch(exception& e) {
 415                 m->errorOut(e, "GetGroupsCommand", "readList");
 416                 exit(1);
 417         }
 418 }
 419 //**********************************************************************************************************************
 420 int GetGroupsCommand::readName(){
 421         try {
 422                 string thisOutputDir = outputDir;
 423                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 424                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 425
 426                 ofstream out;
 427                 m->openOutputFile(outputFileName, out);
 428
 429                 ifstream in;
 430                 m->openInputFile(namefile, in);
 431                 string name, firstCol, secondCol;
 432
 433                 bool wroteSomething = false;
 434
 435                 while(!in.eof()){
 436                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 437
 438                         in >> firstCol;         m->gobble(in);
 439                         in >> secondCol;
 440
 441                         vector<string> parsedNames;
 442                         m->splitAtComma(secondCol, parsedNames);
 443
 444                         vector<string> validSecond;  validSecond.clear();
 445                         for (int i = 0; i < parsedNames.size(); i++) {
 446                                 if (names.count(parsedNames[i]) != 0) {
 447                                         validSecond.push_back(parsedNames[i]);
 448                                 }
 449                         }
 450
 451                         //if the name in the first column is in the set then print it and any other names in second column also in set
 452                         if (names.count(firstCol) != 0) {
 453
 454                                 wroteSomething = true;
 455
 456                                 out << firstCol << '\t';
 457
 458                                 //you know you have at least one valid second since first column is valid
 459                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 460                                 out << validSecond[validSecond.size()-1] << endl;
 461
 462                                 //make first name in set you come to first column and then add the remaining names to second column
 463                         }else {
 464
 465                                 //you want part of this row
 466                                 if (validSecond.size() != 0) {
 467
 468                                         wroteSomething = true;
 469
 470                                         out << validSecond[0] << '\t';
 471
 472                                         //you know you have at least one valid second since first column is valid
 473                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 474                                         out << validSecond[validSecond.size()-1] << endl;
 475                                 }
 476                         }
 477
 478                         m->gobble(in);
 479                 }
 480                 in.close();
 481                 out.close();
 482
 483                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 484                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 485
 486                 return 0;
 487         }
 488         catch(exception& e) {
 489                 m->errorOut(e, "GetGroupsCommand", "readName");
 490                 exit(1);
 491         }
 492 }
 493
 494 //**********************************************************************************************************************
 495 int GetGroupsCommand::readGroup(){
 496         try {
 497                 string thisOutputDir = outputDir;
 498                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 499                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 500
 501                 ofstream out;
 502                 m->openOutputFile(outputFileName, out);
 503
 504                 ifstream in;
 505                 m->openInputFile(groupfile, in);
 506                 string name, group;
 507
 508                 bool wroteSomething = false;
 509
 510                 while(!in.eof()){
 511                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 512
 513                         in >> name;                             //read from first column
 514                         in >> group;                    //read from second column
 515
 516                         //if this name is in the accnos file
 517                         if (names.count(name) != 0) {
 518                                 wroteSomething = true;
 519                                 out << name << '\t' << group << endl;
 520                         }
 521
 522                         m->gobble(in);
 523                 }
 524                 in.close();
 525                 out.close();
 526
 527                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 528                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 529
 530                 return 0;
 531         }
 532         catch(exception& e) {
 533                 m->errorOut(e, "GetGroupsCommand", "readGroup");
 534                 exit(1);
 535         }
 536 }
 537 //**********************************************************************************************************************
 538 int GetGroupsCommand::readTax(){
 539         try {
 540                 string thisOutputDir = outputDir;
 541                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 542                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 543                 ofstream out;
 544                 m->openOutputFile(outputFileName, out);
 545
 546                 ifstream in;
 547                 m->openInputFile(taxfile, in);
 548                 string name, tax;
 549
 550                 bool wroteSomething = false;
 551
 552                 while(!in.eof()){
 553                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 554
 555                         in >> name;                             //read from first column
 556                         in >> tax;                      //read from second column
 557
 558                         //if this name is in the accnos file
 559                         if (names.count(name) != 0) {
 560                                 wroteSomething = true;
 561                                 out << name << '\t' << tax << endl;
 562                         }
 563
 564                         m->gobble(in);
 565                 }
 566                 in.close();
 567                 out.close();
 568
 569                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 570                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 571
 572                 return 0;
 573         }
 574         catch(exception& e) {
 575                 m->errorOut(e, "GetGroupsCommand", "readTax");
 576                 exit(1);
 577         }
 578 }
 579 //**********************************************************************************************************************
 580 void GetGroupsCommand::readAccnos(){
 581         try {
 582                 Groups.clear();
 583
 584                 ifstream in;
 585                 m->openInputFile(accnosfile, in);
 586                 string name;
 587
 588                 while(!in.eof()){
 589                         in >> name;
 590
 591                         Groups.push_back(name);
 592
 593                         m->gobble(in);
 594                 }
 595                 in.close();
 596
 597         }
 598         catch(exception& e) {
 599                 m->errorOut(e, "GetGroupsCommand", "readAccnos");
 600                 exit(1);
 601         }
 602 }
 603 //**********************************************************************************************************************
 604 int GetGroupsCommand::fillNames(){
 605         try {
 606                 vector<string> seqs = groupMap->getNamesSeqs();
 607
 608                 for (int i = 0; i < seqs.size(); i++) {
 609
 610                         if (m->control_pressed) { return 0; }
 611
 612                         string group = groupMap->getGroup(seqs[i]);
 613
 614                         if (m->inUsersGroups(group, Groups)) {
 615                                 names.insert(seqs[i]);
 616                         }
 617                 }
 618
 619                 return 0;
 620         }
 621         catch(exception& e) {
 622                 m->errorOut(e, "GetGroupsCommand", "fillNames");
 623                 exit(1);
 624         }
 625 }
 626
 627 //**********************************************************************************************************************
 628
 629