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                         else { m->setAccnosFile(accnosfile); }
 169
 170                         fastafile = validParameter.validFile(parameters, "fasta", true);
 171                         if (fastafile == "not open") { abort = true; }
 172                         else if (fastafile == "not found") {  fastafile = "";  }
 173                         else { m->setFastaFile(fastafile); }
 174
 175                         namefile = validParameter.validFile(parameters, "name", true);
 176                         if (namefile == "not open") { abort = true; }
 177                         else if (namefile == "not found") {  namefile = "";  }
 178                         else { m->setNameFile(namefile); }
 179
 180                         groupfile = validParameter.validFile(parameters, "group", true);
 181                         if (groupfile == "not open") { abort = true; }
 182                         else if (groupfile == "not found") {
 183                                 //if there is a current group file, use it
 184                                 groupfile = m->getGroupFile();
 185                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 186                                 else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
 187                         }else { m->setGroupFile(groupfile); }
 188
 189                         listfile = validParameter.validFile(parameters, "list", true);
 190                         if (listfile == "not open") { abort = true; }
 191                         else if (listfile == "not found") {  listfile = "";  }
 192                         else { m->setListFile(listfile); }
 193
 194                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 195                         if (taxfile == "not open") { abort = true; }
 196                         else if (taxfile == "not found") {  taxfile = "";  }
 197                         else { m->setTaxonomyFile(taxfile); }
 198
 199                         groups = validParameter.validFile(parameters, "groups", false);
 200                         if (groups == "not found") { groups = "all"; }
 201                         m->splitAtDash(groups, Groups);
 202
 203
 204                         if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
 205
 206                         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; }
 207                 }
 208
 209         }
 210         catch(exception& e) {
 211                 m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
 212                 exit(1);
 213         }
 214 }
 215 //**********************************************************************************************************************
 216
 217 int GetGroupsCommand::execute(){
 218         try {
 219
 220                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 221
 222                 groupMap = new GroupMap(groupfile);
 223                 groupMap->readMap();
 224
 225                 //get groups you want to remove
 226                 if (accnosfile != "") { readAccnos(); }
 227
 228                 //make sure groups are valid
 229                 //takes care of user setting groupNames that are invalid or setting groups=all
 230                 SharedUtil* util = new SharedUtil();
 231                 util->setGroups(Groups, groupMap->namesOfGroups);
 232                 delete util;
 233
 234                 //fill names with names of sequences that are from the groups we want to remove
 235                 fillNames();
 236
 237                 if (m->control_pressed) { delete groupMap; return 0; }
 238
 239                 //read through the correct file and output lines you want to keep
 240                 if (namefile != "")                     {               readName();             }
 241                 if (fastafile != "")            {               readFasta();    }
 242                 if (groupfile != "")            {               readGroup();    }
 243                 if (listfile != "")                     {               readList();             }
 244                 if (taxfile != "")                      {               readTax();              }
 245
 246                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 247
 248                 m->mothurOut("Selected " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
 249                 for (int i = 0; i < Groups.size(); i++) {       m->mothurOut(Groups[i]); m->mothurOut("\t" + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine(); }
 250                 m->mothurOutEndLine();
 251
 252                 if (outputNames.size() != 0) {
 253                         m->mothurOutEndLine();
 254                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 255                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 256                         m->mothurOutEndLine();
 257
 258                         //set fasta file as new current fastafile
 259                         string current = "";
 260                         itTypes = outputTypes.find("fasta");
 261                         if (itTypes != outputTypes.end()) {
 262                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 263                         }
 264
 265                         itTypes = outputTypes.find("name");
 266                         if (itTypes != outputTypes.end()) {
 267                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 268                         }
 269
 270                         itTypes = outputTypes.find("group");
 271                         if (itTypes != outputTypes.end()) {
 272                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 273                         }
 274
 275                         itTypes = outputTypes.find("list");
 276                         if (itTypes != outputTypes.end()) {
 277                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 278                         }
 279
 280                         itTypes = outputTypes.find("taxonomy");
 281                         if (itTypes != outputTypes.end()) {
 282                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 283                         }
 284                 }
 285
 286                 return 0;
 287         }
 288
 289         catch(exception& e) {
 290                 m->errorOut(e, "GetGroupsCommand", "execute");
 291                 exit(1);
 292         }
 293 }
 294
 295 //**********************************************************************************************************************
 296 int GetGroupsCommand::readFasta(){
 297         try {
 298                 string thisOutputDir = outputDir;
 299                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 300                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 301
 302                 ofstream out;
 303                 m->openOutputFile(outputFileName, out);
 304
 305                 ifstream in;
 306                 m->openInputFile(fastafile, in);
 307                 string name;
 308
 309                 bool wroteSomething = false;
 310
 311                 while(!in.eof()){
 312                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 313
 314                         Sequence currSeq(in);
 315                         name = currSeq.getName();
 316
 317                         if (name != "") {
 318                                 //if this name is in the accnos file
 319                                 if (names.count(name) != 0) {
 320                                         wroteSomething = true;
 321
 322                                         currSeq.printSequence(out);
 323                                 }
 324                         }
 325                         m->gobble(in);
 326                 }
 327                 in.close();
 328                 out.close();
 329
 330                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 331                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 332
 333                 return 0;
 334
 335         }
 336         catch(exception& e) {
 337                 m->errorOut(e, "GetGroupsCommand", "readFasta");
 338                 exit(1);
 339         }
 340 }
 341
 342 //**********************************************************************************************************************
 343 int GetGroupsCommand::readList(){
 344         try {
 345                 string thisOutputDir = outputDir;
 346                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 347                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 348
 349                 ofstream out;
 350                 m->openOutputFile(outputFileName, out);
 351
 352                 ifstream in;
 353                 m->openInputFile(listfile, in);
 354
 355                 bool wroteSomething = false;
 356
 357                 while(!in.eof()){
 358                         //read in list vector
 359                         ListVector list(in);
 360
 361                         //make a new list vector
 362                         ListVector newList;
 363                         newList.setLabel(list.getLabel());
 364
 365                         //for each bin
 366                         for (int i = 0; i < list.getNumBins(); i++) {
 367                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 368
 369                                 //parse out names that are in accnos file
 370                                 string binnames = list.get(i);
 371
 372                                 string newNames = "";
 373                                 while (binnames.find_first_of(',') != -1) {
 374                                         string name = binnames.substr(0,binnames.find_first_of(','));
 375                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 376
 377                                         //if that name is in the .accnos file, add it
 378                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 379                                 }
 380
 381                                 //get last name
 382                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 383
 384                                 //if there are names in this bin add to new list
 385                                 if (newNames != "") {
 386                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 387                                         newList.push_back(newNames);
 388                                 }
 389                         }
 390
 391                         //print new listvector
 392                         if (newList.getNumBins() != 0) {
 393                                 wroteSomething = true;
 394                                 newList.print(out);
 395                         }
 396
 397                         m->gobble(in);
 398                 }
 399                 in.close();
 400                 out.close();
 401
 402                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 403                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 404
 405                 return 0;
 406
 407         }
 408         catch(exception& e) {
 409                 m->errorOut(e, "GetGroupsCommand", "readList");
 410                 exit(1);
 411         }
 412 }
 413 //**********************************************************************************************************************
 414 int GetGroupsCommand::readName(){
 415         try {
 416                 string thisOutputDir = outputDir;
 417                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 418                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 419
 420                 ofstream out;
 421                 m->openOutputFile(outputFileName, out);
 422
 423                 ifstream in;
 424                 m->openInputFile(namefile, in);
 425                 string name, firstCol, secondCol;
 426
 427                 bool wroteSomething = false;
 428
 429                 while(!in.eof()){
 430                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 431
 432                         in >> firstCol;         m->gobble(in);
 433                         in >> secondCol;
 434
 435                         vector<string> parsedNames;
 436                         m->splitAtComma(secondCol, parsedNames);
 437
 438                         vector<string> validSecond;  validSecond.clear();
 439                         for (int i = 0; i < parsedNames.size(); i++) {
 440                                 if (names.count(parsedNames[i]) != 0) {
 441                                         validSecond.push_back(parsedNames[i]);
 442                                 }
 443                         }
 444
 445                         //if the name in the first column is in the set then print it and any other names in second column also in set
 446                         if (names.count(firstCol) != 0) {
 447
 448                                 wroteSomething = true;
 449
 450                                 out << firstCol << '\t';
 451
 452                                 //you know you have at least one valid second since first column is valid
 453                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 454                                 out << validSecond[validSecond.size()-1] << endl;
 455
 456                                 //make first name in set you come to first column and then add the remaining names to second column
 457                         }else {
 458
 459                                 //you want part of this row
 460                                 if (validSecond.size() != 0) {
 461
 462                                         wroteSomething = true;
 463
 464                                         out << validSecond[0] << '\t';
 465
 466                                         //you know you have at least one valid second since first column is valid
 467                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 468                                         out << validSecond[validSecond.size()-1] << endl;
 469                                 }
 470                         }
 471
 472                         m->gobble(in);
 473                 }
 474                 in.close();
 475                 out.close();
 476
 477                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 478                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 479
 480                 return 0;
 481         }
 482         catch(exception& e) {
 483                 m->errorOut(e, "GetGroupsCommand", "readName");
 484                 exit(1);
 485         }
 486 }
 487
 488 //**********************************************************************************************************************
 489 int GetGroupsCommand::readGroup(){
 490         try {
 491                 string thisOutputDir = outputDir;
 492                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 493                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 494
 495                 ofstream out;
 496                 m->openOutputFile(outputFileName, out);
 497
 498                 ifstream in;
 499                 m->openInputFile(groupfile, in);
 500                 string name, group;
 501
 502                 bool wroteSomething = false;
 503
 504                 while(!in.eof()){
 505                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 506
 507                         in >> name;                             //read from first column
 508                         in >> group;                    //read from second column
 509
 510                         //if this name is in the accnos file
 511                         if (names.count(name) != 0) {
 512                                 wroteSomething = true;
 513                                 out << name << '\t' << group << endl;
 514                         }
 515
 516                         m->gobble(in);
 517                 }
 518                 in.close();
 519                 out.close();
 520
 521                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 522                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 523
 524                 return 0;
 525         }
 526         catch(exception& e) {
 527                 m->errorOut(e, "GetGroupsCommand", "readGroup");
 528                 exit(1);
 529         }
 530 }
 531 //**********************************************************************************************************************
 532 int GetGroupsCommand::readTax(){
 533         try {
 534                 string thisOutputDir = outputDir;
 535                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 536                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 537                 ofstream out;
 538                 m->openOutputFile(outputFileName, out);
 539
 540                 ifstream in;
 541                 m->openInputFile(taxfile, in);
 542                 string name, tax;
 543
 544                 bool wroteSomething = false;
 545
 546                 while(!in.eof()){
 547                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 548
 549                         in >> name;                             //read from first column
 550                         in >> tax;                      //read from second column
 551
 552                         //if this name is in the accnos file
 553                         if (names.count(name) != 0) {
 554                                 wroteSomething = true;
 555                                 out << name << '\t' << tax << endl;
 556                         }
 557
 558                         m->gobble(in);
 559                 }
 560                 in.close();
 561                 out.close();
 562
 563                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 564                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 565
 566                 return 0;
 567         }
 568         catch(exception& e) {
 569                 m->errorOut(e, "GetGroupsCommand", "readTax");
 570                 exit(1);
 571         }
 572 }
 573 //**********************************************************************************************************************
 574 void GetGroupsCommand::readAccnos(){
 575         try {
 576                 Groups.clear();
 577
 578                 ifstream in;
 579                 m->openInputFile(accnosfile, in);
 580                 string name;
 581
 582                 while(!in.eof()){
 583                         in >> name;
 584
 585                         Groups.push_back(name);
 586
 587                         m->gobble(in);
 588                 }
 589                 in.close();
 590
 591         }
 592         catch(exception& e) {
 593                 m->errorOut(e, "GetGroupsCommand", "readAccnos");
 594                 exit(1);
 595         }
 596 }
 597 //**********************************************************************************************************************
 598 int GetGroupsCommand::fillNames(){
 599         try {
 600                 vector<string> seqs = groupMap->getNamesSeqs();
 601
 602                 for (int i = 0; i < seqs.size(); i++) {
 603
 604                         if (m->control_pressed) { return 0; }
 605
 606                         string group = groupMap->getGroup(seqs[i]);
 607
 608                         if (m->inUsersGroups(group, Groups)) {
 609                                 names.insert(seqs[i]);
 610                         }
 611                 }
 612
 613                 return 0;
 614         }
 615         catch(exception& e) {
 616                 m->errorOut(e, "GetGroupsCommand", "fillNames");
 617                 exit(1);
 618         }
 619 }
 620
 621 //**********************************************************************************************************************
 622
 623