removegroupscommand.cpp

   1 /*
   2  *  removegroupscommand.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 "removegroupscommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13 #include "sharedutilities.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> RemoveGroupsCommand::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, "RemoveGroupsCommand", "setParameters");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 string RemoveGroupsCommand::getHelpString(){
  39         try {
  40                 string helpString = "";
  41                 helpString += "The remove.groups command removes 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 NOT in the those specified groups.\n";
  43                 helpString += "The remove.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 remove or set the groups parameter to the groups you wish to remove.\n";
  45                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like removed.  You can separate group names with dashes.\n";
  46                 helpString += "The remove.groups command should be in the following format: remove.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
  47                 helpString += "Example remove.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n";
  48                 helpString += "or remove.groups(groups=pasture, fasta=amazon.fasta, 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, "RemoveGroupsCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57
  58 //**********************************************************************************************************************
  59 RemoveGroupsCommand::RemoveGroupsCommand(){
  60         try {
  61                 abort = true; calledHelp = true;
  62                 setParameters();
  63                 vector<string> tempOutNames;
  64                 outputTypes["fasta"] = tempOutNames;
  65                 outputTypes["taxonomy"] = tempOutNames;
  66                 outputTypes["name"] = tempOutNames;
  67                 outputTypes["group"] = tempOutNames;
  68                 outputTypes["list"] = tempOutNames;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
  77         try {
  78                 abort = false; calledHelp = false;
  79
  80                 //allow user to run help
  81                 if(option == "help") { help(); abort = true; calledHelp = true; }
  82                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  83
  84                 else {
  85                         vector<string> myArray = setParameters();
  86
  87                         OptionParser parser(option);
  88                         map<string,string> parameters = parser.getParameters();
  89
  90                         ValidParameters validParameter;
  91                         map<string,string>::iterator it;
  92
  93                         //check to make sure all parameters are valid for command
  94                         for (it = parameters.begin(); it != parameters.end(); it++) {
  95                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  96                         }
  97
  98                         //initialize outputTypes
  99                         vector<string> tempOutNames;
 100                         outputTypes["fasta"] = tempOutNames;
 101                         outputTypes["taxonomy"] = tempOutNames;
 102                         outputTypes["name"] = tempOutNames;
 103                         outputTypes["group"] = tempOutNames;
 104                         outputTypes["list"] = tempOutNames;
 105
 106
 107                         //if the user changes the output directory command factory will send this info to us in the output parameter
 108                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 109
 110                         //if the user changes the input directory command factory will send this info to us in the output parameter
 111                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 112                         if (inputDir == "not found"){   inputDir = "";          }
 113                         else {
 114                                 string path;
 115                                 it = parameters.find("fasta");
 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["fasta"] = inputDir + it->second;            }
 121                                 }
 122
 123                                 it = parameters.find("accnos");
 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["accnos"] = inputDir + it->second;           }
 129                                 }
 130
 131                                 it = parameters.find("list");
 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["list"] = inputDir + it->second;             }
 137                                 }
 138
 139                                 it = parameters.find("name");
 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["name"] = inputDir + it->second;             }
 145                                 }
 146
 147                                 it = parameters.find("group");
 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["group"] = inputDir + it->second;            }
 153                                 }
 154
 155                                 it = parameters.find("taxonomy");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 161                                 }
 162                         }
 163
 164
 165                         //check for required parameters
 166                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 167                         if (accnosfile == "not open") { abort = true; }
 168                         else if (accnosfile == "not found") {  accnosfile = ""; }
 169
 170                         fastafile = validParameter.validFile(parameters, "fasta", true);
 171                         if (fastafile == "not open") { abort = true; }
 172                         else if (fastafile == "not found") {  fastafile = "";  }
 173
 174                         namefile = validParameter.validFile(parameters, "name", true);
 175                         if (namefile == "not open") { abort = true; }
 176                         else if (namefile == "not found") {  namefile = "";  }
 177
 178                         groupfile = validParameter.validFile(parameters, "group", true);
 179                         if (groupfile == "not open") { abort = true; }
 180                         else if (groupfile == "not found") {
 181                                 //if there is a current group file, use it
 182                                 groupfile = m->getGroupFile();
 183                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 184                                 else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
 185                         }
 186
 187                         listfile = validParameter.validFile(parameters, "list", true);
 188                         if (listfile == "not open") { abort = true; }
 189                         else if (listfile == "not found") {  listfile = "";  }
 190
 191                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 192                         if (taxfile == "not open") { abort = true; }
 193                         else if (taxfile == "not found") {  taxfile = "";  }
 194
 195                         groups = validParameter.validFile(parameters, "groups", false);
 196                         if (groups == "not found") { groups = ""; }
 197                         else {
 198                                 m->splitAtDash(groups, Groups);
 199                         }
 200
 201                         if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
 202
 203                         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; }
 204                 }
 205
 206         }
 207         catch(exception& e) {
 208                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 209                 exit(1);
 210         }
 211 }
 212 //**********************************************************************************************************************
 213
 214 int RemoveGroupsCommand::execute(){
 215         try {
 216
 217                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 218
 219                 groupMap = new GroupMap(groupfile);
 220                 groupMap->readMap();
 221
 222                 //get groups you want to remove
 223                 if (accnosfile != "") { readAccnos(); }
 224
 225                 //make sure groups are valid
 226                 //takes care of user setting groupNames that are invalid or setting groups=all
 227                 SharedUtil* util = new SharedUtil();
 228                 util->setGroups(Groups, groupMap->namesOfGroups);
 229                 delete util;
 230
 231                 //fill names with names of sequences that are from the groups we want to remove
 232                 fillNames();
 233
 234                 if (m->control_pressed) { delete groupMap; return 0; }
 235
 236                 //read through the correct file and output lines you want to keep
 237                 if (namefile != "")                     {               readName();             }
 238                 if (fastafile != "")            {               readFasta();    }
 239                 if (groupfile != "")            {               readGroup();    }
 240                 if (listfile != "")                     {               readList();             }
 241                 if (taxfile != "")                      {               readTax();              }
 242
 243                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 244
 245                 m->mothurOut("Removed " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
 246                 for (int i = 0; i < Groups.size(); i++) {       m->mothurOut(Groups[i]); m->mothurOut("\t" + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine(); }
 247                 m->mothurOutEndLine();
 248
 249                 if (outputNames.size() != 0) {
 250                         m->mothurOutEndLine();
 251                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 252                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 253                         m->mothurOutEndLine();
 254
 255                         //set fasta file as new current fastafile
 256                         string current = "";
 257                         itTypes = outputTypes.find("fasta");
 258                         if (itTypes != outputTypes.end()) {
 259                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 260                         }
 261
 262                         itTypes = outputTypes.find("name");
 263                         if (itTypes != outputTypes.end()) {
 264                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 265                         }
 266
 267                         itTypes = outputTypes.find("group");
 268                         if (itTypes != outputTypes.end()) {
 269                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 270                         }
 271
 272                         itTypes = outputTypes.find("list");
 273                         if (itTypes != outputTypes.end()) {
 274                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 275                         }
 276
 277                         itTypes = outputTypes.find("taxonomy");
 278                         if (itTypes != outputTypes.end()) {
 279                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 280                         }
 281                 }
 282
 283                 return 0;
 284         }
 285
 286         catch(exception& e) {
 287                 m->errorOut(e, "RemoveGroupsCommand", "execute");
 288                 exit(1);
 289         }
 290 }
 291
 292 //**********************************************************************************************************************
 293 int RemoveGroupsCommand::readFasta(){
 294         try {
 295                 string thisOutputDir = outputDir;
 296                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 297                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 298
 299                 ofstream out;
 300                 m->openOutputFile(outputFileName, out);
 301
 302                 ifstream in;
 303                 m->openInputFile(fastafile, in);
 304                 string name;
 305
 306                 bool wroteSomething = false;
 307
 308                 while(!in.eof()){
 309                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 310
 311                         Sequence currSeq(in);
 312                         name = currSeq.getName();
 313
 314                         if (name != "") {
 315                                 //if this name is in the accnos file
 316                                 if (names.count(name) == 0) {
 317                                         wroteSomething = true;
 318
 319                                         currSeq.printSequence(out);
 320                                 }
 321                         }
 322                         m->gobble(in);
 323                 }
 324                 in.close();
 325                 out.close();
 326
 327                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 328                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 329
 330                 return 0;
 331
 332         }
 333         catch(exception& e) {
 334                 m->errorOut(e, "RemoveGroupsCommand", "readFasta");
 335                 exit(1);
 336         }
 337 }
 338
 339 //**********************************************************************************************************************
 340 int RemoveGroupsCommand::readList(){
 341         try {
 342                 string thisOutputDir = outputDir;
 343                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 344                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 345
 346                 ofstream out;
 347                 m->openOutputFile(outputFileName, out);
 348
 349                 ifstream in;
 350                 m->openInputFile(listfile, in);
 351
 352                 bool wroteSomething = false;
 353
 354                 while(!in.eof()){
 355                         //read in list vector
 356                         ListVector list(in);
 357
 358                         //make a new list vector
 359                         ListVector newList;
 360                         newList.setLabel(list.getLabel());
 361
 362                         //for each bin
 363                         for (int i = 0; i < list.getNumBins(); i++) {
 364                                 if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 365
 366                                 //parse out names that are in accnos file
 367                                 string binnames = list.get(i);
 368
 369                                 string newNames = "";
 370                                 while (binnames.find_first_of(',') != -1) {
 371                                         string name = binnames.substr(0,binnames.find_first_of(','));
 372                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 373
 374                                         //if that name is in the .accnos file, add it
 375                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 376                                 }
 377
 378                                 //get last name
 379                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 380
 381                                 //if there are names in this bin add to new list
 382                                 if (newNames != "") {
 383                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 384                                         newList.push_back(newNames);
 385                                 }
 386                         }
 387
 388                         //print new listvector
 389                         if (newList.getNumBins() != 0) {
 390                                 wroteSomething = true;
 391                                 newList.print(out);
 392                         }
 393
 394                         m->gobble(in);
 395                 }
 396                 in.close();
 397                 out.close();
 398
 399                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 400                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 401
 402                 return 0;
 403
 404         }
 405         catch(exception& e) {
 406                 m->errorOut(e, "RemoveGroupsCommand", "readList");
 407                 exit(1);
 408         }
 409 }
 410 //**********************************************************************************************************************
 411 int RemoveGroupsCommand::readName(){
 412         try {
 413                 string thisOutputDir = outputDir;
 414                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 415                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 416
 417                 ofstream out;
 418                 m->openOutputFile(outputFileName, out);
 419
 420                 ifstream in;
 421                 m->openInputFile(namefile, in);
 422                 string name, firstCol, secondCol;
 423
 424                 bool wroteSomething = false;
 425
 426                 while(!in.eof()){
 427                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 428
 429                         in >> firstCol;         m->gobble(in);
 430                         in >> secondCol;
 431
 432                         vector<string> parsedNames;
 433                         m->splitAtComma(secondCol, parsedNames);
 434
 435                         vector<string> validSecond;  validSecond.clear();
 436                         for (int i = 0; i < parsedNames.size(); i++) {
 437                                 if (names.count(parsedNames[i]) == 0) {
 438                                         validSecond.push_back(parsedNames[i]);
 439                                 }
 440                         }
 441
 442
 443                         //if the name in the first column is in the set then print it and any other names in second column also in set
 444                         if (names.count(firstCol) == 0) {
 445
 446                                 wroteSomething = true;
 447
 448                                 out << firstCol << '\t';
 449
 450                                 //you know you have at least one valid second since first column is valid
 451                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 452                                 out << validSecond[validSecond.size()-1] << endl;
 453
 454                                 //make first name in set you come to first column and then add the remaining names to second column
 455                         }else {
 456
 457                                 //you want part of this row
 458                                 if (validSecond.size() != 0) {
 459
 460                                         wroteSomething = true;
 461
 462                                         out << validSecond[0] << '\t';
 463
 464                                         //you know you have at least one valid second since first column is valid
 465                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 466                                         out << validSecond[validSecond.size()-1] << endl;
 467                                 }
 468                         }
 469
 470                         m->gobble(in);
 471                 }
 472                 in.close();
 473                 out.close();
 474
 475                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 476                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 477
 478                 return 0;
 479         }
 480         catch(exception& e) {
 481                 m->errorOut(e, "RemoveGroupsCommand", "readName");
 482                 exit(1);
 483         }
 484 }
 485
 486 //**********************************************************************************************************************
 487 int RemoveGroupsCommand::readGroup(){
 488         try {
 489                 string thisOutputDir = outputDir;
 490                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 491                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 492
 493                 ofstream out;
 494                 m->openOutputFile(outputFileName, out);
 495
 496                 ifstream in;
 497                 m->openInputFile(groupfile, in);
 498                 string name, group;
 499
 500                 bool wroteSomething = false;
 501
 502                 while(!in.eof()){
 503                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 504
 505                         in >> name;                             //read from first column
 506                         in >> group;                    //read from second column
 507
 508                         //if this name is in the accnos file
 509                         if (names.count(name) == 0) {
 510                                 wroteSomething = true;
 511                                 out << name << '\t' << group << endl;
 512                         }
 513
 514                         m->gobble(in);
 515                 }
 516                 in.close();
 517                 out.close();
 518
 519                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 520                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 521
 522                 return 0;
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "RemoveGroupsCommand", "readGroup");
 526                 exit(1);
 527         }
 528 }
 529 //**********************************************************************************************************************
 530 int RemoveGroupsCommand::readTax(){
 531         try {
 532                 string thisOutputDir = outputDir;
 533                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 534                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 535                 ofstream out;
 536                 m->openOutputFile(outputFileName, out);
 537
 538                 ifstream in;
 539                 m->openInputFile(taxfile, in);
 540                 string name, tax;
 541
 542                 bool wroteSomething = false;
 543
 544                 while(!in.eof()){
 545                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 546
 547                         in >> name;                             //read from first column
 548                         in >> tax;                      //read from second column
 549
 550                         //if this name is in the accnos file
 551                         if (names.count(name) == 0) {
 552                                 wroteSomething = true;
 553                                 out << name << '\t' << tax << endl;
 554                         }
 555
 556                         m->gobble(in);
 557                 }
 558                 in.close();
 559                 out.close();
 560
 561                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 562                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 563
 564                 return 0;
 565         }
 566         catch(exception& e) {
 567                 m->errorOut(e, "RemoveGroupsCommand", "readTax");
 568                 exit(1);
 569         }
 570 }
 571 //**********************************************************************************************************************
 572 void RemoveGroupsCommand::readAccnos(){
 573         try {
 574                 Groups.clear();
 575
 576                 ifstream in;
 577                 m->openInputFile(accnosfile, in);
 578                 string name;
 579
 580                 while(!in.eof()){
 581                         in >> name;
 582
 583                         Groups.push_back(name);
 584
 585                         m->gobble(in);
 586                 }
 587                 in.close();
 588
 589         }
 590         catch(exception& e) {
 591                 m->errorOut(e, "RemoveGroupsCommand", "readAccnos");
 592                 exit(1);
 593         }
 594 }
 595 //**********************************************************************************************************************
 596 int RemoveGroupsCommand::fillNames(){
 597         try {
 598                 vector<string> seqs = groupMap->getNamesSeqs();
 599
 600                 for (int i = 0; i < seqs.size(); i++) {
 601
 602                         if (m->control_pressed) { return 0; }
 603
 604                         string group = groupMap->getGroup(seqs[i]);
 605
 606                         if (m->inUsersGroups(group, Groups)) {
 607                                 names.insert(seqs[i]);
 608                         }
 609                 }
 610
 611                 return 0;
 612         }
 613         catch(exception& e) {
 614                 m->errorOut(e, "RemoveGroupsCommand", "fillNames");
 615                 exit(1);
 616         }
 617 }
 618
 619 //**********************************************************************************************************************
 620
 621
 622