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