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                         else { m->setAccnosFile(accnosfile); }
 170
 171                         fastafile = validParameter.validFile(parameters, "fasta", true);
 172                         if (fastafile == "not open") { abort = true; }
 173                         else if (fastafile == "not found") {  fastafile = "";  }
 174                         else { m->setFastaFile(fastafile); }
 175
 176                         namefile = validParameter.validFile(parameters, "name", true);
 177                         if (namefile == "not open") { abort = true; }
 178                         else if (namefile == "not found") {  namefile = "";  }
 179                         else { m->setNameFile(namefile); }
 180
 181                         groupfile = validParameter.validFile(parameters, "group", true);
 182                         if (groupfile == "not open") { abort = true; }
 183                         else if (groupfile == "not found") {
 184                                 //if there is a current group file, use it
 185                                 groupfile = m->getGroupFile();
 186                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 187                                 else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
 188                         }else { m->setGroupFile(groupfile); }
 189
 190                         listfile = validParameter.validFile(parameters, "list", true);
 191                         if (listfile == "not open") { abort = true; }
 192                         else if (listfile == "not found") {  listfile = "";  }
 193                         else { m->setListFile(listfile); }
 194
 195                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 196                         if (taxfile == "not open") { abort = true; }
 197                         else if (taxfile == "not found") {  taxfile = "";  }
 198                         else { m->setTaxonomyFile(taxfile); }
 199
 200                         groups = validParameter.validFile(parameters, "groups", false);
 201                         if (groups == "not found") { groups = ""; }
 202                         else {
 203                                 m->splitAtDash(groups, Groups);
 204                         }
 205
 206                         if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
 207
 208                         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; }
 209                 }
 210
 211         }
 212         catch(exception& e) {
 213                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 214                 exit(1);
 215         }
 216 }
 217 //**********************************************************************************************************************
 218
 219 int RemoveGroupsCommand::execute(){
 220         try {
 221
 222                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 223
 224                 groupMap = new GroupMap(groupfile);
 225                 groupMap->readMap();
 226
 227                 //get groups you want to remove
 228                 if (accnosfile != "") { readAccnos(); }
 229
 230                 //make sure groups are valid
 231                 //takes care of user setting groupNames that are invalid or setting groups=all
 232                 SharedUtil* util = new SharedUtil();
 233                 util->setGroups(Groups, groupMap->namesOfGroups);
 234                 delete util;
 235
 236                 //fill names with names of sequences that are from the groups we want to remove
 237                 fillNames();
 238
 239                 if (m->control_pressed) { delete groupMap; return 0; }
 240
 241                 //read through the correct file and output lines you want to keep
 242                 if (namefile != "")                     {               readName();             }
 243                 if (fastafile != "")            {               readFasta();    }
 244                 if (groupfile != "")            {               readGroup();    }
 245                 if (listfile != "")                     {               readList();             }
 246                 if (taxfile != "")                      {               readTax();              }
 247
 248                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 249
 250                 m->mothurOut("Removed " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
 251                 for (int i = 0; i < Groups.size(); i++) {       m->mothurOut(Groups[i]); m->mothurOut("\t" + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine(); }
 252                 m->mothurOutEndLine();
 253
 254                 if (outputNames.size() != 0) {
 255                         m->mothurOutEndLine();
 256                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 257                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 258                         m->mothurOutEndLine();
 259
 260                         //set fasta file as new current fastafile
 261                         string current = "";
 262                         itTypes = outputTypes.find("fasta");
 263                         if (itTypes != outputTypes.end()) {
 264                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 265                         }
 266
 267                         itTypes = outputTypes.find("name");
 268                         if (itTypes != outputTypes.end()) {
 269                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 270                         }
 271
 272                         itTypes = outputTypes.find("group");
 273                         if (itTypes != outputTypes.end()) {
 274                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 275                         }
 276
 277                         itTypes = outputTypes.find("list");
 278                         if (itTypes != outputTypes.end()) {
 279                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 280                         }
 281
 282                         itTypes = outputTypes.find("taxonomy");
 283                         if (itTypes != outputTypes.end()) {
 284                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 285                         }
 286                 }
 287
 288                 return 0;
 289         }
 290
 291         catch(exception& e) {
 292                 m->errorOut(e, "RemoveGroupsCommand", "execute");
 293                 exit(1);
 294         }
 295 }
 296
 297 //**********************************************************************************************************************
 298 int RemoveGroupsCommand::readFasta(){
 299         try {
 300                 string thisOutputDir = outputDir;
 301                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 302                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 303
 304                 ofstream out;
 305                 m->openOutputFile(outputFileName, out);
 306
 307                 ifstream in;
 308                 m->openInputFile(fastafile, in);
 309                 string name;
 310
 311                 bool wroteSomething = false;
 312
 313                 while(!in.eof()){
 314                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 315
 316                         Sequence currSeq(in);
 317                         name = currSeq.getName();
 318
 319                         if (name != "") {
 320                                 //if this name is in the accnos file
 321                                 if (names.count(name) == 0) {
 322                                         wroteSomething = true;
 323
 324                                         currSeq.printSequence(out);
 325                                 }
 326                         }
 327                         m->gobble(in);
 328                 }
 329                 in.close();
 330                 out.close();
 331
 332                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 333                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 334
 335                 return 0;
 336
 337         }
 338         catch(exception& e) {
 339                 m->errorOut(e, "RemoveGroupsCommand", "readFasta");
 340                 exit(1);
 341         }
 342 }
 343
 344 //**********************************************************************************************************************
 345 int RemoveGroupsCommand::readList(){
 346         try {
 347                 string thisOutputDir = outputDir;
 348                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 349                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 350
 351                 ofstream out;
 352                 m->openOutputFile(outputFileName, out);
 353
 354                 ifstream in;
 355                 m->openInputFile(listfile, in);
 356
 357                 bool wroteSomething = false;
 358
 359                 while(!in.eof()){
 360                         //read in list vector
 361                         ListVector list(in);
 362
 363                         //make a new list vector
 364                         ListVector newList;
 365                         newList.setLabel(list.getLabel());
 366
 367                         //for each bin
 368                         for (int i = 0; i < list.getNumBins(); i++) {
 369                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 370
 371                                 //parse out names that are in accnos file
 372                                 string binnames = list.get(i);
 373
 374                                 string newNames = "";
 375                                 while (binnames.find_first_of(',') != -1) {
 376                                         string name = binnames.substr(0,binnames.find_first_of(','));
 377                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 378
 379                                         //if that name is in the .accnos file, add it
 380                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 381                                 }
 382
 383                                 //get last name
 384                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 385
 386                                 //if there are names in this bin add to new list
 387                                 if (newNames != "") {
 388                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 389                                         newList.push_back(newNames);
 390                                 }
 391                         }
 392
 393                         //print new listvector
 394                         if (newList.getNumBins() != 0) {
 395                                 wroteSomething = true;
 396                                 newList.print(out);
 397                         }
 398
 399                         m->gobble(in);
 400                 }
 401                 in.close();
 402                 out.close();
 403
 404                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 405                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 406
 407                 return 0;
 408
 409         }
 410         catch(exception& e) {
 411                 m->errorOut(e, "RemoveGroupsCommand", "readList");
 412                 exit(1);
 413         }
 414 }
 415 //**********************************************************************************************************************
 416 int RemoveGroupsCommand::readName(){
 417         try {
 418                 string thisOutputDir = outputDir;
 419                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 420                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 421
 422                 ofstream out;
 423                 m->openOutputFile(outputFileName, out);
 424
 425                 ifstream in;
 426                 m->openInputFile(namefile, in);
 427                 string name, firstCol, secondCol;
 428
 429                 bool wroteSomething = false;
 430
 431                 while(!in.eof()){
 432                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 433
 434                         in >> firstCol;         m->gobble(in);
 435                         in >> secondCol;
 436
 437                         vector<string> parsedNames;
 438                         m->splitAtComma(secondCol, parsedNames);
 439
 440                         vector<string> validSecond;  validSecond.clear();
 441                         for (int i = 0; i < parsedNames.size(); i++) {
 442                                 if (names.count(parsedNames[i]) == 0) {
 443                                         validSecond.push_back(parsedNames[i]);
 444                                 }
 445                         }
 446
 447
 448                         //if the name in the first column is in the set then print it and any other names in second column also in set
 449                         if (names.count(firstCol) == 0) {
 450
 451                                 wroteSomething = true;
 452
 453                                 out << firstCol << '\t';
 454
 455                                 //you know you have at least one valid second since first column is valid
 456                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 457                                 out << validSecond[validSecond.size()-1] << endl;
 458
 459                                 //make first name in set you come to first column and then add the remaining names to second column
 460                         }else {
 461
 462                                 //you want part of this row
 463                                 if (validSecond.size() != 0) {
 464
 465                                         wroteSomething = true;
 466
 467                                         out << validSecond[0] << '\t';
 468
 469                                         //you know you have at least one valid second since first column is valid
 470                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 471                                         out << validSecond[validSecond.size()-1] << endl;
 472                                 }
 473                         }
 474
 475                         m->gobble(in);
 476                 }
 477                 in.close();
 478                 out.close();
 479
 480                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 481                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 482
 483                 return 0;
 484         }
 485         catch(exception& e) {
 486                 m->errorOut(e, "RemoveGroupsCommand", "readName");
 487                 exit(1);
 488         }
 489 }
 490
 491 //**********************************************************************************************************************
 492 int RemoveGroupsCommand::readGroup(){
 493         try {
 494                 string thisOutputDir = outputDir;
 495                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 496                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 497
 498                 ofstream out;
 499                 m->openOutputFile(outputFileName, out);
 500
 501                 ifstream in;
 502                 m->openInputFile(groupfile, in);
 503                 string name, group;
 504
 505                 bool wroteSomething = false;
 506
 507                 while(!in.eof()){
 508                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 509
 510                         in >> name;                             //read from first column
 511                         in >> group;                    //read from second column
 512
 513                         //if this name is in the accnos file
 514                         if (names.count(name) == 0) {
 515                                 wroteSomething = true;
 516                                 out << name << '\t' << group << endl;
 517                         }
 518
 519                         m->gobble(in);
 520                 }
 521                 in.close();
 522                 out.close();
 523
 524                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 525                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 526
 527                 return 0;
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "RemoveGroupsCommand", "readGroup");
 531                 exit(1);
 532         }
 533 }
 534 //**********************************************************************************************************************
 535 int RemoveGroupsCommand::readTax(){
 536         try {
 537                 string thisOutputDir = outputDir;
 538                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 539                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 540                 ofstream out;
 541                 m->openOutputFile(outputFileName, out);
 542
 543                 ifstream in;
 544                 m->openInputFile(taxfile, in);
 545                 string name, tax;
 546
 547                 bool wroteSomething = false;
 548
 549                 while(!in.eof()){
 550                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 551
 552                         in >> name;                             //read from first column
 553                         in >> tax;                      //read from second column
 554
 555                         //if this name is in the accnos file
 556                         if (names.count(name) == 0) {
 557                                 wroteSomething = true;
 558                                 out << name << '\t' << tax << endl;
 559                         }
 560
 561                         m->gobble(in);
 562                 }
 563                 in.close();
 564                 out.close();
 565
 566                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 567                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 568
 569                 return 0;
 570         }
 571         catch(exception& e) {
 572                 m->errorOut(e, "RemoveGroupsCommand", "readTax");
 573                 exit(1);
 574         }
 575 }
 576 //**********************************************************************************************************************
 577 void RemoveGroupsCommand::readAccnos(){
 578         try {
 579                 Groups.clear();
 580
 581                 ifstream in;
 582                 m->openInputFile(accnosfile, in);
 583                 string name;
 584
 585                 while(!in.eof()){
 586                         in >> name;
 587
 588                         Groups.push_back(name);
 589
 590                         m->gobble(in);
 591                 }
 592                 in.close();
 593
 594         }
 595         catch(exception& e) {
 596                 m->errorOut(e, "RemoveGroupsCommand", "readAccnos");
 597                 exit(1);
 598         }
 599 }
 600 //**********************************************************************************************************************
 601 int RemoveGroupsCommand::fillNames(){
 602         try {
 603                 vector<string> seqs = groupMap->getNamesSeqs();
 604
 605                 for (int i = 0; i < seqs.size(); i++) {
 606
 607                         if (m->control_pressed) { return 0; }
 608
 609                         string group = groupMap->getGroup(seqs[i]);
 610
 611                         if (m->inUsersGroups(group, Groups)) {
 612                                 names.insert(seqs[i]);
 613                         }
 614                 }
 615
 616                 return 0;
 617         }
 618         catch(exception& e) {
 619                 m->errorOut(e, "RemoveGroupsCommand", "fillNames");
 620                 exit(1);
 621         }
 622 }
 623
 624 //**********************************************************************************************************************
 625
 626
 627