5 * Created by westcott on 11/10/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "getgroupscommand.h"
11 #include "sequence.hpp"
12 #include "listvector.hpp"
13 #include "sharedutilities.h"
14 #include "inputdata.h"
16 //**********************************************************************************************************************
17 vector<string> GetGroupsCommand::setParameters(){
19 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
20 CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pshared);
21 CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
22 CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pgroup);
23 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
24 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
25 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
26 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
27 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
28 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
30 vector<string> myArray;
31 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
35 m->errorOut(e, "GetGroupsCommand", "setParameters");
39 //**********************************************************************************************************************
40 string GetGroupsCommand::getHelpString(){
42 string helpString = "";
43 helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy or shared file.\n";
44 helpString += "It outputs a file containing the sequences in the those specified groups, or a sharedfile containing only those groups.\n";
45 helpString += "The get.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared and groups. The group parameter is required, unless you have a current group file, or are using a shared file.\n";
46 helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
47 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n";
48 helpString += "The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
49 helpString += "Example get.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n";
50 helpString += "or get.groups(groups=pasture, fasta=amazon.fasta, group=amazon.groups).\n";
51 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
55 m->errorOut(e, "GetGroupsCommand", "getHelpString");
59 //**********************************************************************************************************************
60 GetGroupsCommand::GetGroupsCommand(){
62 abort = true; calledHelp = true;
64 vector<string> tempOutNames;
65 outputTypes["fasta"] = tempOutNames;
66 outputTypes["taxonomy"] = tempOutNames;
67 outputTypes["name"] = tempOutNames;
68 outputTypes["group"] = tempOutNames;
69 outputTypes["list"] = tempOutNames;
70 outputTypes["shared"] = tempOutNames;
73 m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
77 //**********************************************************************************************************************
78 GetGroupsCommand::GetGroupsCommand(string option) {
80 abort = false; calledHelp = false;
82 //allow user to run help
83 if(option == "help") { help(); abort = true; calledHelp = true; }
84 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
87 vector<string> myArray = setParameters();
89 OptionParser parser(option);
90 map<string,string> parameters = parser.getParameters();
92 ValidParameters validParameter;
93 map<string,string>::iterator it;
95 //check to make sure all parameters are valid for command
96 for (it = parameters.begin(); it != parameters.end(); it++) {
97 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
100 //initialize outputTypes
101 vector<string> tempOutNames;
102 outputTypes["fasta"] = tempOutNames;
103 outputTypes["taxonomy"] = tempOutNames;
104 outputTypes["name"] = tempOutNames;
105 outputTypes["group"] = tempOutNames;
106 outputTypes["list"] = tempOutNames;
107 outputTypes["shared"] = tempOutNames;
110 //if the user changes the output directory command factory will send this info to us in the output parameter
111 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
113 //if the user changes the input directory command factory will send this info to us in the output parameter
114 string inputDir = validParameter.validFile(parameters, "inputdir", false);
115 if (inputDir == "not found"){ inputDir = ""; }
118 it = parameters.find("fasta");
119 //user has given a template file
120 if(it != parameters.end()){
121 path = m->hasPath(it->second);
122 //if the user has not given a path then, add inputdir. else leave path alone.
123 if (path == "") { parameters["fasta"] = inputDir + it->second; }
126 it = parameters.find("accnos");
127 //user has given a template file
128 if(it != parameters.end()){
129 path = m->hasPath(it->second);
130 //if the user has not given a path then, add inputdir. else leave path alone.
131 if (path == "") { parameters["accnos"] = inputDir + it->second; }
134 it = parameters.find("list");
135 //user has given a template file
136 if(it != parameters.end()){
137 path = m->hasPath(it->second);
138 //if the user has not given a path then, add inputdir. else leave path alone.
139 if (path == "") { parameters["list"] = inputDir + it->second; }
142 it = parameters.find("name");
143 //user has given a template file
144 if(it != parameters.end()){
145 path = m->hasPath(it->second);
146 //if the user has not given a path then, add inputdir. else leave path alone.
147 if (path == "") { parameters["name"] = inputDir + it->second; }
150 it = parameters.find("group");
151 //user has given a template file
152 if(it != parameters.end()){
153 path = m->hasPath(it->second);
154 //if the user has not given a path then, add inputdir. else leave path alone.
155 if (path == "") { parameters["group"] = inputDir + it->second; }
158 it = parameters.find("taxonomy");
159 //user has given a template file
160 if(it != parameters.end()){
161 path = m->hasPath(it->second);
162 //if the user has not given a path then, add inputdir. else leave path alone.
163 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
166 it = parameters.find("shared");
167 //user has given a template file
168 if(it != parameters.end()){
169 path = m->hasPath(it->second);
170 //if the user has not given a path then, add inputdir. else leave path alone.
171 if (path == "") { parameters["shared"] = inputDir + it->second; }
176 //check for required parameters
177 accnosfile = validParameter.validFile(parameters, "accnos", true);
178 if (accnosfile == "not open") { abort = true; }
179 else if (accnosfile == "not found") { accnosfile = ""; }
180 else { m->setAccnosFile(accnosfile); }
182 fastafile = validParameter.validFile(parameters, "fasta", true);
183 if (fastafile == "not open") { abort = true; }
184 else if (fastafile == "not found") { fastafile = ""; }
185 else { m->setFastaFile(fastafile); }
187 namefile = validParameter.validFile(parameters, "name", true);
188 if (namefile == "not open") { abort = true; }
189 else if (namefile == "not found") { namefile = ""; }
190 else { m->setNameFile(namefile); }
192 groupfile = validParameter.validFile(parameters, "group", true);
193 if (groupfile == "not open") { abort = true; }
194 else if (groupfile == "not found") {
195 //if there is a current group file, use it
196 groupfile = m->getGroupFile();
197 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
198 else { m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
199 }else { m->setGroupFile(groupfile); }
201 listfile = validParameter.validFile(parameters, "list", true);
202 if (listfile == "not open") { abort = true; }
203 else if (listfile == "not found") { listfile = ""; }
204 else { m->setListFile(listfile); }
206 taxfile = validParameter.validFile(parameters, "taxonomy", true);
207 if (taxfile == "not open") { abort = true; }
208 else if (taxfile == "not found") { taxfile = ""; }
209 else { m->setTaxonomyFile(taxfile); }
211 groups = validParameter.validFile(parameters, "groups", false);
212 if (groups == "not found") { groups = ""; }
214 m->splitAtDash(groups, Groups);
215 m->setGroups(Groups);
218 sharedfile = validParameter.validFile(parameters, "shared", true);
219 if (sharedfile == "not open") { sharedfile = ""; abort = true; }
220 else if (sharedfile == "not found") { sharedfile = ""; }
221 else { m->setSharedFile(sharedfile); }
223 groupfile = validParameter.validFile(parameters, "group", true);
224 if (groupfile == "not open") { groupfile = ""; abort = true; }
225 else if (groupfile == "not found") { groupfile = ""; }
226 else { m->setGroupFile(groupfile); }
228 if ((sharedfile == "") && (groupfile == "")) {
229 //is there are current file available for any of these?
230 if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
231 //give priority to group, then shared
232 groupfile = m->getGroupFile();
233 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
235 sharedfile = m->getSharedFile();
236 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
238 m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
242 //give priority to shared, then group
243 sharedfile = m->getSharedFile();
244 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
246 groupfile = m->getGroupFile();
247 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
249 m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
255 if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
257 if ((fastafile == "") && (namefile == "") && (groupfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared or list."); m->mothurOutEndLine(); abort = true; }
258 if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != ""))) { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; }
263 catch(exception& e) {
264 m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
268 //**********************************************************************************************************************
270 int GetGroupsCommand::execute(){
273 if (abort == true) { if (calledHelp) { return 0; } return 2; }
275 //get groups you want to remove
276 if (accnosfile != "") { readAccnos(); }
278 if (groupfile != "") {
279 groupMap = new GroupMap(groupfile);
282 //make sure groups are valid
283 //takes care of user setting groupNames that are invalid or setting groups=all
284 SharedUtil* util = new SharedUtil();
285 vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
286 util->setGroups(Groups, gNamesOfGroups);
287 groupMap->setNamesOfGroups(gNamesOfGroups);
290 //fill names with names of sequences that are from the groups we want to remove
296 if (m->control_pressed) { return 0; }
298 //read through the correct file and output lines you want to keep
299 if (namefile != "") { readName(); }
300 if (fastafile != "") { readFasta(); }
301 if (groupfile != "") { readGroup(); }
302 if (listfile != "") { readList(); }
303 if (taxfile != "") { readTax(); }
304 if (sharedfile != "") { readShared(); }
306 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
309 if (outputNames.size() != 0) {
310 m->mothurOutEndLine();
311 m->mothurOut("Output File names: "); m->mothurOutEndLine();
312 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
313 m->mothurOutEndLine();
315 //set fasta file as new current fastafile
317 itTypes = outputTypes.find("fasta");
318 if (itTypes != outputTypes.end()) {
319 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
322 itTypes = outputTypes.find("name");
323 if (itTypes != outputTypes.end()) {
324 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
327 itTypes = outputTypes.find("group");
328 if (itTypes != outputTypes.end()) {
329 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
332 itTypes = outputTypes.find("list");
333 if (itTypes != outputTypes.end()) {
334 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
337 itTypes = outputTypes.find("taxonomy");
338 if (itTypes != outputTypes.end()) {
339 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
342 itTypes = outputTypes.find("shared");
343 if (itTypes != outputTypes.end()) {
344 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
351 catch(exception& e) {
352 m->errorOut(e, "GetGroupsCommand", "execute");
357 //**********************************************************************************************************************
358 int GetGroupsCommand::readFasta(){
360 string thisOutputDir = outputDir;
361 if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
362 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
365 m->openOutputFile(outputFileName, out);
368 m->openInputFile(fastafile, in);
371 bool wroteSomething = false;
372 int selectedCount = 0;
375 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
377 Sequence currSeq(in);
378 name = currSeq.getName();
381 //if this name is in the accnos file
382 if (names.count(name) != 0) {
383 wroteSomething = true;
385 currSeq.printSequence(out);
394 if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
395 outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
397 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
403 catch(exception& e) {
404 m->errorOut(e, "GetGroupsCommand", "readFasta");
408 //**********************************************************************************************************************
409 int GetGroupsCommand::readShared(){
411 string thisOutputDir = outputDir;
412 if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
414 InputData input(sharedfile, "sharedfile");
415 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
417 bool wroteSomething = false;
419 while(lookup[0] != NULL) {
421 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".pick" + m->getExtension(sharedfile);
423 m->openOutputFile(outputFileName, out);
424 outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
426 if (m->control_pressed) { out.close(); m->mothurRemove(outputFileName); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
428 lookup[0]->printHeaders(out);
430 for (int i = 0; i < lookup.size(); i++) {
431 out << lookup[i]->getLabel() << '\t' << lookup[i]->getGroup() << '\t';
432 lookup[i]->print(out);
433 wroteSomething = true;
437 //get next line to process
438 //prevent memory leak
439 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
440 lookup = input.getSharedRAbundVectors();
445 if (wroteSomething == false) { m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine(); }
447 string groupsString = "";
448 for (int i = 0; i < Groups.size()-1; i++) { groupsString += Groups[i] + ", "; }
449 groupsString += Groups[Groups.size()-1];
451 m->mothurOut("Selected groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
456 catch(exception& e) {
457 m->errorOut(e, "GetGroupsCommand", "readShared");
461 //**********************************************************************************************************************
462 int GetGroupsCommand::readList(){
464 string thisOutputDir = outputDir;
465 if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
466 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
469 m->openOutputFile(outputFileName, out);
472 m->openInputFile(listfile, in);
474 bool wroteSomething = false;
475 int selectedCount = 0;
481 //read in list vector
484 //make a new list vector
486 newList.setLabel(list.getLabel());
489 for (int i = 0; i < list.getNumBins(); i++) {
490 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
492 //parse out names that are in accnos file
493 string binnames = list.get(i);
495 string newNames = "";
496 while (binnames.find_first_of(',') != -1) {
497 string name = binnames.substr(0,binnames.find_first_of(','));
498 binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
500 //if that name is in the .accnos file, add it
501 if (names.count(name) != 0) { newNames += name + ","; selectedCount++; }
505 if (names.count(binnames) != 0) { newNames += binnames + ","; selectedCount++; }
507 //if there are names in this bin add to new list
508 if (newNames != "") {
509 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
510 newList.push_back(newNames);
514 //print new listvector
515 if (newList.getNumBins() != 0) {
516 wroteSomething = true;
525 if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
526 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
528 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
533 catch(exception& e) {
534 m->errorOut(e, "GetGroupsCommand", "readList");
538 //**********************************************************************************************************************
539 int GetGroupsCommand::readName(){
541 string thisOutputDir = outputDir;
542 if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
543 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
546 m->openOutputFile(outputFileName, out);
549 m->openInputFile(namefile, in);
550 string name, firstCol, secondCol;
552 bool wroteSomething = false;
553 int selectedCount = 0;
556 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
558 in >> firstCol; m->gobble(in);
561 vector<string> parsedNames;
562 m->splitAtComma(secondCol, parsedNames);
564 vector<string> validSecond; validSecond.clear();
565 for (int i = 0; i < parsedNames.size(); i++) {
566 if (names.count(parsedNames[i]) != 0) {
567 validSecond.push_back(parsedNames[i]);
571 selectedCount += validSecond.size();
573 //if the name in the first column is in the set then print it and any other names in second column also in set
574 if (names.count(firstCol) != 0) {
576 wroteSomething = true;
578 out << firstCol << '\t';
580 //you know you have at least one valid second since first column is valid
581 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
582 out << validSecond[validSecond.size()-1] << endl;
584 //make first name in set you come to first column and then add the remaining names to second column
587 //you want part of this row
588 if (validSecond.size() != 0) {
590 wroteSomething = true;
592 out << validSecond[0] << '\t';
594 //you know you have at least one valid second since first column is valid
595 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
596 out << validSecond[validSecond.size()-1] << endl;
605 if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
606 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
608 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
612 catch(exception& e) {
613 m->errorOut(e, "GetGroupsCommand", "readName");
618 //**********************************************************************************************************************
619 int GetGroupsCommand::readGroup(){
621 string thisOutputDir = outputDir;
622 if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
623 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
626 m->openOutputFile(outputFileName, out);
629 m->openInputFile(groupfile, in);
632 bool wroteSomething = false;
633 int selectedCount = 0;
636 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
638 in >> name; //read from first column
639 in >> group; //read from second column
641 //if this name is in the accnos file
642 if (names.count(name) != 0) {
643 wroteSomething = true;
644 out << name << '\t' << group << endl;
653 if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
654 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
656 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
660 catch(exception& e) {
661 m->errorOut(e, "GetGroupsCommand", "readGroup");
665 //**********************************************************************************************************************
666 int GetGroupsCommand::readTax(){
668 string thisOutputDir = outputDir;
669 if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
670 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
672 m->openOutputFile(outputFileName, out);
675 m->openInputFile(taxfile, in);
678 bool wroteSomething = false;
681 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
683 in >> name; //read from first column
684 in >> tax; //read from second column
686 //if this name is in the accnos file
687 if (names.count(name) != 0) {
688 wroteSomething = true;
689 out << name << '\t' << tax << endl;
697 if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
698 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
702 catch(exception& e) {
703 m->errorOut(e, "GetGroupsCommand", "readTax");
707 //**********************************************************************************************************************
708 void GetGroupsCommand::readAccnos(){
713 m->openInputFile(accnosfile, in);
719 Groups.push_back(name);
725 m->setGroups(Groups);
728 catch(exception& e) {
729 m->errorOut(e, "GetGroupsCommand", "readAccnos");
733 //**********************************************************************************************************************
734 int GetGroupsCommand::fillNames(){
736 vector<string> seqs = groupMap->getNamesSeqs();
738 for (int i = 0; i < seqs.size(); i++) {
740 if (m->control_pressed) { return 0; }
742 string group = groupMap->getGroup(seqs[i]);
744 if (m->inUsersGroups(group, Groups)) {
745 names.insert(seqs[i]);
751 catch(exception& e) {
752 m->errorOut(e, "GetGroupsCommand", "fillNames");
757 //**********************************************************************************************************************