sharedcommand.cpp

   1 /*
   2  *  sharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedcommand.h"
  11 //********************************************************************************************************************
  12 //sorts lowest to highest
  13 inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){
  14         return (left->getGroup() < right->getGroup());
  15 }
  16 //**********************************************************************************************************************
  17 vector<string> SharedCommand::setParameters(){
  18         try {
  19                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
  21                 CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
  22                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  23                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  24                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  25                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "SharedCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string SharedCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The make.shared command reads a list and group file and creates a shared file, as well as a rabund file for each group.\n";
  41                 helpString += "The make.shared command parameters are list, group, ordergroup, groups and label. list and group are required unless a current file is available.\n";
  42                 helpString += "The groups parameter allows you to indicate which groups you want to include, group names should be separated by dashes. ex. groups=A-B-C. Default is all groups in your groupfile.\n";
  43                 helpString += "The label parameter allows you to indicate which labels you want to include, label names should be separated by dashes. Default is all labels in your list file.\n";
  44                 helpString += "The ordergroup parameter allows you to indicate the order of the groups in the sharedfile, by default the groups are listed alphabetically.\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "SharedCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 SharedCommand::SharedCommand(){
  54         try {
  55                 abort = true; calledHelp = true;
  56                 setParameters();
  57                 //initialize outputTypes
  58                 vector<string> tempOutNames;
  59                 outputTypes["rabund"] = tempOutNames;
  60                 outputTypes["shared"] = tempOutNames;
  61                 outputTypes["group"] = tempOutNames;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "SharedCommand", "SharedCommand");
  65                 exit(1);
  66         }
  67 }
  68 //**********************************************************************************************************************
  69 SharedCommand::SharedCommand(string option)  {
  70         try {
  71                 abort = false; calledHelp = false;
  72                 allLines = 1;
  73
  74                 //allow user to run help
  75                 if(option == "help") { help(); abort = true; calledHelp = true; }
  76                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  77
  78                 else {
  79
  80                          vector<string> myArray = setParameters();
  81
  82                          OptionParser parser(option);
  83                          map<string, string> parameters = parser.getParameters();
  84
  85                          ValidParameters validParameter;
  86                          map<string, string>::iterator it;
  87
  88                          //check to make sure all parameters are valid for command
  89                          for (it = parameters.begin(); it != parameters.end(); it++) {
  90                                  if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  91                          }
  92
  93                          //if the user changes the input directory command factory will send this info to us in the output parameter
  94                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  95                          if (inputDir == "not found"){  inputDir = "";          }
  96                          else {
  97                                  string path;
  98                                  it = parameters.find("list");
  99                                  //user has given a template file
 100                                  if(it != parameters.end()){
 101                                          path = m->hasPath(it->second);
 102                                          //if the user has not given a path then, add inputdir. else leave path alone.
 103                                          if (path == "") {      parameters["list"] = inputDir + it->second;             }
 104                                  }
 105
 106                                  it = parameters.find("group");
 107                                  //user has given a template file
 108                                  if(it != parameters.end()){
 109                                          path = m->hasPath(it->second);
 110                                          //if the user has not given a path then, add inputdir. else leave path alone.
 111                                          if (path == "") {      parameters["group"] = inputDir + it->second;            }
 112                                  }
 113
 114                                  it = parameters.find("ordergroup");
 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["ordergroup"] = inputDir + it->second;               }
 120                                  }
 121                          }
 122
 123
 124                          //if the user changes the output directory command factory will send this info to us in the output parameter
 125                          outputDir = validParameter.validFile(parameters, "outputdir", false);          if (outputDir == "not found"){  outputDir = ""; }
 126
 127                          //check for required parameters
 128                          listfile = validParameter.validFile(parameters, "list", true);
 129                          if (listfile == "not open") { listfile = ""; abort = true; }
 130                          else if (listfile == "not found") {
 131                                  listfile = m->getListFile();
 132                                  if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 133                                  else {         m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 134                          }else { m->setListFile(listfile); }
 135
 136                          ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 137                          if (ordergroupfile == "not open") { abort = true; }
 138                          else if (ordergroupfile == "not found") { ordergroupfile = ""; }
 139
 140                          groupfile = validParameter.validFile(parameters, "group", true);
 141                          if (groupfile == "not open") { groupfile = ""; abort = true; }
 142                          else if (groupfile == "not found") {
 143                                  groupfile = m->getGroupFile();
 144                                  if (groupfile != "") {
 145                                          m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine();
 146                                          groupMap = new GroupMap(groupfile);
 147
 148                                          int error = groupMap->readMap();
 149                                          if (error == 1) { abort = true; }
 150                                          m->namesOfGroups = groupMap->namesOfGroups;
 151                                  }
 152                                  else {         m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
 153                          }else {
 154                                  groupMap = new GroupMap(groupfile);
 155
 156                                  int error = groupMap->readMap();
 157                                  if (error == 1) { abort = true; }
 158                                  m->namesOfGroups = groupMap->namesOfGroups;
 159                                  m->setGroupFile(groupfile);
 160                          }
 161
 162                          string groups = validParameter.validFile(parameters, "groups", false);
 163                          if (groups == "not found") { groups = ""; }
 164                          else {
 165                                  m->splitAtDash(groups, Groups);
 166                                  m->Groups = Groups;
 167                          }
 168
 169                          //check for optional parameter and set defaults
 170                          // ...at some point should added some additional type checking...
 171                          string label = validParameter.validFile(parameters, "label", false);
 172                          if (label == "not found") { label = ""; }
 173                          else {
 174                                  if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 175                                  else { allLines = 1;  }
 176                          }
 177                 }
 178
 179         }
 180         catch(exception& e) {
 181                 m->errorOut(e, "SharedCommand", "SharedCommand");
 182                 exit(1);
 183         }
 184 }
 185 //**********************************************************************************************************************
 186
 187 int SharedCommand::execute(){
 188         try {
 189
 190                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 191
 192                 //getting output filename
 193                 filename = listfile;
 194
 195                 if (outputDir == "") { outputDir += m->hasPath(filename); }
 196
 197                 filename = outputDir + m->getRootName(m->getSimpleName(filename));
 198                 filename = filename + "shared";
 199                 outputTypes["shared"].push_back(filename);
 200
 201                 m->openOutputFile(filename, out);
 202                 pickedGroups = false;
 203
 204                 //if hte user has not specified any groups then use them all
 205                 if (Groups.size() == 0) {
 206                         Groups = groupMap->namesOfGroups; m->Groups = Groups;
 207                 }else { pickedGroups = true; }
 208
 209                 //fill filehandles with neccessary ofstreams
 210                 int i;
 211                 ofstream* temp;
 212                 for (i=0; i<Groups.size(); i++) {
 213                         temp = new ofstream;
 214                         filehandles[Groups[i]] = temp;
 215                 }
 216
 217                 //set fileroot
 218                 fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
 219
 220                 //clears file before we start to write to it below
 221                 for (int i=0; i<Groups.size(); i++) {
 222                         m->mothurRemove((fileroot + Groups[i] + ".rabund"));
 223                         outputNames.push_back((fileroot + Groups[i] + ".rabund"));
 224                         outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
 225                 }
 226
 227                 //lookup.clear();
 228                 string errorOff = "no error";
 229                 //errorOff = "";
 230
 231                 //if user provided an order file containing the order the shared file should be in read it
 232                 if (ordergroupfile != "") { readOrderFile(); }
 233
 234                 input = new InputData(listfile, "shared");
 235                 SharedList = input->getSharedListVector();
 236                 string lastLabel = SharedList->getLabel();
 237                 vector<SharedRAbundVector*> lookup;
 238
 239                 if (m->control_pressed) {
 240                         delete input; delete SharedList; delete groupMap;
 241                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 242                         out.close(); m->mothurRemove(filename);
 243                         for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
 244                         return 0;
 245                 }
 246
 247                 if ((m->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) {  //if the user has not specified any groups and their files don't match exit with error
 248                         m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
 249
 250                         out.close();
 251                         m->mothurRemove(filename); //remove blank shared file you made
 252
 253                         createMisMatchFile();
 254
 255                         //delete memory
 256                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 257                                 delete it3->second;
 258                         }
 259
 260                         delete input; delete SharedList; delete groupMap;
 261
 262                         return 0;
 263                 }
 264
 265                 //if user has specified groups make new groupfile for them
 266                 if (pickedGroups) { //make new group file
 267                         string groups = "";
 268                         if (m->Groups.size() < 4) {
 269                                 for (int i = 0; i < m->Groups.size(); i++) {
 270                                         groups += m->Groups[i] + ".";
 271                                 }
 272                         }else { groups = "merge"; }
 273
 274                         string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + "groups";
 275                         outputTypes["group"].push_back(newGroupFile);
 276                         outputNames.push_back(newGroupFile);
 277                         ofstream outGroups;
 278                         m->openOutputFile(newGroupFile, outGroups);
 279
 280                         vector<string> names = groupMap->getNamesSeqs();
 281                         string groupName;
 282                         for (int i = 0; i < names.size(); i++) {
 283                                 groupName = groupMap->getGroup(names[i]);
 284                                 if (isValidGroup(groupName, m->Groups)) {
 285                                         outGroups << names[i] << '\t' << groupName << endl;
 286                                 }
 287                         }
 288                         outGroups.close();
 289                 }
 290
 291                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 292                 set<string> processedLabels;
 293                 set<string> userLabels = labels;
 294
 295                 while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 296                         if (m->control_pressed) {
 297                                 delete input; delete SharedList; delete groupMap;
 298                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 299                                 out.close(); m->mothurRemove(filename);
 300                                 for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
 301                                 return 0;
 302                         }
 303
 304                         if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
 305
 306                                         lookup = SharedList->getSharedRAbundVector();
 307
 308                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 309                                         if (pickedGroups) { //check for otus with no seqs in them
 310                                                 eliminateZeroOTUS(lookup);
 311                                         }
 312
 313                                         if (m->control_pressed) {
 314                                                 delete input; delete SharedList; delete groupMap;
 315                                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 316                                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 317                                                 out.close(); m->mothurRemove(filename);
 318                                                 for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
 319                                                 return 0;
 320                                         }
 321
 322                                         if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 323                                         printSharedData(lookup); //prints info to the .shared file
 324                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 325
 326                                         processedLabels.insert(SharedList->getLabel());
 327                                         userLabels.erase(SharedList->getLabel());
 328                         }
 329
 330                         if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
 331                                         string saveLabel = SharedList->getLabel();
 332
 333                                         delete SharedList;
 334                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 335
 336                                         lookup = SharedList->getSharedRAbundVector();
 337                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 338                                         if (pickedGroups) { //check for otus with no seqs in them
 339                                                 eliminateZeroOTUS(lookup);
 340                                         }
 341
 342
 343                                         if (m->control_pressed) {
 344                                                 delete input; delete SharedList; delete groupMap;
 345                                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 346                                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 347                                                 out.close(); m->mothurRemove(filename);
 348                                                 for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
 349                                                 return 0;
 350                                         }
 351
 352                                         if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 353                                         printSharedData(lookup); //prints info to the .shared file
 354                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 355
 356                                         processedLabels.insert(SharedList->getLabel());
 357                                         userLabels.erase(SharedList->getLabel());
 358
 359                                         //restore real lastlabel to save below
 360                                         SharedList->setLabel(saveLabel);
 361                         }
 362
 363
 364                         lastLabel = SharedList->getLabel();
 365
 366                         delete SharedList;
 367                         SharedList = input->getSharedListVector(); //get new list vector to process
 368                 }
 369
 370                 //output error messages about any remaining user labels
 371                 set<string>::iterator it;
 372                 bool needToRun = false;
 373                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 374                         if (processedLabels.count(lastLabel) != 1) {
 375                                 needToRun = true;
 376                         }
 377                 }
 378
 379                 //run last label if you need to
 380                 if (needToRun == true)  {
 381                         if (SharedList != NULL) {       delete SharedList;      }
 382                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 383
 384                         lookup = SharedList->getSharedRAbundVector();
 385                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 386                         if (pickedGroups) { //check for otus with no seqs in them
 387                                 eliminateZeroOTUS(lookup);
 388                         }
 389
 390                         if (m->control_pressed) {
 391                                 delete input;  delete groupMap;
 392                                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;   }
 393                                         out.close(); m->mothurRemove(filename);
 394                                         for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
 395                                         return 0;
 396                         }
 397
 398                         if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 399                         printSharedData(lookup); //prints info to the .shared file
 400                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 401                         delete SharedList;
 402                 }
 403
 404                 out.close();
 405
 406                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 407                         delete it3->second;
 408                 }
 409
 410                 delete input; delete groupMap;
 411
 412                 if (m->control_pressed) {
 413                                 m->mothurRemove(filename);
 414                                 for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
 415                                 return 0;
 416                 }
 417
 418                 //set rabund file as new current rabundfile
 419                 string current = "";
 420                 itTypes = outputTypes.find("rabund");
 421                 if (itTypes != outputTypes.end()) {
 422                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 423                 }
 424
 425                 itTypes = outputTypes.find("shared");
 426                 if (itTypes != outputTypes.end()) {
 427                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 428                 }
 429
 430                 itTypes = outputTypes.find("group");
 431                 if (itTypes != outputTypes.end()) {
 432                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 433                 }
 434
 435                 m->mothurOutEndLine();
 436                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 437                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 438                 m->mothurOut(filename); m->mothurOutEndLine();
 439                 m->mothurOutEndLine();
 440
 441                 return 0;
 442         }
 443         catch(exception& e) {
 444                 m->errorOut(e, "SharedCommand", "execute");
 445                 exit(1);
 446         }
 447 }
 448 //**********************************************************************************************************************
 449 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 450         try {
 451
 452                 if (order.size() == 0) { //user has not specified an order so do aplabetically
 453                         sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
 454
 455                         m->Groups.clear();
 456
 457                         //initialize bin values
 458                         for (int i = 0; i < thislookup.size(); i++) {
 459                                 out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 460                                 thislookup[i]->print(out);
 461
 462                                 m->Groups.push_back(thislookup[i]->getGroup());
 463
 464                                 RAbundVector rav = thislookup[i]->getRAbundVector();
 465                                 m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 466                                 rav.print(*(filehandles[thislookup[i]->getGroup()]));
 467                                 (*(filehandles[thislookup[i]->getGroup()])).close();
 468                         }
 469                 }else{
 470                         //create a map from groupName to each sharedrabund
 471                         map<string, SharedRAbundVector*> myMap;
 472                         map<string, SharedRAbundVector*>::iterator myIt;
 473
 474                         for (int i = 0; i < thislookup.size(); i++) {
 475                                 myMap[thislookup[i]->getGroup()] = thislookup[i];
 476                         }
 477
 478                         m->Groups.clear();
 479
 480                         //loop through ordered list and print the rabund
 481                         for (int i = 0; i < order.size(); i++) {
 482                                 myIt = myMap.find(order[i]);
 483
 484                                 if(myIt != myMap.end()) { //we found it
 485                                         out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
 486                                         (myIt->second)->print(out);
 487
 488                                         m->Groups.push_back((myIt->second)->getGroup());
 489
 490                                         RAbundVector rav = (myIt->second)->getRAbundVector();
 491                                         m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
 492                                         rav.print(*(filehandles[(myIt->second)->getGroup()]));
 493                                         (*(filehandles[(myIt->second)->getGroup()])).close();
 494                                 }else{
 495                                         m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
 496                                 }
 497                         }
 498
 499                 }
 500
 501         }
 502         catch(exception& e) {
 503                 m->errorOut(e, "SharedCommand", "printSharedData");
 504                 exit(1);
 505         }
 506 }
 507 //**********************************************************************************************************************
 508 int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 509         try {
 510
 511                 vector<SharedRAbundVector*> newLookup;
 512                 for (int i = 0; i < thislookup.size(); i++) {
 513                         SharedRAbundVector* temp = new SharedRAbundVector();
 514                         temp->setLabel(thislookup[i]->getLabel());
 515                         temp->setGroup(thislookup[i]->getGroup());
 516                         newLookup.push_back(temp);
 517                 }
 518
 519                 //for each bin
 520                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 521                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 522
 523                         //look at each sharedRabund and make sure they are not all zero
 524                         bool allZero = true;
 525                         for (int j = 0; j < thislookup.size(); j++) {
 526                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 527                         }
 528
 529                         //if they are not all zero add this bin
 530                         if (!allZero) {
 531                                 for (int j = 0; j < thislookup.size(); j++) {
 532                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 533                                 }
 534                         }
 535                         //else{  cout << "bin # " << i << " is all zeros" << endl;  }
 536                 }
 537
 538                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 539                 thislookup = newLookup;
 540
 541                 return 0;
 542
 543         }
 544         catch(exception& e) {
 545                 m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
 546                 exit(1);
 547         }
 548 }
 549 //**********************************************************************************************************************
 550 int SharedCommand::createMisMatchFile() {
 551         try {
 552                 ofstream outMisMatch;
 553                 string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(listfile));
 554
 555                 //you have sequences in your list file that are not in your group file
 556                 if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
 557                         outputMisMatchName += "missing.group";
 558                         m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
 559
 560                         m->openOutputFile(outputMisMatchName, outMisMatch);
 561
 562                         map<string, string> listNames;
 563                         map<string, string>::iterator itList;
 564
 565                         //go through list and if group returns "not found" output it
 566                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 567                                 if (m->control_pressed) { outMisMatch.close(); m->mothurRemove(outputMisMatchName); return 0; }
 568
 569                                 string names = SharedList->get(i);
 570
 571                                 while (names.find_first_of(',') != -1) {
 572                                         string name = names.substr(0,names.find_first_of(','));
 573                                         names = names.substr(names.find_first_of(',')+1, names.length());
 574                                         string group = groupMap->getGroup(name);
 575
 576                                         if(group == "not found") {      outMisMatch << name << endl;  }
 577
 578                                         itList = listNames.find(name);
 579                                         if (itList != listNames.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 580                                         else { listNames[name] = name; }
 581                                 }
 582
 583                                 //get last name
 584                                 string group = groupMap->getGroup(names);
 585                                 if(group == "not found") {      outMisMatch << names << endl;  }
 586
 587                                 itList = listNames.find(names);
 588                                 if (itList != listNames.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 589                                 else { listNames[names] = names; }
 590
 591                         }
 592
 593                         outMisMatch.close();
 594
 595
 596                 }else {//you have sequences in your group file that are not in you list file
 597
 598                         outputMisMatchName += "missing.name";
 599                         m->mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
 600
 601                         map<string, string> namesInList;
 602                         map<string, string>::iterator itList;
 603
 604                         //go through listfile and get names
 605                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 606                                 if (m->control_pressed) {  return 0; }
 607
 608
 609                                 string names = SharedList->get(i);
 610
 611                                 while (names.find_first_of(',') != -1) {
 612                                         string name = names.substr(0,names.find_first_of(','));
 613                                         names = names.substr(names.find_first_of(',')+1, names.length());
 614
 615                                         itList = namesInList.find(name);
 616                                         if (itList != namesInList.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 617
 618                                         namesInList[name] = name;
 619
 620                                 }
 621
 622                                 itList = namesInList.find(names);
 623                                 if (itList != namesInList.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 624
 625                                 //get last name
 626                                 namesInList[names] = names;
 627                         }
 628
 629                         //get names of sequences in groupfile
 630                         vector<string> seqNames = groupMap->getNamesSeqs();
 631
 632                         map<string, string>::iterator itMatch;
 633
 634                         m->openOutputFile(outputMisMatchName, outMisMatch);
 635
 636                         //loop through names in seqNames and if they aren't in namesIn list output them
 637                         for (int i = 0; i < seqNames.size(); i++) {
 638                                 if (m->control_pressed) { outMisMatch.close(); m->mothurRemove(outputMisMatchName); return 0; }
 639
 640                                 itMatch = namesInList.find(seqNames[i]);
 641
 642                                 if (itMatch == namesInList.end()) {
 643
 644                                         outMisMatch << seqNames[i] << endl;
 645                                 }
 646                         }
 647                         outMisMatch.close();
 648                 }
 649
 650                 return 0;
 651         }
 652         catch(exception& e) {
 653                 m->errorOut(e, "SharedCommand", "createMisMatchFile");
 654                 exit(1);
 655         }
 656 }
 657
 658 //**********************************************************************************************************************
 659
 660 SharedCommand::~SharedCommand(){
 661         //delete list;
 662
 663
 664 }
 665 //**********************************************************************************************************************
 666 int SharedCommand::readOrderFile() {
 667         try {
 668                 //remove old names
 669                 order.clear();
 670
 671                 ifstream in;
 672                 m->openInputFile(ordergroupfile, in);
 673                 string thisGroup;
 674
 675                 while(!in.eof()){
 676                         in >> thisGroup; m->gobble(in);
 677
 678                         order.push_back(thisGroup);
 679
 680                         if (m->control_pressed) { order.clear(); break; }
 681                 }
 682                 in.close();
 683
 684                 return 0;
 685         }
 686         catch(exception& e) {
 687                 m->errorOut(e, "SharedCommand", "readOrderFile");
 688                 exit(1);
 689         }
 690 }
 691 //**********************************************************************************************************************
 692
 693 bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
 694         try {
 695                 for (int i = 0; i < groups.size(); i++) {
 696                         if (groupname == groups[i]) { return true; }
 697                 }
 698
 699                 return false;
 700         }
 701         catch(exception& e) {
 702                 m->errorOut(e, "SharedCommand", "isValidGroup");
 703                 exit(1);
 704         }
 705 }
 706 /************************************************************/
 707
 708