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                          }
 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                         remove((fileroot + Groups[i] + ".rabund").c_str());
 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(); remove(filename.c_str());
 243                         for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 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                         remove(filename.c_str()); //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(); remove(filename.c_str());
 300                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 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(); remove(filename.c_str());
 318                                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 319                                                 return 0;
 320                                         }
 321
 322                                         printSharedData(lookup); //prints info to the .shared file
 323                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 324
 325                                         processedLabels.insert(SharedList->getLabel());
 326                                         userLabels.erase(SharedList->getLabel());
 327                         }
 328
 329                         if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
 330                                         string saveLabel = SharedList->getLabel();
 331
 332                                         delete SharedList;
 333                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 334
 335                                         lookup = SharedList->getSharedRAbundVector();
 336                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 337                                         if (pickedGroups) { //check for otus with no seqs in them
 338                                                 eliminateZeroOTUS(lookup);
 339                                         }
 340
 341
 342                                         if (m->control_pressed) {
 343                                                 delete input; delete SharedList; delete groupMap;
 344                                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 345                                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 346                                                 out.close(); remove(filename.c_str());
 347                                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 348                                                 return 0;
 349                                         }
 350
 351                                         printSharedData(lookup); //prints info to the .shared file
 352                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 353
 354                                         processedLabels.insert(SharedList->getLabel());
 355                                         userLabels.erase(SharedList->getLabel());
 356
 357                                         //restore real lastlabel to save below
 358                                         SharedList->setLabel(saveLabel);
 359                         }
 360
 361
 362                         lastLabel = SharedList->getLabel();
 363
 364                         delete SharedList;
 365                         SharedList = input->getSharedListVector(); //get new list vector to process
 366                 }
 367
 368                 //output error messages about any remaining user labels
 369                 set<string>::iterator it;
 370                 bool needToRun = false;
 371                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 372                         if (processedLabels.count(lastLabel) != 1) {
 373                                 needToRun = true;
 374                         }
 375                 }
 376
 377                 //run last label if you need to
 378                 if (needToRun == true)  {
 379                         if (SharedList != NULL) {       delete SharedList;      }
 380                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 381
 382                         lookup = SharedList->getSharedRAbundVector();
 383                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 384                         if (pickedGroups) { //check for otus with no seqs in them
 385                                 eliminateZeroOTUS(lookup);
 386                         }
 387
 388                         if (m->control_pressed) {
 389                                 delete input;  delete groupMap;
 390                                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;   }
 391                                         out.close(); remove(filename.c_str());
 392                                         for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 393                                         return 0;
 394                         }
 395
 396                         printSharedData(lookup); //prints info to the .shared file
 397                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 398                         delete SharedList;
 399                 }
 400
 401                 out.close();
 402
 403                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 404                         delete it3->second;
 405                 }
 406
 407                 delete input; delete groupMap;
 408
 409                 if (m->control_pressed) {
 410                                 remove(filename.c_str());
 411                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 412                                 return 0;
 413                 }
 414
 415                 //set rabund file as new current rabundfile
 416                 string current = "";
 417                 itTypes = outputTypes.find("rabund");
 418                 if (itTypes != outputTypes.end()) {
 419                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 420                 }
 421
 422                 itTypes = outputTypes.find("shared");
 423                 if (itTypes != outputTypes.end()) {
 424                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 425                 }
 426
 427                 itTypes = outputTypes.find("group");
 428                 if (itTypes != outputTypes.end()) {
 429                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 430                 }
 431
 432                 m->mothurOutEndLine();
 433                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 434                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 435                 m->mothurOut(filename); m->mothurOutEndLine();
 436                 m->mothurOutEndLine();
 437
 438                 return 0;
 439         }
 440         catch(exception& e) {
 441                 m->errorOut(e, "SharedCommand", "execute");
 442                 exit(1);
 443         }
 444 }
 445 //**********************************************************************************************************************
 446 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 447         try {
 448
 449                 if (order.size() == 0) { //user has not specified an order so do aplabetically
 450                         sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
 451
 452                         m->Groups.clear();
 453
 454                         //initialize bin values
 455                         for (int i = 0; i < thislookup.size(); i++) {
 456                                 out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 457                                 thislookup[i]->print(out);
 458
 459                                 m->Groups.push_back(thislookup[i]->getGroup());
 460
 461                                 RAbundVector rav = thislookup[i]->getRAbundVector();
 462                                 m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 463                                 rav.print(*(filehandles[thislookup[i]->getGroup()]));
 464                                 (*(filehandles[thislookup[i]->getGroup()])).close();
 465                         }
 466                 }else{
 467                         //create a map from groupName to each sharedrabund
 468                         map<string, SharedRAbundVector*> myMap;
 469                         map<string, SharedRAbundVector*>::iterator myIt;
 470
 471                         for (int i = 0; i < thislookup.size(); i++) {
 472                                 myMap[thislookup[i]->getGroup()] = thislookup[i];
 473                         }
 474
 475                         m->Groups.clear();
 476
 477                         //loop through ordered list and print the rabund
 478                         for (int i = 0; i < order.size(); i++) {
 479                                 myIt = myMap.find(order[i]);
 480
 481                                 if(myIt != myMap.end()) { //we found it
 482                                         out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
 483                                         (myIt->second)->print(out);
 484
 485                                         m->Groups.push_back((myIt->second)->getGroup());
 486
 487                                         RAbundVector rav = (myIt->second)->getRAbundVector();
 488                                         m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
 489                                         rav.print(*(filehandles[(myIt->second)->getGroup()]));
 490                                         (*(filehandles[(myIt->second)->getGroup()])).close();
 491                                 }else{
 492                                         m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
 493                                 }
 494                         }
 495
 496                 }
 497
 498         }
 499         catch(exception& e) {
 500                 m->errorOut(e, "SharedCommand", "printSharedData");
 501                 exit(1);
 502         }
 503 }
 504 //**********************************************************************************************************************
 505 int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 506         try {
 507
 508                 vector<SharedRAbundVector*> newLookup;
 509                 for (int i = 0; i < thislookup.size(); i++) {
 510                         SharedRAbundVector* temp = new SharedRAbundVector();
 511                         temp->setLabel(thislookup[i]->getLabel());
 512                         temp->setGroup(thislookup[i]->getGroup());
 513                         newLookup.push_back(temp);
 514                 }
 515
 516                 //for each bin
 517                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 518                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 519
 520                         //look at each sharedRabund and make sure they are not all zero
 521                         bool allZero = true;
 522                         for (int j = 0; j < thislookup.size(); j++) {
 523                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 524                         }
 525
 526                         //if they are not all zero add this bin
 527                         if (!allZero) {
 528                                 for (int j = 0; j < thislookup.size(); j++) {
 529                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 530                                 }
 531                         }
 532                         //else{  cout << "bin # " << i << " is all zeros" << endl;  }
 533                 }
 534
 535                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 536                 thislookup = newLookup;
 537
 538                 return 0;
 539
 540         }
 541         catch(exception& e) {
 542                 m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
 543                 exit(1);
 544         }
 545 }
 546 //**********************************************************************************************************************
 547 int SharedCommand::createMisMatchFile() {
 548         try {
 549                 ofstream outMisMatch;
 550                 string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(listfile));
 551
 552                 //you have sequences in your list file that are not in your group file
 553                 if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
 554                         outputMisMatchName += "missing.group";
 555                         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();
 556
 557                         m->openOutputFile(outputMisMatchName, outMisMatch);
 558
 559                         map<string, string> listNames;
 560                         map<string, string>::iterator itList;
 561
 562                         //go through list and if group returns "not found" output it
 563                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 564                                 if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
 565
 566                                 string names = SharedList->get(i);
 567
 568                                 while (names.find_first_of(',') != -1) {
 569                                         string name = names.substr(0,names.find_first_of(','));
 570                                         names = names.substr(names.find_first_of(',')+1, names.length());
 571                                         string group = groupMap->getGroup(name);
 572
 573                                         if(group == "not found") {      outMisMatch << name << endl;  }
 574
 575                                         itList = listNames.find(name);
 576                                         if (itList != listNames.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 577                                         else { listNames[name] = name; }
 578                                 }
 579
 580                                 //get last name
 581                                 string group = groupMap->getGroup(names);
 582                                 if(group == "not found") {      outMisMatch << names << endl;  }
 583
 584                                 itList = listNames.find(names);
 585                                 if (itList != listNames.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 586                                 else { listNames[names] = names; }
 587
 588                         }
 589
 590                         outMisMatch.close();
 591
 592
 593                 }else {//you have sequences in your group file that are not in you list file
 594
 595                         outputMisMatchName += "missing.name";
 596                         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();
 597
 598                         map<string, string> namesInList;
 599                         map<string, string>::iterator itList;
 600
 601                         //go through listfile and get names
 602                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 603                                 if (m->control_pressed) {  return 0; }
 604
 605
 606                                 string names = SharedList->get(i);
 607
 608                                 while (names.find_first_of(',') != -1) {
 609                                         string name = names.substr(0,names.find_first_of(','));
 610                                         names = names.substr(names.find_first_of(',')+1, names.length());
 611
 612                                         itList = namesInList.find(name);
 613                                         if (itList != namesInList.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 614
 615                                         namesInList[name] = name;
 616
 617                                 }
 618
 619                                 itList = namesInList.find(names);
 620                                 if (itList != namesInList.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 621
 622                                 //get last name
 623                                 namesInList[names] = names;
 624                         }
 625
 626                         //get names of sequences in groupfile
 627                         vector<string> seqNames = groupMap->getNamesSeqs();
 628
 629                         map<string, string>::iterator itMatch;
 630
 631                         m->openOutputFile(outputMisMatchName, outMisMatch);
 632
 633                         //loop through names in seqNames and if they aren't in namesIn list output them
 634                         for (int i = 0; i < seqNames.size(); i++) {
 635                                 if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
 636
 637                                 itMatch = namesInList.find(seqNames[i]);
 638
 639                                 if (itMatch == namesInList.end()) {
 640
 641                                         outMisMatch << seqNames[i] << endl;
 642                                 }
 643                         }
 644                         outMisMatch.close();
 645                 }
 646
 647                 return 0;
 648         }
 649         catch(exception& e) {
 650                 m->errorOut(e, "SharedCommand", "createMisMatchFile");
 651                 exit(1);
 652         }
 653 }
 654
 655 //**********************************************************************************************************************
 656
 657 SharedCommand::~SharedCommand(){
 658         //delete list;
 659
 660
 661 }
 662 //**********************************************************************************************************************
 663 int SharedCommand::readOrderFile() {
 664         try {
 665                 //remove old names
 666                 order.clear();
 667
 668                 ifstream in;
 669                 m->openInputFile(ordergroupfile, in);
 670                 string thisGroup;
 671
 672                 while(!in.eof()){
 673                         in >> thisGroup; m->gobble(in);
 674
 675                         order.push_back(thisGroup);
 676
 677                         if (m->control_pressed) { order.clear(); break; }
 678                 }
 679                 in.close();
 680
 681                 return 0;
 682         }
 683         catch(exception& e) {
 684                 m->errorOut(e, "SharedCommand", "readOrderFile");
 685                 exit(1);
 686         }
 687 }
 688 //**********************************************************************************************************************
 689
 690 bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
 691         try {
 692                 for (int i = 0; i < groups.size(); i++) {
 693                         if (groupname == groups[i]) { return true; }
 694                 }
 695
 696                 return false;
 697         }
 698         catch(exception& e) {
 699                 m->errorOut(e, "SharedCommand", "isValidGroup");
 700                 exit(1);
 701         }
 702 }
 703 /************************************************************/
 704
 705