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         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "SharedCommand", "SharedCommand");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68 SharedCommand::SharedCommand(string option)  {
  69         try {
  70                 abort = false; calledHelp = false;
  71                 allLines = 1;
  72
  73                 //allow user to run help
  74                 if(option == "help") { help(); abort = true; calledHelp = true; }
  75
  76                 else {
  77
  78                          //valid paramters for this command
  79                          string Array[] =  {"list","label","group","groups","ordergroup","outputdir","inputdir"};
  80                          vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  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") { 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") { 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                         //getting output filename
 179                         filename = listfile;
 180                         if (outputDir == "") { outputDir += m->hasPath(filename); }
 181
 182                         filename = outputDir + m->getRootName(m->getSimpleName(filename));
 183                         filename = filename + "shared";
 184                         outputTypes["shared"].push_back(filename);
 185
 186                         m->openOutputFile(filename, out);
 187                         pickedGroups = false;
 188
 189                         //if hte user has not specified any groups then use them all
 190                         if (Groups.size() == 0) {
 191                                 Groups = groupMap->namesOfGroups; m->Groups = Groups;
 192                         }
 193
 194                         //fill filehandles with neccessary ofstreams
 195                         int i;
 196                         ofstream* temp;
 197                         for (i=0; i<Groups.size(); i++) {
 198                                 temp = new ofstream;
 199                                 filehandles[Groups[i]] = temp;
 200                         }
 201
 202                         //set fileroot
 203                         fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
 204
 205                         //clears file before we start to write to it below
 206                         for (int i=0; i<Groups.size(); i++) {
 207                                 remove((fileroot + Groups[i] + ".rabund").c_str());
 208                                 outputNames.push_back((fileroot + Groups[i] + ".rabund"));
 209                                 outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
 210                         }
 211
 212                 }
 213
 214         }
 215         catch(exception& e) {
 216                 m->errorOut(e, "SharedCommand", "SharedCommand");
 217                 exit(1);
 218         }
 219 }
 220 //**********************************************************************************************************************
 221
 222 int SharedCommand::execute(){
 223         try {
 224
 225                 //lookup.clear();
 226                 string errorOff = "no error";
 227                 //errorOff = "";
 228
 229                 //if user provided an order file containing the order the shared file should be in read it
 230                 if (ordergroupfile != "") { readOrderFile(); }
 231
 232                 input = new InputData(listfile, "shared");
 233                 SharedList = input->getSharedListVector();
 234                 string lastLabel = SharedList->getLabel();
 235                 vector<SharedRAbundVector*> lookup;
 236
 237                 if (m->control_pressed) {
 238                         delete input; delete SharedList; delete groupMap;
 239                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 240                         out.close(); remove(filename.c_str());
 241                         for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 242                         return 0;
 243                 }
 244
 245                 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
 246                         m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
 247
 248                         out.close();
 249                         remove(filename.c_str()); //remove blank shared file you made
 250
 251                         createMisMatchFile();
 252
 253                         //delete memory
 254                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 255                                 delete it3->second;
 256                         }
 257
 258                         delete input; delete SharedList; delete groupMap;
 259
 260                         return 0;
 261                 }
 262
 263                 //if user has specified groups make new groupfile for them
 264                 if (m->Groups.size() != 0) { //make new group file
 265                         string groups = "";
 266                         if (m->Groups.size() < 4) {
 267                                 for (int i = 0; i < m->Groups.size(); i++) {
 268                                         groups += m->Groups[i] + ".";
 269                                 }
 270                         }else { groups = "merge"; }
 271
 272                         string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + "groups";
 273                         ofstream outGroups;
 274                         m->openOutputFile(newGroupFile, outGroups);
 275
 276                         vector<string> names = groupMap->getNamesSeqs();
 277                         string groupName;
 278                         for (int i = 0; i < names.size(); i++) {
 279                                 groupName = groupMap->getGroup(names[i]);
 280                                 if (isValidGroup(groupName, m->Groups)) {
 281                                         outGroups << names[i] << '\t' << groupName << endl;
 282                                 }
 283                         }
 284                         outGroups.close();
 285                 }
 286
 287                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 288                 set<string> processedLabels;
 289                 set<string> userLabels = labels;
 290
 291                 while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 292                         if (m->control_pressed) {
 293                                 delete input; delete SharedList; delete groupMap;
 294                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 295                                 out.close(); remove(filename.c_str());
 296                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 297                                 return 0;
 298                         }
 299
 300                         if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
 301
 302                                         lookup = SharedList->getSharedRAbundVector();
 303
 304                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 305                                         if (pickedGroups) { //check for otus with no seqs in them
 306                                                 eliminateZeroOTUS(lookup);
 307                                         }
 308
 309                                         if (m->control_pressed) {
 310                                                 delete input; delete SharedList; delete groupMap;
 311                                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 312                                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 313                                                 out.close(); remove(filename.c_str());
 314                                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 315                                                 return 0;
 316                                         }
 317
 318                                         printSharedData(lookup); //prints info to the .shared file
 319                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 320
 321                                         processedLabels.insert(SharedList->getLabel());
 322                                         userLabels.erase(SharedList->getLabel());
 323                         }
 324
 325                         if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
 326                                         string saveLabel = SharedList->getLabel();
 327
 328                                         delete SharedList;
 329                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 330
 331                                         lookup = SharedList->getSharedRAbundVector();
 332                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 333                                         if (pickedGroups) { //check for otus with no seqs in them
 334                                                 eliminateZeroOTUS(lookup);
 335                                         }
 336
 337
 338                                         if (m->control_pressed) {
 339                                                 delete input; delete SharedList; delete groupMap;
 340                                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 341                                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 342                                                 out.close(); remove(filename.c_str());
 343                                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 344                                                 return 0;
 345                                         }
 346
 347                                         printSharedData(lookup); //prints info to the .shared file
 348                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 349
 350                                         processedLabels.insert(SharedList->getLabel());
 351                                         userLabels.erase(SharedList->getLabel());
 352
 353                                         //restore real lastlabel to save below
 354                                         SharedList->setLabel(saveLabel);
 355                         }
 356
 357
 358                         lastLabel = SharedList->getLabel();
 359
 360                         delete SharedList;
 361                         SharedList = input->getSharedListVector(); //get new list vector to process
 362                 }
 363
 364                 //output error messages about any remaining user labels
 365                 set<string>::iterator it;
 366                 bool needToRun = false;
 367                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 368                         if (processedLabels.count(lastLabel) != 1) {
 369                                 needToRun = true;
 370                         }
 371                 }
 372
 373                 //run last label if you need to
 374                 if (needToRun == true)  {
 375                         if (SharedList != NULL) {       delete SharedList;      }
 376                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 377
 378                         lookup = SharedList->getSharedRAbundVector();
 379                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 380                         if (pickedGroups) { //check for otus with no seqs in them
 381                                 eliminateZeroOTUS(lookup);
 382                         }
 383
 384                         if (m->control_pressed) {
 385                                 delete input;  delete groupMap;
 386                                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;   }
 387                                         out.close(); remove(filename.c_str());
 388                                         for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 389                                         return 0;
 390                         }
 391
 392                         printSharedData(lookup); //prints info to the .shared file
 393                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 394                         delete SharedList;
 395                 }
 396
 397                 out.close();
 398
 399                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 400                         delete it3->second;
 401                 }
 402
 403                 delete input; delete groupMap;
 404
 405                 if (m->control_pressed) {
 406                                 remove(filename.c_str());
 407                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 408                                 return 0;
 409                 }
 410
 411                 //set rabund file as new current rabundfile
 412                 string current = "";
 413                 itTypes = outputTypes.find("rabund");
 414                 if (itTypes != outputTypes.end()) {
 415                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 416                 }
 417
 418                 itTypes = outputTypes.find("shared");
 419                 if (itTypes != outputTypes.end()) {
 420                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 421                 }
 422
 423                 m->mothurOutEndLine();
 424                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 425                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 426                 m->mothurOut(filename); m->mothurOutEndLine();
 427                 m->mothurOutEndLine();
 428
 429                 return 0;
 430         }
 431         catch(exception& e) {
 432                 m->errorOut(e, "SharedCommand", "execute");
 433                 exit(1);
 434         }
 435 }
 436 //**********************************************************************************************************************
 437 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 438         try {
 439
 440                 if (order.size() == 0) { //user has not specified an order so do aplabetically
 441                         sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
 442
 443                         m->Groups.clear();
 444
 445                         //initialize bin values
 446                         for (int i = 0; i < thislookup.size(); i++) {
 447                                 out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 448                                 thislookup[i]->print(out);
 449
 450                                 m->Groups.push_back(thislookup[i]->getGroup());
 451
 452                                 RAbundVector rav = thislookup[i]->getRAbundVector();
 453                                 m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 454                                 rav.print(*(filehandles[thislookup[i]->getGroup()]));
 455                                 (*(filehandles[thislookup[i]->getGroup()])).close();
 456                         }
 457                 }else{
 458                         //create a map from groupName to each sharedrabund
 459                         map<string, SharedRAbundVector*> myMap;
 460                         map<string, SharedRAbundVector*>::iterator myIt;
 461
 462                         for (int i = 0; i < thislookup.size(); i++) {
 463                                 myMap[thislookup[i]->getGroup()] = thislookup[i];
 464                         }
 465
 466                         m->Groups.clear();
 467
 468                         //loop through ordered list and print the rabund
 469                         for (int i = 0; i < order.size(); i++) {
 470                                 myIt = myMap.find(order[i]);
 471
 472                                 if(myIt != myMap.end()) { //we found it
 473                                         out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
 474                                         (myIt->second)->print(out);
 475
 476                                         m->Groups.push_back((myIt->second)->getGroup());
 477
 478                                         RAbundVector rav = (myIt->second)->getRAbundVector();
 479                                         m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
 480                                         rav.print(*(filehandles[(myIt->second)->getGroup()]));
 481                                         (*(filehandles[(myIt->second)->getGroup()])).close();
 482                                 }else{
 483                                         m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
 484                                 }
 485                         }
 486
 487                 }
 488
 489         }
 490         catch(exception& e) {
 491                 m->errorOut(e, "SharedCommand", "printSharedData");
 492                 exit(1);
 493         }
 494 }
 495 //**********************************************************************************************************************
 496 int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 497         try {
 498
 499                 vector<SharedRAbundVector*> newLookup;
 500                 for (int i = 0; i < thislookup.size(); i++) {
 501                         SharedRAbundVector* temp = new SharedRAbundVector();
 502                         temp->setLabel(thislookup[i]->getLabel());
 503                         temp->setGroup(thislookup[i]->getGroup());
 504                         newLookup.push_back(temp);
 505                 }
 506
 507                 //for each bin
 508                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 509                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 510
 511                         //look at each sharedRabund and make sure they are not all zero
 512                         bool allZero = true;
 513                         for (int j = 0; j < thislookup.size(); j++) {
 514                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 515                         }
 516
 517                         //if they are not all zero add this bin
 518                         if (!allZero) {
 519                                 for (int j = 0; j < thislookup.size(); j++) {
 520                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 521                                 }
 522                         }
 523                         //else{  cout << "bin # " << i << " is all zeros" << endl;  }
 524                 }
 525
 526                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 527                 thislookup = newLookup;
 528
 529                 return 0;
 530
 531         }
 532         catch(exception& e) {
 533                 m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
 534                 exit(1);
 535         }
 536 }
 537 //**********************************************************************************************************************
 538 int SharedCommand::createMisMatchFile() {
 539         try {
 540                 ofstream outMisMatch;
 541                 string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(listfile));
 542
 543                 //you have sequences in your list file that are not in your group file
 544                 if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
 545                         outputMisMatchName += "missing.group";
 546                         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();
 547
 548                         m->openOutputFile(outputMisMatchName, outMisMatch);
 549
 550                         map<string, string> listNames;
 551                         map<string, string>::iterator itList;
 552
 553                         //go through list and if group returns "not found" output it
 554                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 555                                 if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
 556
 557                                 string names = SharedList->get(i);
 558
 559                                 while (names.find_first_of(',') != -1) {
 560                                         string name = names.substr(0,names.find_first_of(','));
 561                                         names = names.substr(names.find_first_of(',')+1, names.length());
 562                                         string group = groupMap->getGroup(name);
 563
 564                                         if(group == "not found") {      outMisMatch << name << endl;  }
 565
 566                                         itList = listNames.find(name);
 567                                         if (itList != listNames.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 568                                         else { listNames[name] = name; }
 569                                 }
 570
 571                                 //get last name
 572                                 string group = groupMap->getGroup(names);
 573                                 if(group == "not found") {      outMisMatch << names << endl;  }
 574
 575                                 itList = listNames.find(names);
 576                                 if (itList != listNames.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 577                                 else { listNames[names] = names; }
 578
 579                         }
 580
 581                         outMisMatch.close();
 582
 583
 584                 }else {//you have sequences in your group file that are not in you list file
 585
 586                         outputMisMatchName += "missing.name";
 587                         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();
 588
 589                         map<string, string> namesInList;
 590                         map<string, string>::iterator itList;
 591
 592                         //go through listfile and get names
 593                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 594                                 if (m->control_pressed) {  return 0; }
 595
 596
 597                                 string names = SharedList->get(i);
 598
 599                                 while (names.find_first_of(',') != -1) {
 600                                         string name = names.substr(0,names.find_first_of(','));
 601                                         names = names.substr(names.find_first_of(',')+1, names.length());
 602
 603                                         itList = namesInList.find(name);
 604                                         if (itList != namesInList.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 605
 606                                         namesInList[name] = name;
 607
 608                                 }
 609
 610                                 itList = namesInList.find(names);
 611                                 if (itList != namesInList.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 612
 613                                 //get last name
 614                                 namesInList[names] = names;
 615                         }
 616
 617                         //get names of sequences in groupfile
 618                         vector<string> seqNames = groupMap->getNamesSeqs();
 619
 620                         map<string, string>::iterator itMatch;
 621
 622                         m->openOutputFile(outputMisMatchName, outMisMatch);
 623
 624                         //loop through names in seqNames and if they aren't in namesIn list output them
 625                         for (int i = 0; i < seqNames.size(); i++) {
 626                                 if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
 627
 628                                 itMatch = namesInList.find(seqNames[i]);
 629
 630                                 if (itMatch == namesInList.end()) {
 631
 632                                         outMisMatch << seqNames[i] << endl;
 633                                 }
 634                         }
 635                         outMisMatch.close();
 636                 }
 637
 638                 return 0;
 639         }
 640         catch(exception& e) {
 641                 m->errorOut(e, "SharedCommand", "createMisMatchFile");
 642                 exit(1);
 643         }
 644 }
 645
 646 //**********************************************************************************************************************
 647
 648 SharedCommand::~SharedCommand(){
 649         //delete list;
 650
 651
 652 }
 653 //**********************************************************************************************************************
 654 int SharedCommand::readOrderFile() {
 655         try {
 656                 //remove old names
 657                 order.clear();
 658
 659                 ifstream in;
 660                 m->openInputFile(ordergroupfile, in);
 661                 string thisGroup;
 662
 663                 while(!in.eof()){
 664                         in >> thisGroup; m->gobble(in);
 665
 666                         order.push_back(thisGroup);
 667
 668                         if (m->control_pressed) { order.clear(); break; }
 669                 }
 670                 in.close();
 671
 672                 return 0;
 673         }
 674         catch(exception& e) {
 675                 m->errorOut(e, "SharedCommand", "readOrderFile");
 676                 exit(1);
 677         }
 678 }
 679 //**********************************************************************************************************************
 680
 681 bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
 682         try {
 683                 for (int i = 0; i < groups.size(); i++) {
 684                         if (groupname == groups[i]) { return true; }
 685                 }
 686
 687                 return false;
 688         }
 689         catch(exception& e) {
 690                 m->errorOut(e, "SharedCommand", "isValidGroup");
 691                 exit(1);
 692         }
 693 }
 694 /************************************************************/
 695
 696