bayesian.cpp

   1 /*
   2  *  bayesian.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/3/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "bayesian.h"
  11 #include "kmer.hpp"
  12 #include "phylosummary.h"
  13
  14 /**************************************************************************************************/
  15 Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i) :
  16 Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
  17         try {
  18
  19                 /************calculate the probablity that each word will be in a specific taxonomy*************/
  20                 string tfileroot = tfile.substr(0,tfile.find_last_of(".")+1);
  21                 string tempfileroot = m->getRootName(m->getSimpleName(tempFile));
  22                 string phyloTreeName = tfileroot + "tree.train";
  23                 string phyloTreeSumName = tfileroot + "tree.sum";
  24                 string probFileName = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.prob";
  25                 string probFileName2 = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.numNonZero";
  26
  27                 ofstream out;
  28                 ofstream out2;
  29
  30                 ifstream phyloTreeTest(phyloTreeName.c_str());
  31                 ifstream probFileTest2(probFileName2.c_str());
  32                 ifstream probFileTest(probFileName.c_str());
  33                 ifstream probFileTest3(phyloTreeSumName.c_str());
  34
  35                 int start = time(NULL);
  36
  37                 //if they are there make sure they were created after this release date
  38                 bool FilesGood = false;
  39                 if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3){
  40                         FilesGood = checkReleaseDate(probFileTest, probFileTest2, phyloTreeTest, probFileTest3);
  41                 }
  42
  43                 if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood){
  44                         m->mothurOut("Reading template taxonomy...     "); cout.flush();
  45
  46                         phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
  47
  48                         m->mothurOut("DONE."); m->mothurOutEndLine();
  49
  50                         genusNodes = phyloTree->getGenusNodes();
  51                         genusTotals = phyloTree->getGenusTotals();
  52
  53                         m->mothurOut("Reading template probabilities...     "); cout.flush();
  54                         readProbFile(probFileTest, probFileTest2, probFileName, probFileName2);
  55
  56                 }else{
  57
  58                         //create search database and names vector
  59                         generateDatabaseAndNames(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0);
  60
  61                         //prevents errors caused by creating shortcut files if you had an error in the sanity check.
  62                         if (m->control_pressed) {  remove(phyloTreeName.c_str());  remove(probFileName.c_str()); remove(probFileName2.c_str()); }
  63                         else{
  64                                 genusNodes = phyloTree->getGenusNodes();
  65                                 genusTotals = phyloTree->getGenusTotals();
  66
  67                                 m->mothurOut("Calculating template taxonomy tree...     "); cout.flush();
  68
  69                                 phyloTree->printTreeNodes(phyloTreeName);
  70
  71                                 m->mothurOut("DONE."); m->mothurOutEndLine();
  72
  73                                 m->mothurOut("Calculating template probabilities...     "); cout.flush();
  74
  75                                 numKmers = database->getMaxKmer() + 1;
  76
  77                                 //initialze probabilities
  78                                 wordGenusProb.resize(numKmers);
  79                         //cout << numKmers << '\t' << genusNodes.size() << endl;
  80                                 for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
  81                         //cout << numKmers << '\t' << genusNodes.size() << endl;
  82                                 ofstream out;
  83                                 ofstream out2;
  84
  85                                 #ifdef USE_MPI
  86                                         int pid;
  87                                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  88
  89                                         if (pid == 0) {
  90                                 #endif
  91
  92
  93                                 m->openOutputFile(probFileName, out);
  94
  95                                 //output mothur version
  96                                 out << "#" << m->getVersion() << endl;
  97
  98                                 out << numKmers << endl;
  99
 100                                 m->openOutputFile(probFileName2, out2);
 101
 102                                 //output mothur version
 103                                 out2 << "#" << m->getVersion() << endl;
 104
 105                                 #ifdef USE_MPI
 106                                         }
 107                                 #endif
 108
 109
 110                                 //for each word
 111                                 for (int i = 0; i < numKmers; i++) {
 112                                         if (m->control_pressed) {  break; }
 113
 114                                         #ifdef USE_MPI
 115                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 116
 117                                                 if (pid == 0) {
 118                                         #endif
 119
 120                                         out << i << '\t';
 121
 122                                         #ifdef USE_MPI
 123                                                 }
 124                                         #endif
 125
 126                                         vector<int> seqsWithWordi = database->getSequencesWithKmer(i);
 127
 128                                         map<int, int> count;
 129                                         for (int k = 0; k < genusNodes.size(); k++) {  count[genusNodes[k]] = 0;  }
 130
 131                                         //for each sequence with that word
 132                                         for (int j = 0; j < seqsWithWordi.size(); j++) {
 133                                                 int temp = phyloTree->getIndex(names[seqsWithWordi[j]]);
 134                                                 count[temp]++;  //increment count of seq in this genus who have this word
 135                                         }
 136
 137                                         //probabilityInTemplate = (# of seqs with that word in template + 0.50) / (total number of seqs in template + 1);
 138                                         float probabilityInTemplate = (seqsWithWordi.size() + 0.50) / (float) (names.size() + 1);
 139
 140                                         int numNotZero = 0;
 141                                         for (int k = 0; k < genusNodes.size(); k++) {
 142                                                 //probabilityInThisTaxonomy = (# of seqs with that word in this taxonomy + probabilityInTemplate) / (total number of seqs in this taxonomy + 1);
 143
 144
 145                                                 wordGenusProb[i][k] = log((count[genusNodes[k]] + probabilityInTemplate) / (float) (genusTotals[k] + 1));
 146
 147                                                 if (count[genusNodes[k]] != 0) {
 148                                                         #ifdef USE_MPI
 149                                                                 int pid;
 150                                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 151
 152                                                                 if (pid == 0) {
 153                                                         #endif
 154
 155                                                         out << k << '\t' << wordGenusProb[i][k] << '\t';
 156
 157                                                         #ifdef USE_MPI
 158                                                                 }
 159                                                         #endif
 160
 161                                                         numNotZero++;
 162                                                 }
 163                                         }
 164
 165                                         #ifdef USE_MPI
 166                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 167
 168                                                 if (pid == 0) {
 169                                         #endif
 170
 171                                         out << endl;
 172                                         out2 << probabilityInTemplate << '\t' << numNotZero << endl;
 173
 174                                         #ifdef USE_MPI
 175                                                 }
 176                                         #endif
 177                                 }
 178
 179                                 #ifdef USE_MPI
 180                                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 181
 182                                         if (pid == 0) {
 183                                 #endif
 184
 185                                 out.close();
 186                                 out2.close();
 187
 188                                 #ifdef USE_MPI
 189                                         }
 190                                 #endif
 191
 192                                 //read in new phylotree with less info. - its faster
 193                                 ifstream phyloTreeTest(phyloTreeName.c_str());
 194                                 delete phyloTree;
 195
 196                                 phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
 197                         }
 198                 }
 199
 200                 m->mothurOut("DONE."); m->mothurOutEndLine();
 201                 m->mothurOut("It took " + toString(time(NULL) - start) + " seconds get probabilities. "); m->mothurOutEndLine();
 202         }
 203         catch(exception& e) {
 204                 m->errorOut(e, "Bayesian", "Bayesian");
 205                 exit(1);
 206         }
 207 }
 208 /**************************************************************************************************/
 209 Bayesian::~Bayesian() {
 210         try {
 211
 212                  delete phyloTree;
 213                  if (database != NULL) {  delete database; }
 214         }
 215         catch(exception& e) {
 216                 m->errorOut(e, "Bayesian", "~Bayesian");
 217                 exit(1);
 218         }
 219 }
 220
 221 /**************************************************************************************************/
 222 string Bayesian::getTaxonomy(Sequence* seq) {
 223         try {
 224                 string tax = "";
 225                 Kmer kmer(kmerSize);
 226
 227                 //get words contained in query
 228                 //getKmerString returns a string where the index in the string is hte kmer number
 229                 //and the character at that index can be converted to be the number of times that kmer was seen
 230
 231                 string queryKmerString = kmer.getKmerString(seq->getUnaligned());
 232
 233                 vector<int> queryKmers;
 234                 for (int i = 0; i < queryKmerString.length()-1; i++) {  // the -1 is to ignore any kmer with an N in it
 235                         if (queryKmerString[i] != '!') { //this kmer is in the query
 236                                 queryKmers.push_back(i);
 237                         }
 238                 }
 239
 240                 if (queryKmers.size() == 0) {  m->mothurOut(seq->getName() + "is bad."); m->mothurOutEndLine(); return "bad seq"; }
 241
 242
 243                 int index = getMostProbableTaxonomy(queryKmers);
 244
 245                 if (m->control_pressed) { return tax; }
 246
 247                 //bootstrap - to set confidenceScore
 248                 int numToSelect = queryKmers.size() / 8;
 249
 250                 tax = bootstrapResults(queryKmers, index, numToSelect);
 251
 252                 return tax;
 253         }
 254         catch(exception& e) {
 255                 m->errorOut(e, "Bayesian", "getTaxonomy");
 256                 exit(1);
 257         }
 258 }
 259 /**************************************************************************************************/
 260 string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
 261         try {
 262
 263                 map<int, int> confidenceScores;
 264
 265                 //initialize confidences to 0
 266                 int seqIndex = tax;
 267                 TaxNode seq = phyloTree->get(tax);
 268                 confidenceScores[tax] = 0;
 269
 270                 while (seq.level != 0) { //while you are not at the root
 271                         seqIndex = seq.parent;
 272                         confidenceScores[seqIndex] = 0;
 273                         seq = phyloTree->get(seq.parent);
 274                 }
 275
 276                 map<int, int>::iterator itBoot;
 277                 map<int, int>::iterator itBoot2;
 278                 map<int, int>::iterator itConvert;
 279
 280                 for (int i = 0; i < iters; i++) {
 281                         if (m->control_pressed) { return "control"; }
 282
 283                         vector<int> temp;
 284                         for (int j = 0; j < numToSelect; j++) {
 285                                 int index = int(rand() % kmers.size());
 286
 287                                 //add word to temp
 288                                 temp.push_back(kmers[index]);
 289                         }
 290
 291                         //get taxonomy
 292                         int newTax = getMostProbableTaxonomy(temp);
 293                         //int newTax = 1;
 294                         TaxNode taxonomyTemp = phyloTree->get(newTax);
 295
 296                         //add to confidence results
 297                         while (taxonomyTemp.level != 0) { //while you are not at the root
 298                                 itBoot2 = confidenceScores.find(newTax); //is this a classification we already have a count on
 299
 300                                 if (itBoot2 != confidenceScores.end()) { //this is a classification we need a confidence for
 301                                         (itBoot2->second)++;
 302                                 }
 303
 304                                 newTax = taxonomyTemp.parent;
 305                                 taxonomyTemp = phyloTree->get(newTax);
 306                         }
 307
 308                 }
 309
 310                 string confidenceTax = "";
 311                 simpleTax = "";
 312
 313                 int seqTaxIndex = tax;
 314                 TaxNode seqTax = phyloTree->get(tax);
 315
 316                 while (seqTax.level != 0) { //while you are not at the root
 317
 318                                 itBoot2 = confidenceScores.find(seqTaxIndex); //is this a classification we already have a count on
 319
 320                                 int confidence = 0;
 321                                 if (itBoot2 != confidenceScores.end()) { //already in confidence scores
 322                                         confidence = itBoot2->second;
 323                                 }
 324
 325                                 if (((confidence/(float)iters) * 100) >= confidenceThreshold) {
 326                                         confidenceTax = seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");" + confidenceTax;
 327                                         simpleTax = seqTax.name + ";" + simpleTax;
 328                                 }
 329
 330                                 seqTaxIndex = seqTax.parent;
 331                                 seqTax = phyloTree->get(seqTax.parent);
 332                 }
 333
 334                 if (confidenceTax == "") { confidenceTax = "unclassified;"; simpleTax = "unclassified;"; }
 335                 return confidenceTax;
 336
 337         }
 338         catch(exception& e) {
 339                 m->errorOut(e, "Bayesian", "bootstrapResults");
 340                 exit(1);
 341         }
 342 }
 343 /**************************************************************************************************/
 344 int Bayesian::getMostProbableTaxonomy(vector<int> queryKmer) {
 345         try {
 346                 int indexofGenus = 0;
 347
 348                 double maxProbability = -1000000.0;
 349                 //find taxonomy with highest probability that this sequence is from it
 350
 351
 352 //              cout << genusNodes.size() << endl;
 353
 354
 355                 for (int k = 0; k < genusNodes.size(); k++) {
 356                         //for each taxonomy calc its probability
 357
 358                         double prob = 0.0000;
 359                         for (int i = 0; i < queryKmer.size(); i++) {
 360                                 prob += wordGenusProb[queryKmer[i]][k];
 361                         }
 362
 363 //                      cout << phyloTree->get(genusNodes[k]).name << '\t' << prob << endl;
 364
 365                         //is this the taxonomy with the greatest probability?
 366                         if (prob > maxProbability) {
 367                                 indexofGenus = genusNodes[k];
 368                                 maxProbability = prob;
 369                         }
 370                 }
 371
 372
 373                 return indexofGenus;
 374         }
 375         catch(exception& e) {
 376                 m->errorOut(e, "Bayesian", "getMostProbableTaxonomy");
 377                 exit(1);
 378         }
 379 }
 380 /*************************************************************************************************
 381 map<string, int> Bayesian::parseTaxMap(string newTax) {
 382         try{
 383
 384                 map<string, int> parsed;
 385
 386                 newTax = newTax.substr(0, newTax.length()-1);  //get rid of last ';'
 387
 388                 //parse taxonomy
 389                 string individual;
 390                 while (newTax.find_first_of(';') != -1) {
 391                         individual = newTax.substr(0,newTax.find_first_of(';'));
 392                         newTax = newTax.substr(newTax.find_first_of(';')+1, newTax.length());
 393                         parsed[individual] = 1;
 394                 }
 395
 396                 //get last one
 397                 parsed[newTax] = 1;
 398
 399                 return parsed;
 400
 401         }
 402         catch(exception& e) {
 403                 m->errorOut(e, "Bayesian", "parseTax");
 404                 exit(1);
 405         }
 406 }
 407 /**************************************************************************************************/
 408 void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string inNumName) {
 409         try{
 410
 411                 #ifdef USE_MPI
 412
 413                         int pid, num, num2, processors;
 414                         vector<unsigned long int> positions;
 415                         vector<unsigned long int> positions2;
 416
 417                         MPI_Status status;
 418                         MPI_File inMPI;
 419                         MPI_File inMPI2;
 420                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 421                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 422                         int tag = 2001;
 423
 424                         char inFileName[1024];
 425                         strcpy(inFileName, inNumName.c_str());
 426
 427                         char inFileName2[1024];
 428                         strcpy(inFileName2, inName.c_str());
 429
 430                         MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 431                         MPI_File_open(MPI_COMM_WORLD, inFileName2, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI2);  //comm, filename, mode, info, filepointer
 432
 433                         if (pid == 0) {
 434                                 positions = m->setFilePosEachLine(inNumName, num);
 435                                 positions2 = m->setFilePosEachLine(inName, num2);
 436
 437                                 for(int i = 1; i < processors; i++) {
 438                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 439                                         MPI_Send(&positions[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 440
 441                                         MPI_Send(&num2, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 442                                         MPI_Send(&positions2[0], (num2+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 443                                 }
 444
 445                         }else{
 446                                 MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 447                                 positions.resize(num+1);
 448                                 MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 449
 450                                 MPI_Recv(&num2, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 451                                 positions2.resize(num2+1);
 452                                 MPI_Recv(&positions2[0], (num2+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 453                         }
 454
 455                         //read version
 456                         int length = positions2[1] - positions2[0];
 457                         char* buf5 = new char[length];
 458
 459                         MPI_File_read_at(inMPI2, positions2[0], buf5, length, MPI_CHAR, &status);
 460                         delete buf5;
 461
 462                         //read numKmers
 463                         length = positions2[2] - positions2[1];
 464                         char* buf = new char[length];
 465
 466                         MPI_File_read_at(inMPI2, positions2[1], buf, length, MPI_CHAR, &status);
 467
 468                         string tempBuf = buf;
 469                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 470                         delete buf;
 471
 472                         istringstream iss (tempBuf,istringstream::in);
 473                         iss >> numKmers;
 474
 475                         //initialze probabilities
 476                         wordGenusProb.resize(numKmers);
 477
 478                         for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
 479
 480                         int kmer, name;
 481                         vector<int> numbers; numbers.resize(numKmers);
 482                         float prob;
 483                         vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
 484
 485                         //read version
 486                         length = positions[1] - positions[0];
 487                         char* buf6 = new char[length];
 488
 489                         MPI_File_read_at(inMPI2, positions[0], buf6, length, MPI_CHAR, &status);
 490                         delete buf6;
 491
 492                         //read file
 493                         for(int i=1;i<num;i++){
 494                                 //read next sequence
 495                                 length = positions[i+1] - positions[i];
 496                                 char* buf4 = new char[length];
 497
 498                                 MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
 499
 500                                 tempBuf = buf4;
 501                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 502                                 delete buf4;
 503
 504                                 istringstream iss (tempBuf,istringstream::in);
 505                                 iss >> zeroCountProb[i] >> numbers[i];
 506                         }
 507
 508                         MPI_File_close(&inMPI);
 509
 510                         for(int i=2;i<num2;i++){
 511                                 //read next sequence
 512                                 length = positions2[i+1] - positions2[i];
 513                                 char* buf4 = new char[length];
 514
 515                                 MPI_File_read_at(inMPI2, positions2[i], buf4, length, MPI_CHAR, &status);
 516
 517                                 tempBuf = buf4;
 518                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 519                                 delete buf4;
 520
 521                                 istringstream iss (tempBuf,istringstream::in);
 522
 523                                 iss >> kmer;
 524
 525                                 //set them all to zero value
 526                                 for (int i = 0; i < genusNodes.size(); i++) {
 527                                         wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
 528                                 }
 529
 530                                 //get probs for nonzero values
 531                                 for (int i = 0; i < numbers[kmer]; i++) {
 532                                         iss >> name >> prob;
 533                                         wordGenusProb[kmer][name] = prob;
 534                                 }
 535
 536                         }
 537                         MPI_File_close(&inMPI2);
 538                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 539                 #else
 540                         //read version
 541                         string line = m->getline(in); m->gobble(in);
 542
 543                         in >> numKmers; m->gobble(in);
 544
 545                         //initialze probabilities
 546                         wordGenusProb.resize(numKmers);
 547
 548                         for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
 549
 550                         int kmer, name, count;  count = 0;
 551                         vector<int> num; num.resize(numKmers);
 552                         float prob;
 553                         vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
 554
 555                         //read version
 556                         string line2 = m->getline(inNum); m->gobble(inNum);
 557
 558                         while (inNum) {
 559                                 inNum >> zeroCountProb[count] >> num[count];
 560                                 count++;
 561                                 m->gobble(inNum);
 562                         }
 563                         inNum.close();
 564
 565                         while(in) {
 566                                 in >> kmer;
 567
 568                                 //set them all to zero value
 569                                 for (int i = 0; i < genusNodes.size(); i++) {
 570                                         wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
 571                                 }
 572
 573                                 //get probs for nonzero values
 574                                 for (int i = 0; i < num[kmer]; i++) {
 575                                         in >> name >> prob;
 576                                         wordGenusProb[kmer][name] = prob;
 577                                 }
 578
 579                                 m->gobble(in);
 580                         }
 581                         in.close();
 582
 583                 #endif
 584         }
 585         catch(exception& e) {
 586                 m->errorOut(e, "Bayesian", "readProbFile");
 587                 exit(1);
 588         }
 589 }
 590 /**************************************************************************************************/
 591 bool Bayesian::checkReleaseDate(ifstream& file1, ifstream& file2, ifstream& file3, ifstream& file4) {
 592         try {
 593
 594                 bool good = true;
 595
 596                 vector<string> lines;
 597                 lines.push_back(m->getline(file1));
 598                 lines.push_back(m->getline(file2));
 599                 lines.push_back(m->getline(file3));
 600                 lines.push_back(m->getline(file4));
 601
 602                 //before we added this check
 603                 if ((lines[0][0] != '#') || (lines[1][0] != '#') || (lines[2][0] != '#') || (lines[3][0] != '#')) {  good = false;  }
 604                 else {
 605                         //rip off #
 606                         for (int i = 0; i < lines.size(); i++) { lines[i] = lines[i].substr(1);  }
 607
 608                         //get mothurs current version
 609                         string version = m->getVersion();
 610
 611                         vector<string> versionVector;
 612                         m->splitAtChar(version, versionVector, '.');
 613
 614                         //check each files version
 615                         for (int i = 0; i < lines.size(); i++) {
 616                                 vector<string> linesVector;
 617                                 m->splitAtChar(lines[i], linesVector, '.');
 618
 619                                 if (versionVector.size() != linesVector.size()) { good = false; break; }
 620                                 else {
 621                                         for (int j = 0; j < versionVector.size(); j++) {
 622                                                 int num1, num2;
 623                                                 convert(versionVector[j], num1);
 624                                                 convert(linesVector[j], num2);
 625
 626                                                 //if mothurs version is newer than this files version, then we want to remake it
 627                                                 if (num1 > num2) {  good = false; break;  }
 628                                         }
 629                                 }
 630
 631                                 if (!good) { break; }
 632                         }
 633                 }
 634
 635                 if (!good) {  file1.close(); file2.close(); file3.close(); file4.close();  }
 636                 else { file1.seekg(0);  file2.seekg(0);  file3.seekg(0);  file4.seekg(0);  }
 637
 638                 return good;
 639         }
 640         catch(exception& e) {
 641                 m->errorOut(e, "Bayesian", "checkReleaseDate");
 642                 exit(1);
 643         }
 644 }
 645 /**************************************************************************************************/
 646
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