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 + 0.05) / (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                                                 wordGenusProb[i][k] = log((count[genusNodes[k]] + probabilityInTemplate) / (float) (genusTotals[k] + 1));
 144                                                 if (count[genusNodes[k]] != 0) {
 145                                                         #ifdef USE_MPI
 146                                                                 int pid;
 147                                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 148
 149                                                                 if (pid == 0) {
 150                                                         #endif
 151
 152                                                         out << k << '\t' << wordGenusProb[i][k] << '\t';
 153
 154                                                         #ifdef USE_MPI
 155                                                                 }
 156                                                         #endif
 157
 158                                                         numNotZero++;
 159                                                 }
 160                                         }
 161
 162                                         #ifdef USE_MPI
 163                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 164
 165                                                 if (pid == 0) {
 166                                         #endif
 167
 168                                         out << endl;
 169                                         out2 << probabilityInTemplate << '\t' << numNotZero << endl;
 170
 171                                         #ifdef USE_MPI
 172                                                 }
 173                                         #endif
 174                                 }
 175
 176                                 #ifdef USE_MPI
 177                                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 178
 179                                         if (pid == 0) {
 180                                 #endif
 181
 182                                 out.close();
 183                                 out2.close();
 184
 185                                 #ifdef USE_MPI
 186                                         }
 187                                 #endif
 188
 189                                 //read in new phylotree with less info. - its faster
 190                                 ifstream phyloTreeTest(phyloTreeName.c_str());
 191                                 delete phyloTree;
 192
 193                                 phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
 194                         }
 195                 }
 196
 197                 m->mothurOut("DONE."); m->mothurOutEndLine();
 198                 m->mothurOut("It took " + toString(time(NULL) - start) + " seconds get probabilities. "); m->mothurOutEndLine();
 199         }
 200         catch(exception& e) {
 201                 m->errorOut(e, "Bayesian", "Bayesian");
 202                 exit(1);
 203         }
 204 }
 205 /**************************************************************************************************/
 206 Bayesian::~Bayesian() {
 207         try {
 208
 209                  delete phyloTree;
 210                  if (database != NULL) {  delete database; }
 211         }
 212         catch(exception& e) {
 213                 m->errorOut(e, "Bayesian", "~Bayesian");
 214                 exit(1);
 215         }
 216 }
 217
 218 /**************************************************************************************************/
 219 string Bayesian::getTaxonomy(Sequence* seq) {
 220         try {
 221                 string tax = "";
 222                 Kmer kmer(kmerSize);
 223
 224                 //get words contained in query
 225                 //getKmerString returns a string where the index in the string is hte kmer number
 226                 //and the character at that index can be converted to be the number of times that kmer was seen
 227
 228                 string queryKmerString = kmer.getKmerString(seq->getUnaligned());
 229
 230                 vector<int> queryKmers;
 231                 for (int i = 0; i < queryKmerString.length(); i++) {
 232                         if (queryKmerString[i] != '!') { //this kmer is in the query
 233                                 queryKmers.push_back(i);
 234                         }
 235                 }
 236
 237                 if (queryKmers.size() == 0) {  m->mothurOut(seq->getName() + "is bad."); m->mothurOutEndLine(); return "bad seq"; }
 238
 239
 240                 int index = getMostProbableTaxonomy(queryKmers);
 241
 242                 if (m->control_pressed) { return tax; }
 243
 244                 //bootstrap - to set confidenceScore
 245                 int numToSelect = queryKmers.size() / 8;
 246
 247                 tax = bootstrapResults(queryKmers, index, numToSelect);
 248
 249                 return tax;
 250         }
 251         catch(exception& e) {
 252                 m->errorOut(e, "Bayesian", "getTaxonomy");
 253                 exit(1);
 254         }
 255 }
 256 /**************************************************************************************************/
 257 string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
 258         try {
 259
 260                 map<int, int> confidenceScores;
 261
 262                 //initialize confidences to 0
 263                 int seqIndex = tax;
 264                 TaxNode seq = phyloTree->get(tax);
 265                 confidenceScores[tax] = 0;
 266
 267                 while (seq.level != 0) { //while you are not at the root
 268                         seqIndex = seq.parent;
 269                         confidenceScores[seqIndex] = 0;
 270                         seq = phyloTree->get(seq.parent);
 271                 }
 272
 273                 map<int, int>::iterator itBoot;
 274                 map<int, int>::iterator itBoot2;
 275                 map<int, int>::iterator itConvert;
 276
 277                 for (int i = 0; i < iters; i++) {
 278                         if (m->control_pressed) { return "control"; }
 279
 280                         vector<int> temp;
 281                         for (int j = 0; j < numToSelect; j++) {
 282                                 int index = int(rand() % kmers.size());
 283
 284                                 //add word to temp
 285                                 temp.push_back(kmers[index]);
 286                         }
 287
 288                         //get taxonomy
 289                         int newTax = getMostProbableTaxonomy(temp);
 290                         //int newTax = 1;
 291                         TaxNode taxonomyTemp = phyloTree->get(newTax);
 292
 293                         //add to confidence results
 294                         while (taxonomyTemp.level != 0) { //while you are not at the root
 295                                 itBoot2 = confidenceScores.find(newTax); //is this a classification we already have a count on
 296
 297                                 if (itBoot2 != confidenceScores.end()) { //this is a classification we need a confidence for
 298                                         (itBoot2->second)++;
 299                                 }
 300
 301                                 newTax = taxonomyTemp.parent;
 302                                 taxonomyTemp = phyloTree->get(newTax);
 303                         }
 304
 305                 }
 306
 307                 string confidenceTax = "";
 308                 simpleTax = "";
 309
 310                 int seqTaxIndex = tax;
 311                 TaxNode seqTax = phyloTree->get(tax);
 312
 313                 while (seqTax.level != 0) { //while you are not at the root
 314
 315                                 itBoot2 = confidenceScores.find(seqTaxIndex); //is this a classification we already have a count on
 316
 317                                 int confidence = 0;
 318                                 if (itBoot2 != confidenceScores.end()) { //already in confidence scores
 319                                         confidence = itBoot2->second;
 320                                 }
 321
 322                                 if (((confidence/(float)iters) * 100) >= confidenceThreshold) {
 323                                         confidenceTax = seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");" + confidenceTax;
 324                                         simpleTax = seqTax.name + ";" + simpleTax;
 325                                 }
 326
 327                                 seqTaxIndex = seqTax.parent;
 328                                 seqTax = phyloTree->get(seqTax.parent);
 329                 }
 330
 331                 if (confidenceTax == "") { confidenceTax = "unclassified;"; simpleTax = "unclassified;"; }
 332                 return confidenceTax;
 333
 334         }
 335         catch(exception& e) {
 336                 m->errorOut(e, "Bayesian", "bootstrapResults");
 337                 exit(1);
 338         }
 339 }
 340 /**************************************************************************************************/
 341 int Bayesian::getMostProbableTaxonomy(vector<int> queryKmer) {
 342         try {
 343                 int indexofGenus = 0;
 344
 345                 double maxProbability = -1000000.0;
 346                 //find taxonomy with highest probability that this sequence is from it
 347                 for (int k = 0; k < genusNodes.size(); k++) {
 348                         //for each taxonomy calc its probability
 349                         double prob = 1.0;
 350                         for (int i = 0; i < queryKmer.size(); i++) {
 351                                 prob += wordGenusProb[queryKmer[i]][k];
 352                         }
 353
 354                         //is this the taxonomy with the greatest probability?
 355                         if (prob > maxProbability) {
 356                                 indexofGenus = genusNodes[k];
 357                                 maxProbability = prob;
 358                         }
 359                 }
 360
 361                 return indexofGenus;
 362         }
 363         catch(exception& e) {
 364                 m->errorOut(e, "Bayesian", "getMostProbableTaxonomy");
 365                 exit(1);
 366         }
 367 }
 368 /*************************************************************************************************
 369 map<string, int> Bayesian::parseTaxMap(string newTax) {
 370         try{
 371
 372                 map<string, int> parsed;
 373
 374                 newTax = newTax.substr(0, newTax.length()-1);  //get rid of last ';'
 375
 376                 //parse taxonomy
 377                 string individual;
 378                 while (newTax.find_first_of(';') != -1) {
 379                         individual = newTax.substr(0,newTax.find_first_of(';'));
 380                         newTax = newTax.substr(newTax.find_first_of(';')+1, newTax.length());
 381                         parsed[individual] = 1;
 382                 }
 383
 384                 //get last one
 385                 parsed[newTax] = 1;
 386
 387                 return parsed;
 388
 389         }
 390         catch(exception& e) {
 391                 m->errorOut(e, "Bayesian", "parseTax");
 392                 exit(1);
 393         }
 394 }
 395 /**************************************************************************************************/
 396 void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string inNumName) {
 397         try{
 398
 399                 #ifdef USE_MPI
 400
 401                         int pid, num, num2, processors;
 402                         vector<unsigned long int> positions;
 403                         vector<unsigned long int> positions2;
 404
 405                         MPI_Status status;
 406                         MPI_File inMPI;
 407                         MPI_File inMPI2;
 408                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 409                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 410                         int tag = 2001;
 411
 412                         char inFileName[1024];
 413                         strcpy(inFileName, inNumName.c_str());
 414
 415                         char inFileName2[1024];
 416                         strcpy(inFileName2, inName.c_str());
 417
 418                         MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 419                         MPI_File_open(MPI_COMM_WORLD, inFileName2, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI2);  //comm, filename, mode, info, filepointer
 420
 421                         if (pid == 0) {
 422                                 positions = m->setFilePosEachLine(inNumName, num);
 423                                 positions2 = m->setFilePosEachLine(inName, num2);
 424
 425                                 for(int i = 1; i < processors; i++) {
 426                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 427                                         MPI_Send(&positions[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 428
 429                                         MPI_Send(&num2, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 430                                         MPI_Send(&positions2[0], (num2+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 431                                 }
 432
 433                         }else{
 434                                 MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 435                                 positions.resize(num+1);
 436                                 MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 437
 438                                 MPI_Recv(&num2, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 439                                 positions2.resize(num2+1);
 440                                 MPI_Recv(&positions2[0], (num2+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 441                         }
 442
 443                         //read version
 444                         int length = positions2[1] - positions2[0];
 445                         char* buf5 = new char[length];
 446
 447                         MPI_File_read_at(inMPI2, positions2[0], buf5, length, MPI_CHAR, &status);
 448                         delete buf5;
 449
 450                         //read numKmers
 451                         length = positions2[2] - positions2[1];
 452                         char* buf = new char[length];
 453
 454                         MPI_File_read_at(inMPI2, positions2[1], buf, length, MPI_CHAR, &status);
 455
 456                         string tempBuf = buf;
 457                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 458                         delete buf;
 459
 460                         istringstream iss (tempBuf,istringstream::in);
 461                         iss >> numKmers;
 462
 463                         //initialze probabilities
 464                         wordGenusProb.resize(numKmers);
 465
 466                         for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
 467
 468                         int kmer, name;
 469                         vector<int> numbers; numbers.resize(numKmers);
 470                         float prob;
 471                         vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
 472
 473                         //read version
 474                         length = positions[1] - positions[0];
 475                         char* buf6 = new char[length];
 476
 477                         MPI_File_read_at(inMPI2, positions[0], buf6, length, MPI_CHAR, &status);
 478                         delete buf6;
 479
 480                         //read file
 481                         for(int i=1;i<num;i++){
 482                                 //read next sequence
 483                                 length = positions[i+1] - positions[i];
 484                                 char* buf4 = new char[length];
 485
 486                                 MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
 487
 488                                 tempBuf = buf4;
 489                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 490                                 delete buf4;
 491
 492                                 istringstream iss (tempBuf,istringstream::in);
 493                                 iss >> zeroCountProb[i] >> numbers[i];
 494                         }
 495
 496                         MPI_File_close(&inMPI);
 497
 498                         for(int i=2;i<num2;i++){
 499                                 //read next sequence
 500                                 length = positions2[i+1] - positions2[i];
 501                                 char* buf4 = new char[length];
 502
 503                                 MPI_File_read_at(inMPI2, positions2[i], buf4, length, MPI_CHAR, &status);
 504
 505                                 tempBuf = buf4;
 506                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 507                                 delete buf4;
 508
 509                                 istringstream iss (tempBuf,istringstream::in);
 510
 511                                 iss >> kmer;
 512
 513                                 //set them all to zero value
 514                                 for (int i = 0; i < genusNodes.size(); i++) {
 515                                         wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
 516                                 }
 517
 518                                 //get probs for nonzero values
 519                                 for (int i = 0; i < numbers[kmer]; i++) {
 520                                         iss >> name >> prob;
 521                                         wordGenusProb[kmer][name] = prob;
 522                                 }
 523
 524                         }
 525                         MPI_File_close(&inMPI2);
 526                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 527                 #else
 528                         //read version
 529                         string line = m->getline(in); m->gobble(in);
 530
 531                         in >> numKmers; m->gobble(in);
 532
 533                         //initialze probabilities
 534                         wordGenusProb.resize(numKmers);
 535
 536                         for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
 537
 538                         int kmer, name, count;  count = 0;
 539                         vector<int> num; num.resize(numKmers);
 540                         float prob;
 541                         vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
 542
 543                         //read version
 544                         string line2 = m->getline(inNum); m->gobble(inNum);
 545
 546                         while (inNum) {
 547                                 inNum >> zeroCountProb[count] >> num[count];
 548                                 count++;
 549                                 m->gobble(inNum);
 550                         }
 551                         inNum.close();
 552
 553                         while(in) {
 554                                 in >> kmer;
 555
 556                                 //set them all to zero value
 557                                 for (int i = 0; i < genusNodes.size(); i++) {
 558                                         wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
 559                                 }
 560
 561                                 //get probs for nonzero values
 562                                 for (int i = 0; i < num[kmer]; i++) {
 563                                         in >> name >> prob;
 564                                         wordGenusProb[kmer][name] = prob;
 565                                 }
 566
 567                                 m->gobble(in);
 568                         }
 569                         in.close();
 570
 571                 #endif
 572         }
 573         catch(exception& e) {
 574                 m->errorOut(e, "Bayesian", "readProbFile");
 575                 exit(1);
 576         }
 577 }
 578 /**************************************************************************************************/
 579 bool Bayesian::checkReleaseDate(ifstream& file1, ifstream& file2, ifstream& file3, ifstream& file4) {
 580         try {
 581
 582                 bool good = true;
 583
 584                 vector<string> lines;
 585                 lines.push_back(m->getline(file1));
 586                 lines.push_back(m->getline(file2));
 587                 lines.push_back(m->getline(file3));
 588                 lines.push_back(m->getline(file4));
 589
 590                 //before we added this check
 591                 if ((lines[0][0] != '#') || (lines[1][0] != '#') || (lines[2][0] != '#') || (lines[3][0] != '#')) {  good = false;  }
 592                 else {
 593                         //rip off #
 594                         for (int i = 0; i < lines.size(); i++) { lines[i] = lines[i].substr(1);  }
 595
 596                         //get mothurs current version
 597                         string version = m->getVersion();
 598
 599                         vector<string> versionVector;
 600                         m->splitAtChar(version, versionVector, '.');
 601
 602                         //check each files version
 603                         for (int i = 0; i < lines.size(); i++) {
 604                                 vector<string> linesVector;
 605                                 m->splitAtChar(lines[i], linesVector, '.');
 606
 607                                 if (versionVector.size() != linesVector.size()) { good = false; break; }
 608                                 else {
 609                                         for (int j = 0; j < versionVector.size(); j++) {
 610                                                 int num1, num2;
 611                                                 convert(versionVector[j], num1);
 612                                                 convert(linesVector[j], num2);
 613
 614                                                 //if mothurs version is newer than this files version, then we want to remake it
 615                                                 if (num1 > num2) {  good = false; break;  }
 616                                         }
 617                                 }
 618
 619                                 if (!good) { break; }
 620                         }
 621                 }
 622
 623                 if (!good) {  file1.close(); file2.close(); file3.close(); file4.close();  }
 624                 else { file1.seekg(0);  file2.seekg(0);  file3.seekg(0);  file4.seekg(0);  }
 625
 626                 return good;
 627         }
 628         catch(exception& e) {
 629                 m->errorOut(e, "Bayesian", "checkReleaseDate");
 630                 exit(1);
 631         }
 632 }
 633 /**************************************************************************************************/
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