bellerophon.cpp

   1 /*
   2  *  bellerophon.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 7/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "bellerophon.h"
  11 #include "eachgapdist.h"
  12 #include "ignoregaps.h"
  13 #include "onegapdist.h"
  14
  15
  16 /***************************************************************************************************************/
  17
  18 Bellerophon::Bellerophon(string name, bool filterSeqs,  bool c, int win, int inc, int p, string o) : Chimera() {
  19         try {
  20                 fastafile = name;
  21                 correction = c;
  22                 outputDir = o;
  23                 window = win;
  24                 increment = inc;
  25                 processors = p;
  26
  27                 //read in sequences
  28                 seqs = readSeqs(fastafile);
  29                 numSeqs = seqs.size();
  30                 if (numSeqs == 0) { m->mothurOut("Error in reading you sequences."); m->mothurOutEndLine(); exit(1); }
  31
  32                 //do soft filter
  33                 if (filterSeqs)  {
  34                         createFilter(seqs, 0.5);
  35                         for (int i = 0; i < seqs.size(); i++) {  runFilter(seqs[i]);  }
  36                 }
  37
  38                 distCalculator = new eachGapDist();
  39
  40                 //set default window to 25% of sequence length
  41                 string seq0 = seqs[0]->getAligned();
  42                 if (window == 0) { window = seq0.length() / 4;  }
  43                 else if (window > (seq0.length() / 2)) {
  44                         m->mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); m->mothurOutEndLine();
  45                         window = (seq0.length() / 2);
  46                 }
  47
  48                 if (increment > (seqs[0]->getAlignLength() - (2*window))) {
  49                         if (increment != 10) {
  50
  51                                 m->mothurOut("You have selected a increment that is too large. I will use the default."); m->mothurOutEndLine();
  52                                 increment = 10;
  53                                 if (increment > (seqs[0]->getAlignLength() - (2*window))) {  increment = 0;  }
  54
  55                         }else{ increment = 0; }
  56                 }
  57
  58                 if (increment == 0) { iters = 1; }
  59                 else { iters = ((seqs[0]->getAlignLength() - (2*window)) / increment); }
  60
  61                 //initialize pref
  62                 pref.resize(iters);
  63                 for (int i = 0; i < iters; i++) {
  64                         Preference temp;
  65                         for (int j = 0; j < numSeqs; j++) {
  66                                 pref[i].push_back(temp);
  67                         }
  68                 }
  69
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "Bellerophon", "Bellerophon");
  73                 exit(1);
  74         }
  75 }
  76
  77 //***************************************************************************************************************
  78 int Bellerophon::print(ostream& out, ostream& outAcc) {
  79         try {
  80                 int above1 = 0;
  81
  82                 //sorted "best" preference scores for all seqs
  83                 vector<Preference> best = getBestPref();
  84
  85                 if (m->control_pressed) { return numSeqs; }
  86
  87                 out << "Name\tScore\tLeft\tRight\t" << endl;
  88                 //output prefenence structure to .chimeras file
  89                 for (int i = 0; i < best.size(); i++) {
  90
  91                         if (m->control_pressed) {  return numSeqs; }
  92
  93                         out << best[i].name << '\t' << setprecision(3) << best[i].score << '\t' << best[i].leftParent << '\t' << best[i].rightParent << endl;
  94
  95                         //calc # of seqs with preference above 1.0
  96                         if (best[i].score > 1.0) {
  97                                 above1++;
  98                                 outAcc << best[i].name << endl;
  99                                 m->mothurOut(best[i].name + " is a suspected chimera at breakpoint " + toString(best[i].midpoint)); m->mothurOutEndLine();
 100                                 m->mothurOut("It's score is " + toString(best[i].score) + " with suspected left parent " + best[i].leftParent + " and right parent " + best[i].rightParent); m->mothurOutEndLine();
 101                         }
 102                 }
 103
 104                 //output results to screen
 105                 m->mothurOutEndLine();
 106                 m->mothurOut("Sequence with preference score above 1.0: " + toString(above1)); m->mothurOutEndLine();
 107                 int spot;
 108                 spot = best.size()-1;
 109                 m->mothurOut("Minimum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 110                 spot = best.size() * 0.975;
 111                 m->mothurOut("2.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 112                 spot = best.size() * 0.75;
 113                 m->mothurOut("25%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 114                 spot = best.size() * 0.50;
 115                 m->mothurOut("Median: \t" + toString(best[spot].score)); m->mothurOutEndLine();
 116                 spot = best.size() * 0.25;
 117                 m->mothurOut("75%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 118                 spot = best.size() * 0.025;
 119                 m->mothurOut("97.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 120                 spot = 0;
 121                 m->mothurOut("Maximum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 122
 123                 return numSeqs;
 124
 125         }
 126         catch(exception& e) {
 127                 m->errorOut(e, "Bellerophon", "print");
 128                 exit(1);
 129         }
 130 }
 131 #ifdef USE_MPI
 132 //***************************************************************************************************************
 133 int Bellerophon::print(MPI_File& out, MPI_File& outAcc) {
 134         try {
 135
 136                 int pid;
 137                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 138
 139                 if (pid == 0) {
 140                         string outString = "";
 141
 142                         //sorted "best" preference scores for all seqs
 143                         vector<Preference> best = getBestPref();
 144
 145                         int above1 = 0;
 146                         int ninetyfive = best.size() * 0.05;
 147                         float cutoffScore = best[ninetyfive].score;
 148
 149                         if (m->control_pressed) { return numSeqs; }
 150
 151                         outString += "Name\tScore\tLeft\tRight\n";
 152                         //output prefenence structure to .chimeras file
 153                         for (int i = 0; i < best.size(); i++) {
 154
 155                                 if (m->control_pressed) {  return numSeqs; }
 156
 157                                 outString += best[i].name + "\t" +  toString(best[i].score) + "\t" + best[i].leftParent + "\t" + best[i].rightParent + "\n";
 158
 159                                 MPI_Status status;
 160                                 int length = outString.length();
 161                                 char buf2[length];
 162                                 strcpy(buf2, outString.c_str());
 163
 164                                 MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
 165
 166
 167                                 //calc # of seqs with preference above 95%tile
 168                                 if (best[i].score >= cutoffScore) {
 169                                         above1++;
 170                                         string outAccString;
 171                                          outAccString += best[i].name + "\n";
 172
 173                                         MPI_Status statusAcc;
 174                                         length = outAccString.length();
 175                                         char buf[length];
 176                                         strcpy(buf, outAccString.c_str());
 177
 178                                         MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
 179
 180                                         cout << best[i].name << " is a suspected chimera at breakpoint " << toString(best[i].midpoint) << endl;
 181                                         cout << "It's score is " << toString(best[i].score) << " with suspected left parent " << best[i].leftParent << " and right parent " << best[i].rightParent << endl;
 182                                 }
 183                         }
 184
 185                         //output results to screen
 186                         m->mothurOutEndLine();
 187                         m->mothurOut("Sequence with preference score above " + toString(cutoffScore) +  ": " + toString(above1)); m->mothurOutEndLine();
 188                         int spot;
 189                         spot = best.size()-1;
 190                         m->mothurOut("Minimum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 191                         spot = best.size() * 0.975;
 192                         m->mothurOut("2.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 193                         spot = best.size() * 0.75;
 194                         m->mothurOut("25%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 195                         spot = best.size() * 0.50;
 196                         m->mothurOut("Median: \t" + toString(best[spot].score)); m->mothurOutEndLine();
 197                         spot = best.size() * 0.25;
 198                         m->mothurOut("75%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 199                         spot = best.size() * 0.025;
 200                         m->mothurOut("97.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 201                         spot = 0;
 202                         m->mothurOut("Maximum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 203
 204                 }
 205
 206                 return numSeqs;
 207
 208         }
 209         catch(exception& e) {
 210                 m->errorOut(e, "Bellerophon", "print");
 211                 exit(1);
 212         }
 213 }
 214 #endif
 215 //********************************************************************************************************************
 216 //sorts highest score to lowest
 217 inline bool comparePref(Preference left, Preference right){
 218         return (left.score > right.score);
 219 }
 220 //***************************************************************************************************************
 221 int Bellerophon::getChimeras() {
 222         try {
 223
 224                 //create breaking points
 225                 vector<int> midpoints;   midpoints.resize(iters, window);
 226                 for (int i = 1; i < iters; i++) {  midpoints[i] = midpoints[i-1] + increment;  }
 227
 228         #ifdef USE_MPI
 229                 int pid, numSeqsPerProcessor;
 230
 231                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 232                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 233
 234                 numSeqsPerProcessor = iters / processors;
 235
 236                 //each process hits this only once
 237                 int startPos = pid * numSeqsPerProcessor;
 238                 if(pid == processors - 1){
 239                                 numSeqsPerProcessor = iters - pid * numSeqsPerProcessor;
 240                 }
 241                 lines.push_back(linePair(startPos, numSeqsPerProcessor));
 242
 243                 //fill pref with scores
 244                 driverChimeras(midpoints, lines[0]);
 245
 246                 if (m->control_pressed) { return 0; }
 247
 248                 //each process must send its parts back to pid 0
 249                 if (pid == 0) {
 250
 251                         //receive results
 252                         for (int j = 1; j < processors; j++) {
 253
 254                                 vector<string>  MPIBestSend;
 255                                 for (int i = 0; i < numSeqs; i++) {
 256
 257                                         if (m->control_pressed) { return 0; }
 258
 259                                         MPI_Status status;
 260                                         //receive string
 261                                         int length;
 262                                         MPI_Recv(&length, 1, MPI_INT, j, 2001, MPI_COMM_WORLD, &status);
 263
 264                                         char buf[length];
 265                                         MPI_Recv(&buf, length, MPI_CHAR, j, 2001, MPI_COMM_WORLD, &status);
 266
 267                                         string temp = buf;
 268                                         if (temp.length() > length) { temp = temp.substr(0, length); }
 269
 270                                         MPIBestSend.push_back(temp);
 271                                 }
 272
 273                                 fillPref(j, MPIBestSend);
 274
 275                                 if (m->control_pressed) { return 0; }
 276                         }
 277
 278                 }else {
 279                         //takes best window for each sequence and turns Preference to string that can be parsed by pid 0.
 280                         //played with this a bit, but it may be better to try user-defined datatypes with set string lengths??
 281                         vector<string> MPIBestSend = getBestWindow(lines[0]);
 282                         pref.clear();
 283
 284                         //send your result to parent
 285                         for (int i = 0; i < numSeqs; i++) {
 286
 287                                 if (m->control_pressed) { return 0; }
 288
 289                                 int bestLength = MPIBestSend[i].length();
 290                                 char buf[bestLength];
 291                                 strcpy(buf, MPIBestSend[i].c_str());
 292
 293                                 MPI_Send(&bestLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD);
 294                                 MPI_Send(buf, bestLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD);
 295                         }
 296
 297                         MPIBestSend.clear();
 298                 }
 299
 300         #else
 301
 302                 //divide breakpoints between processors
 303                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 304                         if(processors == 1){
 305                                 lines.push_back(linePair(0, iters));
 306
 307                                 //fill pref with scores
 308                                 driverChimeras(midpoints, lines[0]);
 309
 310                         }else{
 311
 312                                 int numSeqsPerProcessor = iters / processors;
 313
 314                                 for (int i = 0; i < processors; i++) {
 315                                         int startPos = i * numSeqsPerProcessor;
 316                                         if(i == processors - 1){
 317                                                 numSeqsPerProcessor = iters - i * numSeqsPerProcessor;
 318                                         }
 319                                         lines.push_back(linePair(startPos, numSeqsPerProcessor));
 320                                 }
 321
 322                                 createProcesses(midpoints);
 323                         }
 324                 #else
 325                         lines.push_back(linePair(0, iters));
 326
 327                         ///fill pref with scores
 328                         driverChimeras(midpoints, lines[0]);
 329                 #endif
 330
 331         #endif
 332
 333                 return 0;
 334
 335         }
 336         catch(exception& e) {
 337                 m->errorOut(e, "Bellerophon", "getChimeras");
 338                 exit(1);
 339         }
 340 }
 341 /**************************************************************************************************/
 342
 343 int Bellerophon::createProcesses(vector<int> mid) {
 344         try {
 345 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 346                 int process = 0;
 347                 int exitCommand = 1;
 348                 vector<int> processIDS;
 349
 350                 //loop through and create all the processes you want
 351                 while (process != processors) {
 352                         int pid = fork();
 353
 354                         if (pid > 0) {
 355                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 356                                 process++;
 357                         }else if (pid == 0){
 358                                 exitCommand = driverChimeras(mid, lines[process]);
 359                                 string tempOut = outputDir + toString(getpid()) + ".temp";
 360                                 writePrefs(tempOut, lines[process]);
 361                                 exit(0);
 362                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 363                 }
 364
 365                 //force parent to wait until all the processes are done
 366                 for (int i=0;i<processors;i++) {
 367                         int temp = processIDS[i];
 368                         wait(&temp);
 369                 }
 370
 371                 //get info that other processes created
 372                 for (int i = 0; i < processIDS.size(); i++) {
 373                         string tempIn = outputDir + toString(processIDS[i]) + ".temp";
 374                         readPrefs(tempIn);
 375                 }
 376
 377                 return exitCommand;
 378 #endif
 379         }
 380         catch(exception& e) {
 381                 m->errorOut(e, "AlignCommand", "createProcesses");
 382                 exit(1);
 383         }
 384 }
 385 //***************************************************************************************************************
 386 int Bellerophon::driverChimeras(vector<int> midpoints, linePair line) {
 387         try {
 388
 389                 for (int h = line.start; h < (line.start + line.num); h++) {
 390                         count = h;
 391                         int midpoint = midpoints[h];
 392
 393                         //initialize pref[count]
 394                         for (int i = 0; i < numSeqs; i++ ) {
 395                                 pref[count][i].name = seqs[i]->getName();
 396                                 pref[count][i].midpoint = midpoint;
 397                         }
 398
 399                         if (m->control_pressed) { return 0; }
 400
 401                         //create 2 vectors of sequences, 1 for left side and one for right side
 402                         vector<Sequence> left;  vector<Sequence> right;
 403
 404                         for (int i = 0; i < seqs.size(); i++) {
 405
 406                                 if (m->control_pressed) { return 0; }
 407
 408                                 //cout << "midpoint = " << midpoint << "\twindow = " << window << endl;
 409                                 //cout << "whole = " << seqs[i]->getAligned().length() << endl;
 410                                 //save left side
 411                                 string seqLeft = seqs[i]->getAligned().substr(midpoint-window, window);
 412                                 Sequence tempLeft;
 413                                 tempLeft.setName(seqs[i]->getName());
 414                                 tempLeft.setAligned(seqLeft);
 415                                 left.push_back(tempLeft);
 416                                 //cout << "left = " << tempLeft.getAligned().length() << endl;
 417                                 //save right side
 418                                 string seqRight = seqs[i]->getAligned().substr(midpoint, window);
 419                                 Sequence tempRight;
 420                                 tempRight.setName(seqs[i]->getName());
 421                                 tempRight.setAligned(seqRight);
 422                                 right.push_back(tempRight);
 423                                 //cout << "right = " << seqRight.length() << endl;
 424                         }
 425
 426                         //this should be parallelized
 427                         //perference = sum of (| distance of my left to sequence j's left - distance of my right to sequence j's right | )
 428                         //create a matrix containing the distance from left to left and right to right
 429                         //calculate distances
 430                         SparseMatrix* SparseLeft = new SparseMatrix();
 431                         SparseMatrix* SparseRight = new SparseMatrix();
 432
 433                         createSparseMatrix(0, left.size(), SparseLeft, left);
 434
 435                         if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 436
 437                         createSparseMatrix(0, right.size(), SparseRight, right);
 438
 439                         if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 440
 441                         left.clear(); right.clear();
 442                         vector<SeqMap> distMapRight;
 443                         vector<SeqMap> distMapLeft;
 444
 445                         // Create a data structure to quickly access the distance information.
 446                         //this is from thallingers reimplementation on get.oturep
 447                         // It consists of a vector of distance maps, where each map contains
 448                         // all distances of a certain sequence. Vector and maps are accessed
 449                         // via the index of a sequence in the distance matrix
 450                         distMapRight = vector<SeqMap>(numSeqs);
 451                         distMapLeft = vector<SeqMap>(numSeqs);
 452                         //cout << "left" << endl << endl;
 453                         for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
 454                                 distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
 455                                 if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 456                                 //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
 457                         }
 458                         //cout << "right" << endl << endl;
 459                         for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
 460                                 distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
 461                                 if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 462                                 //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
 463                         }
 464
 465                         delete SparseLeft;
 466                         delete SparseRight;
 467
 468                         //fill preference structure
 469                         generatePreferences(distMapLeft, distMapRight, midpoint);
 470
 471                         if (m->control_pressed) { return 0; }
 472
 473                         //report progress
 474                         if((h+1) % 10 == 0){    cout << "Processing sliding window: " << toString(h+1) <<  "\n";  m->mothurOutJustToLog("Processing sliding window: " + toString(h+1) + "\n") ;         }
 475
 476                 }
 477
 478                 //report progress
 479                 if((line.start + line.num) % 10 != 0){  cout << "Processing sliding window: " << toString(line.start + line.num) <<  "\n";  m->mothurOutJustToLog("Processing sliding window: " + toString(line.start + line.num) + "\n") ;             }
 480
 481                 return 0;
 482
 483         }
 484         catch(exception& e) {
 485                 m->errorOut(e, "Bellerophon", "driverChimeras");
 486                 exit(1);
 487         }
 488 }
 489
 490 /***************************************************************************************************************/
 491 int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* sparse, vector<Sequence> s){
 492         try {
 493
 494                 for(int i=startSeq; i<endSeq; i++){
 495
 496                         for(int j=0;j<i;j++){
 497
 498                                 if (m->control_pressed) { return 0; }
 499
 500                                 distCalculator->calcDist(s[i], s[j]);
 501                                 float dist = distCalculator->getDist();
 502
 503                                 PCell temp(i, j, dist);
 504                                 sparse->addCell(temp);
 505
 506                         }
 507                 }
 508
 509                 return 1;
 510         }
 511         catch(exception& e) {
 512                 m->errorOut(e, "Bellerophon", "createSparseMatrix");
 513                 exit(1);
 514         }
 515 }
 516 /***************************************************************************************************************/
 517 int Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
 518         try {
 519
 520                 float dme = 0.0;
 521                 SeqMap::iterator itR;
 522                 SeqMap::iterator itL;
 523
 524                 for (int i = 0; i < left.size(); i++) {
 525
 526                         SeqMap currentLeft = left[i];    //example i = 3;   currentLeft is a map of 0 to the distance of sequence 3 to sequence 0,
 527                                                                                                 //                                                                              1 to the distance of sequence 3 to sequence 1,
 528                                                                                                 //                                                                              2 to the distance of sequence 3 to sequence 2.
 529                         SeqMap currentRight = right[i];         // same as left but with distances on the right side.
 530
 531                         for (int j = 0; j < i; j++) {
 532
 533                                 if (m->control_pressed) {  return 0; }
 534
 535                                 itL = currentLeft.find(j);
 536                                 itR = currentRight.find(j);
 537 //cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
 538 //cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
 539
 540                                 //if you can find this entry update the preferences
 541                                 if ((itL != currentLeft.end()) && (itR != currentRight.end())) {
 542
 543                                         if (!correction) {
 544                                                 pref[count][i].score += abs((itL->second - itR->second));
 545                                                 pref[count][j].score += abs((itL->second - itR->second));
 546 //cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
 547 //cout << "abs = " << abs((itL->second - itR->second)) << endl;
 548 //cout << i << " score = " << pref[i].score[1] << endl;
 549 //cout << j << " score = " << pref[j].score[1] << endl;
 550                                         }else {
 551                                                 pref[count][i].score += abs((sqrt(itL->second) - sqrt(itR->second)));
 552                                                 pref[count][j].score += abs((sqrt(itL->second) - sqrt(itR->second)));
 553 //cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
 554 //cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
 555 //cout << i << " score = " << pref[i].score[1] << endl;
 556 //cout << j << " score = " << pref[j].score[1] << endl;
 557                                         }
 558 //cout << "pref[" << i << "].closestLeft[1] = " <<      pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;
 559                                         //are you the closest left sequence
 560                                         if (itL->second < pref[count][i].closestLeft) {
 561
 562                                                 pref[count][i].closestLeft = itL->second;
 563                                                 pref[count][i].leftParent = seqs[j]->getName();
 564 //cout << "updating closest left to " << pref[i].leftParent[1] << endl;
 565                                         }
 566 //cout << "pref[" << j << "].closestLeft[1] = " <<      pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;
 567                                         if (itL->second < pref[count][j].closestLeft) {
 568                                                 pref[count][j].closestLeft = itL->second;
 569                                                 pref[count][j].leftParent = seqs[i]->getName();
 570 //cout << "updating closest left to " << pref[j].leftParent[1] << endl;
 571                                         }
 572
 573                                         //are you the closest right sequence
 574                                         if (itR->second < pref[count][i].closestRight) {
 575                                                 pref[count][i].closestRight = itR->second;
 576                                                 pref[count][i].rightParent = seqs[j]->getName();
 577                                         }
 578                                         if (itR->second < pref[count][j].closestRight) {
 579                                                 pref[count][j].closestRight = itR->second;
 580                                                 pref[count][j].rightParent = seqs[i]->getName();
 581                                         }
 582
 583                                 }
 584                         }
 585
 586                 }
 587
 588
 589                 return 1;
 590
 591         }
 592         catch(exception& e) {
 593                 m->errorOut(e, "Bellerophon", "generatePreferences");
 594                 exit(1);
 595         }
 596 }
 597 /**************************************************************************************************/
 598 vector<Preference> Bellerophon::getBestPref() {
 599         try {
 600
 601                 vector<Preference> best;
 602
 603                 //for each sequence
 604                 for (int i = 0; i < numSeqs; i++) {
 605
 606                         //set best pref score to first one
 607                         Preference temp = pref[0][i];
 608
 609                         if (m->control_pressed) { return best;  }
 610
 611                         //for each window
 612                         for (int j = 1; j < pref.size(); j++) {
 613
 614                                 //is this a better score
 615                                 if (pref[j][i].score > temp.score) {    temp = pref[j][i];              }
 616                         }
 617
 618                         best.push_back(temp);
 619                 }
 620
 621                 //rank preference score to eachother
 622                 float dme = 0.0;
 623                 float expectedPercent = 1 / (float) (best.size());
 624
 625                 for (int i = 0; i < best.size(); i++) {  dme += best[i].score;  }
 626
 627                 for (int i = 0; i < best.size(); i++) {
 628
 629                         if (m->control_pressed) { return best; }
 630
 631                         //gives the actual percentage of the dme this seq adds
 632                         best[i].score = best[i].score / dme;
 633
 634                         //how much higher or lower is this than expected
 635                         best[i].score = best[i].score / expectedPercent;
 636
 637                 }
 638
 639                 //sort Preferences highest to lowest
 640                 sort(best.begin(), best.end(), comparePref);
 641
 642                 return best;
 643         }
 644         catch(exception& e) {
 645                 m->errorOut(e, "Bellerophon", "getBestPref");
 646                 exit(1);
 647         }
 648 }
 649 /**************************************************************************************************/
 650 int Bellerophon::writePrefs(string file, linePair tempLine) {
 651         try {
 652
 653                 ofstream outTemp;
 654                 openOutputFile(file, outTemp);
 655
 656                 //lets you know what part of the pref matrix you are writing
 657                 outTemp << tempLine.start << '\t' << tempLine.num << endl;
 658
 659                 for (int i = tempLine.start; i < (tempLine.start + tempLine.num); i++) {
 660
 661                         for (int j = 0; j < numSeqs; j++) {
 662
 663                                 if (m->control_pressed) { outTemp.close(); remove(file.c_str()); return 0; }
 664
 665                                 outTemp << pref[i][j].name << '\t' << pref[i][j].leftParent << '\t' << pref[i][j].rightParent << '\t';
 666                                 outTemp << pref[i][j].score << '\t' << pref[i][j].closestLeft << '\t' << pref[i][j].closestRight << '\t' << pref[i][j].midpoint <<  endl;
 667                         }
 668                 }
 669
 670                 outTemp.close();
 671
 672                 return 0;
 673         }
 674         catch(exception& e) {
 675                 m->errorOut(e, "Bellerophon", "writePrefs");
 676                 exit(1);
 677         }
 678 }
 679 /**************************************************************************************************/
 680 int Bellerophon::readPrefs(string file) {
 681         try {
 682
 683                 ifstream inTemp;
 684                 openInputFile(file, inTemp);
 685
 686                 int start, num;
 687
 688                 //lets you know what part of the pref matrix you are writing
 689                 inTemp >> start >> num;  gobble(inTemp);
 690
 691                 for (int i = start; i < num; i++) {
 692
 693                         for (int j = 0; j < numSeqs; j++) {
 694
 695                                 if (m->control_pressed) { inTemp.close(); remove(file.c_str()); return 0; }
 696
 697                                 inTemp >> pref[i][j].name >> pref[i][j].leftParent >> pref[i][j].rightParent;
 698                                 inTemp >> pref[i][j].score >> pref[i][j].closestLeft >> pref[i][j].closestRight >> pref[i][j].midpoint;
 699                                 gobble(inTemp);
 700                         }
 701                 }
 702
 703                 inTemp.close();
 704
 705                 remove(file.c_str());
 706
 707                 return 0;
 708         }
 709         catch(exception& e) {
 710                 m->errorOut(e, "Bellerophon", "writePrefs");
 711                 exit(1);
 712         }
 713 }
 714 /**************************************************************************************************/
 715 vector<string> Bellerophon::getBestWindow(linePair line) {
 716         try {
 717
 718                 vector<string> best;
 719
 720                 //for each sequence
 721                 for (int i = 0; i < numSeqs; i++) {
 722
 723                         //set best pref score to first one
 724                         Preference temp = pref[line.start][i];
 725
 726                         if (m->control_pressed) { return best;  }
 727
 728                         //for each window
 729                         for (int j = (line.start+1); j < (line.start+line.num); j++) {
 730
 731                                 //is this a better score
 732                                 if (pref[j][i].score > temp.score) {    temp = pref[j][i];              }
 733                         }
 734
 735                         string tempString = temp.name + '\t' + temp.leftParent + '\t' + temp.rightParent + '\t' + toString(temp.score);
 736                         best.push_back(tempString);
 737                 }
 738
 739                 return best;
 740
 741         }
 742         catch(exception& e) {
 743                 m->errorOut(e, "Bellerophon", "getBestWindow");
 744                 exit(1);
 745         }
 746 }
 747 /**************************************************************************************************/
 748 int Bellerophon::fillPref(int process, vector<string>& best) {
 749         try {
 750                 //figure out where you start so you can put the best scores there
 751                 int numSeqsPerProcessor = iters / processors;
 752                 int start = process * numSeqsPerProcessor;
 753
 754                 for (int i = 0; i < best.size(); i++) {
 755
 756                         if (m->control_pressed) { return 0;  }
 757
 758                         istringstream iss (best[i],istringstream::in);
 759
 760                         string tempScore;
 761                         iss >> pref[start][i].name >> pref[start][i].leftParent >> pref[start][i].rightParent >> tempScore;
 762                         convert(tempScore, pref[start][i].score);
 763                 }
 764
 765                 return 0;
 766         }
 767         catch(exception& e) {
 768                 m->errorOut(e, "Bellerophon", "fillPref");
 769                 exit(1);
 770         }
 771 }
 772
 773 /**************************************************************************************************/
 774