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 = new char[length];\r
 162                                 memcpy(buf2, outString.c_str(), length);
 163
 164                                 MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
 165
 166                                 delete buf2;
 167
 168                                 //calc # of seqs with preference above 95%tile
 169                                 if (best[i].score >= cutoffScore) {
 170                                         above1++;
 171                                         string outAccString;
 172                                          outAccString += best[i].name + "\n";
 173
 174                                         MPI_Status statusAcc;
 175                                         length = outAccString.length();
 176                                         char* buf = new char[length];\r
 177                                         memcpy(buf, outAccString.c_str(), length);
 178
 179                                         MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
 180
 181                                         delete buf;
 182
 183                                         cout << best[i].name << " is a suspected chimera at breakpoint " << toString(best[i].midpoint) << endl;
 184                                         cout << "It's score is " << toString(best[i].score) << " with suspected left parent " << best[i].leftParent << " and right parent " << best[i].rightParent << endl;
 185                                 }
 186                         }
 187
 188                         //output results to screen
 189                         m->mothurOutEndLine();
 190                         m->mothurOut("Sequence with preference score above " + toString(cutoffScore) +  ": " + toString(above1)); m->mothurOutEndLine();
 191                         int spot;
 192                         spot = best.size()-1;
 193                         m->mothurOut("Minimum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 194                         spot = best.size() * 0.975;
 195                         m->mothurOut("2.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 196                         spot = best.size() * 0.75;
 197                         m->mothurOut("25%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 198                         spot = best.size() * 0.50;
 199                         m->mothurOut("Median: \t" + toString(best[spot].score)); m->mothurOutEndLine();
 200                         spot = best.size() * 0.25;
 201                         m->mothurOut("75%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 202                         spot = best.size() * 0.025;
 203                         m->mothurOut("97.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 204                         spot = 0;
 205                         m->mothurOut("Maximum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
 206
 207                 }
 208
 209                 return numSeqs;
 210
 211         }
 212         catch(exception& e) {
 213                 m->errorOut(e, "Bellerophon", "print");
 214                 exit(1);
 215         }
 216 }
 217 #endif
 218 //********************************************************************************************************************
 219 //sorts highest score to lowest
 220 inline bool comparePref(Preference left, Preference right){
 221         return (left.score > right.score);
 222 }
 223 //***************************************************************************************************************
 224 int Bellerophon::getChimeras() {
 225         try {
 226
 227                 //create breaking points
 228                 vector<int> midpoints;   midpoints.resize(iters, window);
 229                 for (int i = 1; i < iters; i++) {  midpoints[i] = midpoints[i-1] + increment;  }
 230
 231         #ifdef USE_MPI
 232                 int pid, numSeqsPerProcessor;
 233
 234                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 235                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 236
 237                 numSeqsPerProcessor = iters / processors;
 238
 239                 //each process hits this only once
 240                 int startPos = pid * numSeqsPerProcessor;
 241                 if(pid == processors - 1){
 242                                 numSeqsPerProcessor = iters - pid * numSeqsPerProcessor;
 243                 }
 244                 lines.push_back(linePair(startPos, numSeqsPerProcessor));
 245
 246                 //fill pref with scores
 247                 driverChimeras(midpoints, lines[0]);
 248
 249                 if (m->control_pressed) { return 0; }
 250
 251                 //each process must send its parts back to pid 0
 252                 if (pid == 0) {
 253
 254                         //receive results
 255                         for (int j = 1; j < processors; j++) {
 256
 257                                 vector<string>  MPIBestSend;
 258                                 for (int i = 0; i < numSeqs; i++) {
 259
 260                                         if (m->control_pressed) { return 0; }
 261
 262                                         MPI_Status status;
 263                                         //receive string
 264                                         int length;
 265                                         MPI_Recv(&length, 1, MPI_INT, j, 2001, MPI_COMM_WORLD, &status);
 266
 267                                         char* buf = new char[length];
 268                                         MPI_Recv(&buf, length, MPI_CHAR, j, 2001, MPI_COMM_WORLD, &status);
 269
 270                                         string temp = buf;
 271                                         if (temp.length() > length) { temp = temp.substr(0, length); }
 272                                         delete buf;
 273
 274                                         MPIBestSend.push_back(temp);
 275                                 }
 276
 277                                 fillPref(j, MPIBestSend);
 278
 279                                 if (m->control_pressed) { return 0; }
 280                         }
 281
 282                 }else {
 283                         //takes best window for each sequence and turns Preference to string that can be parsed by pid 0.
 284                         //played with this a bit, but it may be better to try user-defined datatypes with set string lengths??
 285                         vector<string> MPIBestSend = getBestWindow(lines[0]);
 286                         pref.clear();
 287
 288                         //send your result to parent
 289                         for (int i = 0; i < numSeqs; i++) {
 290
 291                                 if (m->control_pressed) { return 0; }
 292
 293                                 int bestLength = MPIBestSend[i].length();
 294                                 char* buf = new char[bestLength];\r
 295                                 memcpy(buf, MPIBestSend[i].c_str(), bestLength);
 296
 297                                 MPI_Send(&bestLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD);
 298                                 MPI_Send(buf, bestLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD);
 299                                 delete buf;
 300                         }
 301
 302                         MPIBestSend.clear();
 303                 }
 304
 305         #else
 306
 307                 //divide breakpoints between processors
 308                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 309                         if(processors == 1){
 310                                 lines.push_back(linePair(0, iters));
 311
 312                                 //fill pref with scores
 313                                 driverChimeras(midpoints, lines[0]);
 314
 315                         }else{
 316
 317                                 int numSeqsPerProcessor = iters / processors;
 318
 319                                 for (int i = 0; i < processors; i++) {
 320                                         int startPos = i * numSeqsPerProcessor;
 321                                         if(i == processors - 1){
 322                                                 numSeqsPerProcessor = iters - i * numSeqsPerProcessor;
 323                                         }
 324                                         lines.push_back(linePair(startPos, numSeqsPerProcessor));
 325                                 }
 326
 327                                 createProcesses(midpoints);
 328                         }
 329                 #else
 330                         lines.push_back(linePair(0, iters));
 331
 332                         ///fill pref with scores
 333                         driverChimeras(midpoints, lines[0]);
 334                 #endif
 335
 336         #endif
 337
 338                 return 0;
 339
 340         }
 341         catch(exception& e) {
 342                 m->errorOut(e, "Bellerophon", "getChimeras");
 343                 exit(1);
 344         }
 345 }
 346 /**************************************************************************************************/
 347
 348 int Bellerophon::createProcesses(vector<int> mid) {
 349         try {
 350 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 351                 int process = 0;
 352                 int exitCommand = 1;
 353                 vector<int> processIDS;
 354
 355                 //loop through and create all the processes you want
 356                 while (process != processors) {
 357                         int pid = fork();
 358
 359                         if (pid > 0) {
 360                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 361                                 process++;
 362                         }else if (pid == 0){
 363                                 exitCommand = driverChimeras(mid, lines[process]);
 364                                 string tempOut = outputDir + toString(getpid()) + ".temp";
 365                                 writePrefs(tempOut, lines[process]);
 366                                 exit(0);
 367                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 368                 }
 369
 370                 //force parent to wait until all the processes are done
 371                 for (int i=0;i<processors;i++) {
 372                         int temp = processIDS[i];
 373                         wait(&temp);
 374                 }
 375
 376                 //get info that other processes created
 377                 for (int i = 0; i < processIDS.size(); i++) {
 378                         string tempIn = outputDir + toString(processIDS[i]) + ".temp";
 379                         readPrefs(tempIn);
 380                 }
 381
 382                 return exitCommand;
 383 #endif
 384         }
 385         catch(exception& e) {
 386                 m->errorOut(e, "AlignCommand", "createProcesses");
 387                 exit(1);
 388         }
 389 }
 390 //***************************************************************************************************************
 391 int Bellerophon::driverChimeras(vector<int> midpoints, linePair line) {
 392         try {
 393
 394                 for (int h = line.start; h < (line.start + line.num); h++) {
 395                         count = h;
 396                         int midpoint = midpoints[h];
 397
 398                         //initialize pref[count]
 399                         for (int i = 0; i < numSeqs; i++ ) {
 400                                 pref[count][i].name = seqs[i]->getName();
 401                                 pref[count][i].midpoint = midpoint;
 402                         }
 403
 404                         if (m->control_pressed) { return 0; }
 405
 406                         //create 2 vectors of sequences, 1 for left side and one for right side
 407                         vector<Sequence> left;  vector<Sequence> right;
 408
 409                         for (int i = 0; i < seqs.size(); i++) {
 410
 411                                 if (m->control_pressed) { return 0; }
 412
 413                                 //cout << "midpoint = " << midpoint << "\twindow = " << window << endl;
 414                                 //cout << "whole = " << seqs[i]->getAligned().length() << endl;
 415                                 //save left side
 416                                 string seqLeft = seqs[i]->getAligned().substr(midpoint-window, window);
 417                                 Sequence tempLeft;
 418                                 tempLeft.setName(seqs[i]->getName());
 419                                 tempLeft.setAligned(seqLeft);
 420                                 left.push_back(tempLeft);
 421                                 //cout << "left = " << tempLeft.getAligned().length() << endl;
 422                                 //save right side
 423                                 string seqRight = seqs[i]->getAligned().substr(midpoint, window);
 424                                 Sequence tempRight;
 425                                 tempRight.setName(seqs[i]->getName());
 426                                 tempRight.setAligned(seqRight);
 427                                 right.push_back(tempRight);
 428                                 //cout << "right = " << seqRight.length() << endl;
 429                         }
 430
 431                         //this should be parallelized
 432                         //perference = sum of (| distance of my left to sequence j's left - distance of my right to sequence j's right | )
 433                         //create a matrix containing the distance from left to left and right to right
 434                         //calculate distances
 435                         SparseMatrix* SparseLeft = new SparseMatrix();
 436                         SparseMatrix* SparseRight = new SparseMatrix();
 437
 438                         createSparseMatrix(0, left.size(), SparseLeft, left);
 439
 440                         if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 441
 442                         createSparseMatrix(0, right.size(), SparseRight, right);
 443
 444                         if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 445
 446                         left.clear(); right.clear();
 447                         vector<SeqMap> distMapRight;
 448                         vector<SeqMap> distMapLeft;
 449
 450                         // Create a data structure to quickly access the distance information.
 451                         //this is from thallingers reimplementation on get.oturep
 452                         // It consists of a vector of distance maps, where each map contains
 453                         // all distances of a certain sequence. Vector and maps are accessed
 454                         // via the index of a sequence in the distance matrix
 455                         distMapRight = vector<SeqMap>(numSeqs);
 456                         distMapLeft = vector<SeqMap>(numSeqs);
 457                         //cout << "left" << endl << endl;
 458                         for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
 459                                 distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
 460                                 if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 461                                 //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
 462                         }
 463                         //cout << "right" << endl << endl;
 464                         for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
 465                                 distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
 466                                 if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 467                                 //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
 468                         }
 469
 470                         delete SparseLeft;
 471                         delete SparseRight;
 472
 473                         //fill preference structure
 474                         generatePreferences(distMapLeft, distMapRight, midpoint);
 475
 476                         if (m->control_pressed) { return 0; }
 477
 478                         //report progress
 479                         if((h+1) % 10 == 0){    cout << "Processing sliding window: " << toString(h+1) <<  "\n";  m->mothurOutJustToLog("Processing sliding window: " + toString(h+1) + "\n") ;         }
 480
 481                 }
 482
 483                 //report progress
 484                 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") ;             }
 485
 486                 return 0;
 487
 488         }
 489         catch(exception& e) {
 490                 m->errorOut(e, "Bellerophon", "driverChimeras");
 491                 exit(1);
 492         }
 493 }
 494
 495 /***************************************************************************************************************/
 496 int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* sparse, vector<Sequence> s){
 497         try {
 498
 499                 for(int i=startSeq; i<endSeq; i++){
 500
 501                         for(int j=0;j<i;j++){
 502
 503                                 if (m->control_pressed) { return 0; }
 504
 505                                 distCalculator->calcDist(s[i], s[j]);
 506                                 float dist = distCalculator->getDist();
 507
 508                                 PCell temp(i, j, dist);
 509                                 sparse->addCell(temp);
 510
 511                         }
 512                 }
 513
 514                 return 1;
 515         }
 516         catch(exception& e) {
 517                 m->errorOut(e, "Bellerophon", "createSparseMatrix");
 518                 exit(1);
 519         }
 520 }
 521 /***************************************************************************************************************/
 522 int Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
 523         try {
 524
 525                 float dme = 0.0;
 526                 SeqMap::iterator itR;
 527                 SeqMap::iterator itL;
 528
 529                 for (int i = 0; i < left.size(); i++) {
 530
 531                         SeqMap currentLeft = left[i];    //example i = 3;   currentLeft is a map of 0 to the distance of sequence 3 to sequence 0,
 532                                                                                                 //                                                                              1 to the distance of sequence 3 to sequence 1,
 533                                                                                                 //                                                                              2 to the distance of sequence 3 to sequence 2.
 534                         SeqMap currentRight = right[i];         // same as left but with distances on the right side.
 535
 536                         for (int j = 0; j < i; j++) {
 537
 538                                 if (m->control_pressed) {  return 0; }
 539
 540                                 itL = currentLeft.find(j);
 541                                 itR = currentRight.find(j);
 542 //cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
 543 //cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
 544
 545                                 //if you can find this entry update the preferences
 546                                 if ((itL != currentLeft.end()) && (itR != currentRight.end())) {
 547
 548                                         if (!correction) {
 549                                                 pref[count][i].score += abs((itL->second - itR->second));
 550                                                 pref[count][j].score += abs((itL->second - itR->second));
 551 //cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
 552 //cout << "abs = " << abs((itL->second - itR->second)) << endl;
 553 //cout << i << " score = " << pref[i].score[1] << endl;
 554 //cout << j << " score = " << pref[j].score[1] << endl;
 555                                         }else {
 556                                                 pref[count][i].score += abs((sqrt(itL->second) - sqrt(itR->second)));
 557                                                 pref[count][j].score += abs((sqrt(itL->second) - sqrt(itR->second)));
 558 //cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
 559 //cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
 560 //cout << i << " score = " << pref[i].score[1] << endl;
 561 //cout << j << " score = " << pref[j].score[1] << endl;
 562                                         }
 563 //cout << "pref[" << i << "].closestLeft[1] = " <<      pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;
 564                                         //are you the closest left sequence
 565                                         if (itL->second < pref[count][i].closestLeft) {
 566
 567                                                 pref[count][i].closestLeft = itL->second;
 568                                                 pref[count][i].leftParent = seqs[j]->getName();
 569 //cout << "updating closest left to " << pref[i].leftParent[1] << endl;
 570                                         }
 571 //cout << "pref[" << j << "].closestLeft[1] = " <<      pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;
 572                                         if (itL->second < pref[count][j].closestLeft) {
 573                                                 pref[count][j].closestLeft = itL->second;
 574                                                 pref[count][j].leftParent = seqs[i]->getName();
 575 //cout << "updating closest left to " << pref[j].leftParent[1] << endl;
 576                                         }
 577
 578                                         //are you the closest right sequence
 579                                         if (itR->second < pref[count][i].closestRight) {
 580                                                 pref[count][i].closestRight = itR->second;
 581                                                 pref[count][i].rightParent = seqs[j]->getName();
 582                                         }
 583                                         if (itR->second < pref[count][j].closestRight) {
 584                                                 pref[count][j].closestRight = itR->second;
 585                                                 pref[count][j].rightParent = seqs[i]->getName();
 586                                         }
 587
 588                                 }
 589                         }
 590
 591                 }
 592
 593
 594                 return 1;
 595
 596         }
 597         catch(exception& e) {
 598                 m->errorOut(e, "Bellerophon", "generatePreferences");
 599                 exit(1);
 600         }
 601 }
 602 /**************************************************************************************************/
 603 vector<Preference> Bellerophon::getBestPref() {
 604         try {
 605
 606                 vector<Preference> best;
 607
 608                 //for each sequence
 609                 for (int i = 0; i < numSeqs; i++) {
 610
 611                         //set best pref score to first one
 612                         Preference temp = pref[0][i];
 613
 614                         if (m->control_pressed) { return best;  }
 615
 616                         //for each window
 617                         for (int j = 1; j < pref.size(); j++) {
 618
 619                                 //is this a better score
 620                                 if (pref[j][i].score > temp.score) {    temp = pref[j][i];              }
 621                         }
 622
 623                         best.push_back(temp);
 624                 }
 625
 626                 //rank preference score to eachother
 627                 float dme = 0.0;
 628                 float expectedPercent = 1 / (float) (best.size());
 629
 630                 for (int i = 0; i < best.size(); i++) {  dme += best[i].score;  }
 631
 632                 for (int i = 0; i < best.size(); i++) {
 633
 634                         if (m->control_pressed) { return best; }
 635
 636                         //gives the actual percentage of the dme this seq adds
 637                         best[i].score = best[i].score / dme;
 638
 639                         //how much higher or lower is this than expected
 640                         best[i].score = best[i].score / expectedPercent;
 641
 642                 }
 643
 644                 //sort Preferences highest to lowest
 645                 sort(best.begin(), best.end(), comparePref);
 646
 647                 return best;
 648         }
 649         catch(exception& e) {
 650                 m->errorOut(e, "Bellerophon", "getBestPref");
 651                 exit(1);
 652         }
 653 }
 654 /**************************************************************************************************/
 655 int Bellerophon::writePrefs(string file, linePair tempLine) {
 656         try {
 657
 658                 ofstream outTemp;
 659                 openOutputFile(file, outTemp);
 660
 661                 //lets you know what part of the pref matrix you are writing
 662                 outTemp << tempLine.start << '\t' << tempLine.num << endl;
 663
 664                 for (int i = tempLine.start; i < (tempLine.start + tempLine.num); i++) {
 665
 666                         for (int j = 0; j < numSeqs; j++) {
 667
 668                                 if (m->control_pressed) { outTemp.close(); remove(file.c_str()); return 0; }
 669
 670                                 outTemp << pref[i][j].name << '\t' << pref[i][j].leftParent << '\t' << pref[i][j].rightParent << '\t';
 671                                 outTemp << pref[i][j].score << '\t' << pref[i][j].closestLeft << '\t' << pref[i][j].closestRight << '\t' << pref[i][j].midpoint <<  endl;
 672                         }
 673                 }
 674
 675                 outTemp.close();
 676
 677                 return 0;
 678         }
 679         catch(exception& e) {
 680                 m->errorOut(e, "Bellerophon", "writePrefs");
 681                 exit(1);
 682         }
 683 }
 684 /**************************************************************************************************/
 685 int Bellerophon::readPrefs(string file) {
 686         try {
 687
 688                 ifstream inTemp;
 689                 openInputFile(file, inTemp);
 690
 691                 int start, num;
 692
 693                 //lets you know what part of the pref matrix you are writing
 694                 inTemp >> start >> num;  gobble(inTemp);
 695
 696                 for (int i = start; i < num; i++) {
 697
 698                         for (int j = 0; j < numSeqs; j++) {
 699
 700                                 if (m->control_pressed) { inTemp.close(); remove(file.c_str()); return 0; }
 701
 702                                 inTemp >> pref[i][j].name >> pref[i][j].leftParent >> pref[i][j].rightParent;
 703                                 inTemp >> pref[i][j].score >> pref[i][j].closestLeft >> pref[i][j].closestRight >> pref[i][j].midpoint;
 704                                 gobble(inTemp);
 705                         }
 706                 }
 707
 708                 inTemp.close();
 709
 710                 remove(file.c_str());
 711
 712                 return 0;
 713         }
 714         catch(exception& e) {
 715                 m->errorOut(e, "Bellerophon", "writePrefs");
 716                 exit(1);
 717         }
 718 }
 719 /**************************************************************************************************/
 720 vector<string> Bellerophon::getBestWindow(linePair line) {
 721         try {
 722
 723                 vector<string> best;
 724
 725                 //for each sequence
 726                 for (int i = 0; i < numSeqs; i++) {
 727
 728                         //set best pref score to first one
 729                         Preference temp = pref[line.start][i];
 730
 731                         if (m->control_pressed) { return best;  }
 732
 733                         //for each window
 734                         for (int j = (line.start+1); j < (line.start+line.num); j++) {
 735
 736                                 //is this a better score
 737                                 if (pref[j][i].score > temp.score) {    temp = pref[j][i];              }
 738                         }
 739
 740                         string tempString = temp.name + '\t' + temp.leftParent + '\t' + temp.rightParent + '\t' + toString(temp.score);
 741                         best.push_back(tempString);
 742                 }
 743
 744                 return best;
 745
 746         }
 747         catch(exception& e) {
 748                 m->errorOut(e, "Bellerophon", "getBestWindow");
 749                 exit(1);
 750         }
 751 }
 752 /**************************************************************************************************/
 753 int Bellerophon::fillPref(int process, vector<string>& best) {
 754         try {
 755                 //figure out where you start so you can put the best scores there
 756                 int numSeqsPerProcessor = iters / processors;
 757                 int start = process * numSeqsPerProcessor;
 758
 759                 for (int i = 0; i < best.size(); i++) {
 760
 761                         if (m->control_pressed) { return 0;  }
 762
 763                         istringstream iss (best[i],istringstream::in);
 764
 765                         string tempScore;
 766                         iss >> pref[start][i].name >> pref[start][i].leftParent >> pref[start][i].rightParent >> tempScore;
 767                         convert(tempScore, pref[start][i].score);
 768                 }
 769
 770                 return 0;
 771         }
 772         catch(exception& e) {
 773                 m->errorOut(e, "Bellerophon", "fillPref");
 774                 exit(1);
 775         }
 776 }
 777
 778 /**************************************************************************************************/
 779