maligner.cpp

   1 /*
   2  *  maligner.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/23/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "maligner.h"
  11
  12 /***********************************************************************/ //int num, int match, int misMatch, , string mode, Database* dataLeft, Database* dataRight
  13 Maligner::Maligner(vector<Sequence*> temp, int match, int misMatch, float div, int ms, int minCov) : db(temp), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov) {
  14                         //numWanted(num),  , searchMethod(mode), databaseLeft(dataLeft), databaseRight(dataRight)
  15
  16                         m = MothurOut::getInstance();
  17
  18 }
  19 /***********************************************************************/
  20 string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
  21         try {
  22
  23                 outputResults.clear();
  24
  25                 //make copy so trimming doesn't destroy query from calling class - remember to deallocate
  26                 query = new Sequence(q->getName(), q->getAligned());
  27
  28                 string chimera;
  29
  30                 //copy refSeqs so that filter does not effect original
  31                 for(int i = 0; i < db.size(); i++) {
  32                         Sequence* newSeq = new Sequence(db[i]->getName(), db[i]->getAligned());
  33                         refSeqs.push_back(newSeq);
  34                 }
  35
  36                 refSeqs = minCoverageFilter(refSeqs);
  37
  38                 if (refSeqs.size() < 2)  {
  39                         for (int i = 0; i < refSeqs.size(); i++) {  delete refSeqs[i];  }
  40                         percentIdenticalQueryChimera = 0.0;
  41                         return "unknown";
  42                 }
  43
  44                 int chimeraPenalty = computeChimeraPenalty();
  45
  46                 //fills outputResults
  47                 chimera = chimeraMaligner(chimeraPenalty, decalc);
  48
  49                 if (m->control_pressed) { return chimera;  }
  50
  51                 //free memory
  52                 delete query;
  53
  54                 for (int i = 0; i < refSeqs.size(); i++) {  delete refSeqs[i];  }
  55
  56                 return chimera;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "Maligner", "getResults");
  60                 exit(1);
  61         }
  62 }
  63 /***********************************************************************/
  64 string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
  65         try {
  66
  67                 string chimera;
  68
  69                 //trims seqs to first non gap char in all seqs and last non gap char in all seqs
  70                 spotMap = decalc->trimSeqs(query, refSeqs);
  71
  72                 //you trimmed the whole sequence, skip
  73                 if (query->getAligned() == "") { return "no"; }
  74
  75                 vector<Sequence*> temp = refSeqs;
  76                 temp.push_back(query);
  77
  78                 verticalFilter(temp);
  79
  80                 //for (int i = 0; i < refSeqs.size(); i++) { cout << refSeqs[i]->getName() << endl ; }//<< refSeqs[i]->getAligned() << endl
  81
  82                 vector< vector<score_struct> > matrix = buildScoreMatrix(query->getAligned().length(), refSeqs.size()); //builds and initializes
  83
  84                 if (m->control_pressed) { return chimera;  }
  85
  86                 fillScoreMatrix(matrix, refSeqs, chimeraPenalty);
  87
  88                 vector<score_struct> path = extractHighestPath(matrix);
  89
  90                 if (m->control_pressed) { return chimera;  }
  91
  92                 vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
  93
  94                 if (trace.size() > 1) {         chimera = "yes";        }
  95                 else { chimera = "no";  return chimera; }
  96
  97                 int traceStart = path[0].col;
  98                 int traceEnd = path[path.size()-1].col;
  99                 string queryInRange = query->getAligned();
 100                 queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));
 101
 102                 string chimeraSeq = constructChimericSeq(trace, refSeqs);
 103
 104                 percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
 105
 106         /*
 107                 vector<trace_struct> trace = extractHighestPath(matrix);
 108
 109                 //cout << "traces\n";
 110                 //for(int i=0;i<trace.size();i++){
 111                 //      cout << trace[i].col << '\t' << trace[i].oldCol << '\t' << refSeqs[trace[i].row]->getName() << endl;
 112                 //}
 113
 114                 if (trace.size() > 1) {         chimera = "yes";        }
 115                 else { chimera = "no";  return chimera; }
 116
 117                 int traceStart = trace[0].col;
 118                 int traceEnd = trace[trace.size()-1].oldCol;
 119                 string queryInRange = query->getAligned();
 120                 queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));*/
 121
 122                 if (m->control_pressed) { return chimera;  }
 123
 124                 //save output results
 125                 for (int i = 0; i < trace.size(); i++) {
 126                         int regionStart = trace[i].col;
 127                         int regionEnd = trace[i].oldCol;
 128                         int seqIndex = trace[i].row;
 129
 130                         results temp;
 131
 132                         temp.parent = refSeqs[seqIndex]->getName();
 133                         temp.parentAligned = db[seqIndex]->getAligned();
 134                         temp.nastRegionStart = spotMap[regionStart];
 135                         temp.nastRegionEnd = spotMap[regionEnd];
 136                         temp.regionStart = regionStart;
 137                         temp.regionEnd = regionEnd;
 138
 139                         string parentInRange = refSeqs[seqIndex]->getAligned();
 140                         parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart));
 141
 142                         temp.queryToParent = computePercentID(queryInRange, parentInRange);
 143                         temp.divR = (percentIdenticalQueryChimera / temp.queryToParent);
 144
 145                         string queryInRegion = query->getAligned();
 146                         queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart));
 147
 148                         string parentInRegion = refSeqs[seqIndex]->getAligned();
 149                         parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart));
 150
 151                         temp.queryToParentLocal = computePercentID(queryInRegion, parentInRegion);
 152
 153                         //cout << query->getName() << '\t' << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << ", " <<  temp.divR << endl;
 154
 155                         outputResults.push_back(temp);
 156                 }
 157
 158                 return chimera;
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "Maligner", "chimeraMaligner");
 162                 exit(1);
 163         }
 164 }
 165 /***********************************************************************/
 166 //removes top matches that do not have minimum coverage with query.
 167 vector<Sequence*> Maligner::minCoverageFilter(vector<Sequence*> ref){
 168         try {
 169                 vector<Sequence*> newRefs;
 170
 171                 string queryAligned = query->getAligned();
 172
 173                 for (int i = 0; i < ref.size(); i++) {
 174
 175                         string refAligned = ref[i]->getAligned();
 176
 177                         int numBases = 0;
 178                         int numCovered = 0;
 179
 180                         //calculate coverage
 181                         for (int j = 0; j < queryAligned.length(); j++) {
 182
 183                                 if (isalpha(queryAligned[j])) {
 184                                         numBases++;
 185
 186                                         if (isalpha(refAligned[j])) {
 187                                                 numCovered++;
 188                                         }
 189                                 }
 190                         }
 191
 192                         int coverage = ((numCovered/(float)numBases)*100);
 193
 194                         //if coverage above minimum
 195                         if (coverage > minCoverage) {
 196                                 newRefs.push_back(ref[i]);
 197                         }else {
 198                                 delete ref[i];
 199                         }
 200                 }
 201
 202                 return newRefs;
 203         }
 204         catch(exception& e) {
 205                 m->errorOut(e, "Maligner", "minCoverageFilter");
 206                 exit(1);
 207         }
 208 }
 209 /***********************************************************************/
 210 // a breakpoint should yield fewer mismatches than this number with respect to the best parent sequence.
 211 int Maligner::computeChimeraPenalty() {
 212         try {
 213
 214                 int numAllowable = ((1.0 - (1.0/minDivR)) * query->getNumBases());
 215
 216 //              if(numAllowable < 1){   numAllowable = 1;       }
 217
 218                 int penalty = int(numAllowable + 1) * misMatchPenalty;
 219
 220                 return penalty;
 221
 222         }
 223         catch(exception& e) {
 224                 m->errorOut(e, "Maligner", "computeChimeraPenalty");
 225                 exit(1);
 226         }
 227 }
 228 /***********************************************************************/
 229 //this is a vertical filter
 230 void Maligner::verticalFilter(vector<Sequence*> seqs) {
 231         try {
 232                 vector<int> gaps;       gaps.resize(query->getAligned().length(), 0);
 233
 234                 string filterString = (string(query->getAligned().length(), '1'));
 235
 236                 //for each sequence
 237                 for (int i = 0; i < seqs.size(); i++) {
 238
 239                         string seqAligned = seqs[i]->getAligned();
 240
 241                         for (int j = 0; j < seqAligned.length(); j++) {
 242                                 //if this spot is a gap
 243                                 if ((seqAligned[j] == '-') || (seqAligned[j] == '.'))   {       gaps[j]++;      }
 244                         }
 245                 }
 246
 247                 //zero out spot where all sequences have blanks
 248                 int numColRemoved = 0;
 249                 for(int i = 0; i < seqs[0]->getAligned().length(); i++){
 250                         if(gaps[i] == seqs.size())      {       filterString[i] = '0';  numColRemoved++;  }
 251                 }
 252
 253                 map<int, int> newMap;
 254                 //for each sequence
 255                 for (int i = 0; i < seqs.size(); i++) {
 256
 257                         string seqAligned = seqs[i]->getAligned();
 258                         string newAligned = "";
 259                         int count = 0;
 260
 261                         for (int j = 0; j < seqAligned.length(); j++) {
 262                                 //if this spot is not a gap
 263                                 if (filterString[j] == '1') {
 264                                         newAligned += seqAligned[j];
 265                                         newMap[count] = spotMap[j];
 266                                         count++;
 267                                 }
 268                         }
 269
 270                         seqs[i]->setAligned(newAligned);
 271                 }
 272
 273                 spotMap = newMap;
 274         }
 275         catch(exception& e) {
 276                 m->errorOut(e, "Maligner", "verticalFilter");
 277                 exit(1);
 278         }
 279 }
 280 //***************************************************************************************************************
 281 vector< vector<score_struct> > Maligner::buildScoreMatrix(int cols, int rows) {
 282         try{
 283
 284                 vector< vector<score_struct> > m(rows);
 285
 286                 for (int i = 0; i < rows; i++) {
 287                         for (int j = 0; j < cols; j++) {
 288
 289                                 //initialize each cell
 290                                 score_struct temp;
 291                                 temp.prev = -1;
 292                                 temp.score = -9999999;
 293                                 temp.col = j;
 294                                 temp.row = i;
 295
 296                                 m[i].push_back(temp);
 297                         }
 298                 }
 299
 300                 return m;
 301         }
 302         catch(exception& e) {
 303                 m->errorOut(e, "Maligner", "buildScoreMatrix");
 304                 exit(1);
 305         }
 306 }
 307
 308 //***************************************************************************************************************
 309
 310 void Maligner::fillScoreMatrix(vector<vector<score_struct> >& ms, vector<Sequence*> seqs, int penalty) {
 311         try{
 312
 313                 //get matrix dimensions
 314                 int numCols = query->getAligned().length();
 315                 int numRows = seqs.size();
 316
 317                 //initialize first col
 318                 string queryAligned = query->getAligned();
 319                 for (int i = 0; i < numRows; i++) {
 320                         string subjectAligned = seqs[i]->getAligned();
 321
 322                         //are you both gaps?
 323                         if ((!isalpha(queryAligned[0])) && (!isalpha(subjectAligned[0]))) {
 324                                 ms[i][0].score = 0;
 325 //                              ms[i][0].mismatches = 0;
 326                         }else if (queryAligned[0] == subjectAligned[0])  { //|| subjectAligned[0] == 'N')
 327                                 ms[i][0].score = matchScore;
 328 //                              ms[i][0].mismatches = 0;
 329                         }else{
 330                                 ms[i][0].score = 0;
 331 //                              ms[i][0].mismatches = 1;
 332                         }
 333                 }
 334
 335                 //fill rest of matrix
 336                 for (int j = 1; j < numCols; j++) {  //iterate through matrix columns
 337
 338                         for (int i = 0; i < numRows; i++) {  //iterate through matrix rows
 339
 340                                 string subjectAligned = seqs[i]->getAligned();
 341
 342                                 int matchMisMatchScore = 0;
 343                                 //are you both gaps?
 344                                 if ((!isalpha(queryAligned[j])) && (!isalpha(subjectAligned[j]))) {
 345                                         //leave the same
 346                                 }else if ((toupper(queryAligned[j]) == 'N') || (toupper(subjectAligned[j]) == 'N')) {
 347                                         //matchMisMatchScore = matchScore;
 348                                         //leave the same
 349                                 }else if (queryAligned[j] == subjectAligned[j]) {
 350                                         matchMisMatchScore = matchScore;
 351 //                                      ms[i][j].mismatches = ms[i][j-1].mismatches;
 352                                 }else if (queryAligned[j] != subjectAligned[j]) {
 353                                         matchMisMatchScore = misMatchPenalty;
 354 //                                      ms[i][j].mismatches = ms[i][j-1].mismatches + 1;
 355                                 }
 356
 357                                 //compute score based on previous columns scores
 358                                 for (int prevIndex = 0; prevIndex < numRows; prevIndex++) { //iterate through rows
 359
 360                                         int sumScore = matchMisMatchScore + ms[prevIndex][j-1].score;
 361
 362                                         //you are not at yourself
 363                                         if (prevIndex != i) {   sumScore += penalty;    }
 364                                         if (sumScore < 0)       {       sumScore = 0;                   }
 365
 366                                         if (sumScore > ms[i][j].score) {
 367                                                 ms[i][j].score = sumScore;
 368                                                 ms[i][j].prev = prevIndex;
 369                                         }
 370                                 }
 371                         }
 372                 }
 373
 374         /*      for(int i=0;i<numRows;i++){
 375                         cout << seqs[i]->getName();
 376                         for(int j=0;j<numCols;j++){
 377                                 cout << '\t' << ms[i][j].mismatches;
 378                         }
 379                         cout << endl;
 380                 }
 381                 cout << endl;*/
 382                 /*cout << numRows << '\t' << numCols << endl;
 383                 for(int i=0;i<numRows;i++){
 384                         cout << seqs[i]->getName() << endl << seqs[i]->getAligned() << endl << endl;
 385                         if ((seqs[i]->getName() == "S000003470") || (seqs[i]->getName() == "S000383265") || (seqs[i]->getName() == "7000004128191054")) {
 386                         for(int j=0;j<numCols;j++){
 387                                 cout << '\t' << ms[i][j].score;
 388                         }
 389                         cout << endl;
 390                         }
 391                 }
 392                 cout << endl;*/
 393                 /*for(int i=0;i<numRows;i++){
 394                         cout << seqs[i]->getName();
 395                         for(int j=0;j<numCols;j++){
 396                                 cout << '\t' << ms[i][j].prev;
 397                         }
 398                         cout << endl;
 399                 }*/
 400
 401
 402         }
 403         catch(exception& e) {
 404                 m->errorOut(e, "Maligner", "fillScoreMatrix");
 405                 exit(1);
 406         }
 407 }
 408 //***************************************************************************************************************
 409 vector<score_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
 410         try {
 411
 412                 //get matrix dimensions
 413                 int numCols = query->getAligned().length();
 414                 int numRows = ms.size();
 415
 416
 417                 //find highest score scoring matrix
 418                 score_struct highestStruct;
 419                 int highestScore = 0;
 420
 421                 for (int i = 0; i < numRows; i++) {
 422                         for (int j = 0; j < numCols; j++) {
 423                                 if (ms[i][j].score > highestScore) {
 424                                         highestScore = ms[i][j].score;
 425                                         highestStruct = ms[i][j];
 426                                 }
 427                         }
 428                 }
 429
 430                 vector<score_struct> path;
 431
 432                 int rowIndex = highestStruct.row;
 433                 int pos = highestStruct.col;
 434                 int score = highestStruct.score;
 435
 436                 while (pos >= 0 && score > 0) {
 437                         score_struct temp = ms[rowIndex][pos];
 438                         score = temp.score;
 439
 440                         if (score > 0) {        path.push_back(temp);   }
 441
 442                         rowIndex = temp.prev;
 443                         pos--;
 444                 }
 445
 446                 reverse(path.begin(), path.end());
 447
 448                 return path;
 449
 450         }
 451         catch(exception& e) {
 452                 m->errorOut(e, "Maligner", "extractHighestPath");
 453                 exit(1);
 454         }
 455 }
 456 //***************************************************************************************************************
 457 vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path, vector<Sequence*> seqs) {
 458         try {
 459                 vector<trace_struct> trace;
 460
 461                 int region_index = path[0].row;
 462                 int region_start = path[0].col;
 463
 464                 for (int i = 1; i < path.size(); i++) {
 465
 466                         int next_region_index = path[i].row;
 467
 468                         if (next_region_index != region_index) {
 469
 470                                 // add trace region
 471                                 int col_index = path[i].col;
 472                                 trace_struct temp;
 473                                 temp.col = region_start;
 474                                 temp.oldCol = col_index-1;
 475                                 temp.row = region_index;
 476
 477                                 trace.push_back(temp);
 478
 479                                 region_index = path[i].row;
 480                                 region_start = col_index;
 481                         }
 482                 }
 483
 484                 // get last one
 485                 trace_struct temp;
 486                 temp.col = region_start;
 487                 temp.oldCol = path[path.size()-1].col;
 488                 temp.row = region_index;
 489                 trace.push_back(temp);
 490
 491                 return trace;
 492
 493         }
 494         catch(exception& e) {
 495                 m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
 496                 exit(1);
 497         }
 498 }
 499
 500 /***************************************************************************************************************
 501
 502 vector<trace_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
 503         try {
 504
 505
 506                 //get matrix dimensions
 507                 int numCols = query->getAligned().length();
 508                 int numRows = ms.size();
 509
 510
 511                 //find highest score scoring matrix
 512                 vector<score_struct> highestStruct;
 513                 int highestScore = 0;
 514
 515                 for (int i = 0; i < numRows; i++) {
 516                         for (int j = 0; j < numCols; j++) {
 517                                 if (ms[i][j].score > highestScore) {
 518                                         highestScore = ms[i][j].score;
 519                                         highestStruct.resize(0);
 520                                         highestStruct.push_back(ms[i][j]);
 521                                 }
 522                                 else if(ms[i][j].score == highestScore){
 523                                         highestStruct.push_back(ms[i][j]);
 524                                 }
 525                         }
 526                 }
 527
 528                 //cout << endl << highestScore << '\t' << highestStruct.size() << '\t' << highestStruct[0].row << endl;
 529
 530                 vector<trace_struct> maxTrace;
 531                 double maxPercentIdenticalQueryAntiChimera = 0;
 532
 533                 for(int i=0;i<highestStruct.size();i++){
 534
 535                         vector<score_struct> path;
 536
 537                         int rowIndex = highestStruct[i].row;
 538                         int pos = highestStruct[i].col;
 539                         int score = highestStruct[i].score;
 540
 541                         while (pos >= 0 && score > 0) {
 542                                 score_struct temp = ms[rowIndex][pos];
 543                                 score = temp.score;
 544
 545                                 if (score > 0) {        path.push_back(temp);   }
 546
 547                                 rowIndex = temp.prev;
 548                                 pos--;
 549                         }
 550
 551                         reverse(path.begin(), path.end());
 552
 553                         vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
 554
 555                         //cout << "traces\n";
 556                         //for(int j=0;j<trace.size();j++){
 557                         //      cout << trace[j].col << '\t' << trace[j].oldCol << '\t' << refSeqs[trace[j].row]->getName() << endl;
 558                         //}
 559
 560                         int traceStart = path[0].col;
 561                         int traceEnd = path[path.size()-1].col;
 562 //                      cout << "traceStart/End\t" << traceStart << '\t' << traceEnd << endl;
 563
 564                         string queryInRange = query->getAligned();
 565                         queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
 566 //                      cout << "here" << endl;
 567                         string chimeraSeq = constructChimericSeq(trace, refSeqs);
 568                         string antiChimeraSeq = constructAntiChimericSeq(trace, refSeqs);
 569
 570                         percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
 571                         double percentIdenticalQueryAntiChimera = computePercentID(queryInRange, antiChimeraSeq);
 572 //                      cout << i << '\t' << percentIdenticalQueryChimera << '\t' << percentIdenticalQueryAntiChimera << endl;
 573
 574                         if(percentIdenticalQueryAntiChimera > maxPercentIdenticalQueryAntiChimera){
 575                                 maxPercentIdenticalQueryAntiChimera = percentIdenticalQueryAntiChimera;
 576                                 maxTrace = trace;
 577                         }
 578                 }
 579 //              cout << maxPercentIdenticalQueryAntiChimera << endl;
 580                 return maxTrace;
 581
 582
 583         }
 584         catch(exception& e) {
 585                 m->errorOut(e, "Maligner", "extractHighestPath");
 586                 exit(1);
 587         }
 588 }
 589
 590 //***************************************************************************************************************
 591
 592 vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path, vector<Sequence*> seqs) {
 593         try {
 594                 vector<trace_struct> trace;
 595
 596                 int region_index = path[0].row;
 597                 int region_start = path[0].col;
 598
 599                 for (int i = 1; i < path.size(); i++) {
 600
 601                         int next_region_index = path[i].row;
 602
 603                         if (next_region_index != region_index) {
 604
 605                                 // add trace region
 606                                 int col_index = path[i].col;
 607                                 trace_struct temp;
 608                                 temp.col = region_start;
 609                                 temp.oldCol = col_index-1;
 610                                 temp.row = region_index;
 611
 612                                 trace.push_back(temp);
 613
 614                                 region_index = path[i].row;
 615                                 region_start = col_index;
 616                         }
 617                 }
 618
 619                 // get last one
 620                 trace_struct temp;
 621                 temp.col = region_start;
 622                 temp.oldCol = path[path.size()-1].col;
 623                 temp.row = region_index;
 624                 trace.push_back(temp);
 625
 626 //              cout << endl;
 627 //              cout << trace.size() << endl;
 628 //              for(int i=0;i<trace.size();i++){
 629 //                      cout << seqs[trace[i].row]->getName() << endl;
 630 //              }
 631 //              cout << endl;
 632
 633                 return trace;
 634
 635         }
 636         catch(exception& e) {
 637                 m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
 638                 exit(1);
 639         }
 640 }
 641 */
 642 //***************************************************************************************************************
 643
 644 string Maligner::constructChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
 645         try {
 646                 string chimera = "";
 647
 648                 for (int i = 0; i < trace.size(); i++) {
 649 //                      cout << i << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
 650
 651                         string seqAlign = seqs[trace[i].row]->getAligned();
 652                         seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
 653                         chimera += seqAlign;
 654                 }
 655
 656                 if (chimera != "") { chimera = chimera.substr(0, (chimera.length()-1)); }
 657                 return chimera;
 658         }
 659         catch(exception& e) {
 660                 m->errorOut(e, "Maligner", "constructChimericSeq");
 661                 exit(1);
 662         }
 663 }
 664
 665 //***************************************************************************************************************
 666
 667 string Maligner::constructAntiChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
 668         try {
 669                 string antiChimera = "";
 670
 671                 for (int i = 0; i < trace.size(); i++) {
 672 //                      cout << i << '\t' << (trace.size() - i - 1) << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
 673
 674                         int oppositeIndex = trace.size() - i - 1;
 675
 676                         string seqAlign = seqs[trace[oppositeIndex].row]->getAligned();
 677                         seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
 678                         antiChimera += seqAlign;
 679                 }
 680
 681                 return antiChimera;
 682         }
 683         catch(exception& e) {
 684                 m->errorOut(e, "Maligner", "constructChimericSeq");
 685                 exit(1);
 686         }
 687 }
 688
 689 //***************************************************************************************************************
 690 float Maligner::computePercentID(string queryAlign, string chimera) {
 691         try {
 692
 693                 if (queryAlign.length() != chimera.length()) {
 694                         m->mothurOut("Error, alignment strings are of different lengths: "); m->mothurOutEndLine();
 695                         m->mothurOut(toString(queryAlign.length())); m->mothurOutEndLine();
 696                         m->mothurOut(toString(chimera.length())); m->mothurOutEndLine();
 697                         return -1.0;
 698                 }
 699
 700                 int numIdentical = 0;
 701                 int countA = 0;
 702                 int countB = 0;
 703                 for (int i = 0; i < queryAlign.length(); i++) {
 704                         if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
 705                                 ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
 706                         else {
 707
 708                                 bool charA = false; bool charB = false;
 709                                 if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
 710                                 if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
 711
 712                                 if (charA || charB) {
 713
 714                                         if (charA) { countA++; }
 715                                         if (charB) { countB++; }
 716
 717                                         if (queryAlign[i] == chimera[i]) {
 718                                                 numIdentical++;
 719                                         }
 720                                 }
 721                         }
 722                 }
 723
 724                 float numBases = (countA + countB) /(float) 2;
 725
 726                 if (numBases == 0) { return 0; }
 727
 728                 float percentIdentical = (numIdentical/(float)numBases) * 100;
 729
 730                 return percentIdentical;
 731
 732         }
 733         catch(exception& e) {
 734                 m->errorOut(e, "Maligner", "computePercentID");
 735                 exit(1);
 736         }
 737 }
 738 //***************************************************************************************************************