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 << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << endl;
 154                         outputResults.push_back(temp);
 155                 }
 156
 157                 return chimera;
 158         }
 159         catch(exception& e) {
 160                 m->errorOut(e, "Maligner", "chimeraMaligner");
 161                 exit(1);
 162         }
 163 }
 164 /***********************************************************************/
 165 //removes top matches that do not have minimum coverage with query.
 166 vector<Sequence*> Maligner::minCoverageFilter(vector<Sequence*> ref){
 167         try {
 168                 vector<Sequence*> newRefs;
 169
 170                 string queryAligned = query->getAligned();
 171
 172                 for (int i = 0; i < ref.size(); i++) {
 173
 174                         string refAligned = ref[i]->getAligned();
 175
 176                         int numBases = 0;
 177                         int numCovered = 0;
 178
 179                         //calculate coverage
 180                         for (int j = 0; j < queryAligned.length(); j++) {
 181
 182                                 if (isalpha(queryAligned[j])) {
 183                                         numBases++;
 184
 185                                         if (isalpha(refAligned[j])) {
 186                                                 numCovered++;
 187                                         }
 188                                 }
 189                         }
 190
 191                         int coverage = ((numCovered/(float)numBases)*100);
 192
 193                         //if coverage above minimum
 194                         if (coverage > minCoverage) {
 195                                 newRefs.push_back(ref[i]);
 196                         }else {
 197                                 delete ref[i];
 198                         }
 199                 }
 200
 201                 return newRefs;
 202         }
 203         catch(exception& e) {
 204                 m->errorOut(e, "Maligner", "minCoverageFilter");
 205                 exit(1);
 206         }
 207 }
 208 /***********************************************************************/
 209 // a breakpoint should yield fewer mismatches than this number with respect to the best parent sequence.
 210 int Maligner::computeChimeraPenalty() {
 211         try {
 212
 213                 int numAllowable = ((1.0 - (1.0/minDivR)) * query->getNumBases());
 214
 215 //              if(numAllowable < 1){   numAllowable = 1;       }
 216
 217                 int penalty = int(numAllowable + 1) * misMatchPenalty;
 218
 219                 return penalty;
 220
 221         }
 222         catch(exception& e) {
 223                 m->errorOut(e, "Maligner", "computeChimeraPenalty");
 224                 exit(1);
 225         }
 226 }
 227 /***********************************************************************/
 228 //this is a vertical filter
 229 void Maligner::verticalFilter(vector<Sequence*> seqs) {
 230         try {
 231                 vector<int> gaps;       gaps.resize(query->getAligned().length(), 0);
 232
 233                 string filterString = (string(query->getAligned().length(), '1'));
 234
 235                 //for each sequence
 236                 for (int i = 0; i < seqs.size(); i++) {
 237
 238                         string seqAligned = seqs[i]->getAligned();
 239
 240                         for (int j = 0; j < seqAligned.length(); j++) {
 241                                 //if this spot is a gap
 242                                 if ((seqAligned[j] == '-') || (seqAligned[j] == '.'))   {       gaps[j]++;      }
 243                         }
 244                 }
 245
 246                 //zero out spot where all sequences have blanks
 247                 int numColRemoved = 0;
 248                 for(int i = 0; i < seqs[0]->getAligned().length(); i++){
 249                         if(gaps[i] == seqs.size())      {       filterString[i] = '0';  numColRemoved++;  }
 250                 }
 251
 252                 map<int, int> newMap;
 253                 //for each sequence
 254                 for (int i = 0; i < seqs.size(); i++) {
 255
 256                         string seqAligned = seqs[i]->getAligned();
 257                         string newAligned = "";
 258                         int count = 0;
 259
 260                         for (int j = 0; j < seqAligned.length(); j++) {
 261                                 //if this spot is not a gap
 262                                 if (filterString[j] == '1') {
 263                                         newAligned += seqAligned[j];
 264                                         newMap[count] = spotMap[j];
 265                                         count++;
 266                                 }
 267                         }
 268
 269                         seqs[i]->setAligned(newAligned);
 270                 }
 271
 272                 spotMap = newMap;
 273         }
 274         catch(exception& e) {
 275                 m->errorOut(e, "Maligner", "verticalFilter");
 276                 exit(1);
 277         }
 278 }
 279 //***************************************************************************************************************
 280 vector< vector<score_struct> > Maligner::buildScoreMatrix(int cols, int rows) {
 281         try{
 282
 283                 vector< vector<score_struct> > m(rows);
 284
 285                 for (int i = 0; i < rows; i++) {
 286                         for (int j = 0; j < cols; j++) {
 287
 288                                 //initialize each cell
 289                                 score_struct temp;
 290                                 temp.prev = -1;
 291                                 temp.score = -9999999;
 292                                 temp.col = j;
 293                                 temp.row = i;
 294
 295                                 m[i].push_back(temp);
 296                         }
 297                 }
 298
 299                 return m;
 300         }
 301         catch(exception& e) {
 302                 m->errorOut(e, "Maligner", "buildScoreMatrix");
 303                 exit(1);
 304         }
 305 }
 306
 307 //***************************************************************************************************************
 308
 309 void Maligner::fillScoreMatrix(vector<vector<score_struct> >& ms, vector<Sequence*> seqs, int penalty) {
 310         try{
 311
 312                 //get matrix dimensions
 313                 int numCols = query->getAligned().length();
 314                 int numRows = seqs.size();
 315
 316                 //initialize first col
 317                 string queryAligned = query->getAligned();
 318                 for (int i = 0; i < numRows; i++) {
 319                         string subjectAligned = seqs[i]->getAligned();
 320
 321                         //are you both gaps?
 322                         if ((!isalpha(queryAligned[0])) && (!isalpha(subjectAligned[0]))) {
 323                                 ms[i][0].score = 0;
 324 //                              ms[i][0].mismatches = 0;
 325                         }else if (queryAligned[0] == subjectAligned[0])  { //|| subjectAligned[0] == 'N')
 326                                 ms[i][0].score = matchScore;
 327 //                              ms[i][0].mismatches = 0;
 328                         }else{
 329                                 ms[i][0].score = 0;
 330 //                              ms[i][0].mismatches = 1;
 331                         }
 332                 }
 333
 334                 //fill rest of matrix
 335                 for (int j = 1; j < numCols; j++) {  //iterate through matrix columns
 336
 337                         for (int i = 0; i < numRows; i++) {  //iterate through matrix rows
 338
 339                                 string subjectAligned = seqs[i]->getAligned();
 340
 341                                 int matchMisMatchScore = 0;
 342                                 //are you both gaps?
 343                                 if ((!isalpha(queryAligned[j])) && (!isalpha(subjectAligned[j]))) {
 344                                         //leave the same
 345                                 }else if ((toupper(queryAligned[j]) == 'N') || (toupper(subjectAligned[j]) == 'N')) {
 346                                         //matchMisMatchScore = matchScore;
 347                                         //leave the same
 348                                 }else if (queryAligned[j] == subjectAligned[j]) {
 349                                         matchMisMatchScore = matchScore;
 350 //                                      ms[i][j].mismatches = ms[i][j-1].mismatches;
 351                                 }else if (queryAligned[j] != subjectAligned[j]) {
 352                                         matchMisMatchScore = misMatchPenalty;
 353 //                                      ms[i][j].mismatches = ms[i][j-1].mismatches + 1;
 354                                 }
 355
 356                                 //compute score based on previous columns scores
 357                                 for (int prevIndex = 0; prevIndex < numRows; prevIndex++) { //iterate through rows
 358
 359                                         int sumScore = matchMisMatchScore + ms[prevIndex][j-1].score;
 360
 361                                         //you are not at yourself
 362                                         if (prevIndex != i) {   sumScore += penalty;    }
 363                                         if (sumScore < 0)       {       sumScore = 0;                   }
 364
 365                                         if (sumScore > ms[i][j].score) {
 366                                                 ms[i][j].score = sumScore;
 367                                                 ms[i][j].prev = prevIndex;
 368                                         }
 369                                 }
 370                         }
 371                 }
 372
 373         /*      for(int i=0;i<numRows;i++){
 374                         cout << seqs[i]->getName();
 375                         for(int j=0;j<numCols;j++){
 376                                 cout << '\t' << ms[i][j].mismatches;
 377                         }
 378                         cout << endl;
 379                 }
 380                 cout << endl;*/
 381                 /*cout << numRows << '\t' << numCols << endl;
 382                 for(int i=0;i<numRows;i++){
 383                         cout << seqs[i]->getName() << endl << seqs[i]->getAligned() << endl << endl;
 384                         if ((seqs[i]->getName() == "S000003470") || (seqs[i]->getName() == "S000383265") || (seqs[i]->getName() == "7000004128191054")) {
 385                         for(int j=0;j<numCols;j++){
 386                                 cout << '\t' << ms[i][j].score;
 387                         }
 388                         cout << endl;
 389                         }
 390                 }
 391                 cout << endl;*/
 392                 /*for(int i=0;i<numRows;i++){
 393                         cout << seqs[i]->getName();
 394                         for(int j=0;j<numCols;j++){
 395                                 cout << '\t' << ms[i][j].prev;
 396                         }
 397                         cout << endl;
 398                 }*/
 399
 400
 401         }
 402         catch(exception& e) {
 403                 m->errorOut(e, "Maligner", "fillScoreMatrix");
 404                 exit(1);
 405         }
 406 }
 407 //***************************************************************************************************************
 408 vector<score_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
 409         try {
 410
 411                 //get matrix dimensions
 412                 int numCols = query->getAligned().length();
 413                 int numRows = ms.size();
 414
 415
 416                 //find highest score scoring matrix
 417                 score_struct highestStruct;
 418                 int highestScore = 0;
 419
 420                 for (int i = 0; i < numRows; i++) {
 421                         for (int j = 0; j < numCols; j++) {
 422                                 if (ms[i][j].score > highestScore) {
 423                                         highestScore = ms[i][j].score;
 424                                         highestStruct = ms[i][j];
 425                                 }
 426                         }
 427                 }
 428
 429                 vector<score_struct> path;
 430
 431                 int rowIndex = highestStruct.row;
 432                 int pos = highestStruct.col;
 433                 int score = highestStruct.score;
 434
 435                 while (pos >= 0 && score > 0) {
 436                         score_struct temp = ms[rowIndex][pos];
 437                         score = temp.score;
 438
 439                         if (score > 0) {        path.push_back(temp);   }
 440
 441                         rowIndex = temp.prev;
 442                         pos--;
 443                 }
 444
 445                 reverse(path.begin(), path.end());
 446
 447                 return path;
 448
 449         }
 450         catch(exception& e) {
 451                 m->errorOut(e, "Maligner", "extractHighestPath");
 452                 exit(1);
 453         }
 454 }
 455 //***************************************************************************************************************
 456 vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path, vector<Sequence*> seqs) {
 457         try {
 458                 vector<trace_struct> trace;
 459
 460                 int region_index = path[0].row;
 461                 int region_start = path[0].col;
 462
 463                 for (int i = 1; i < path.size(); i++) {
 464
 465                         int next_region_index = path[i].row;
 466
 467                         if (next_region_index != region_index) {
 468
 469                                 // add trace region
 470                                 int col_index = path[i].col;
 471                                 trace_struct temp;
 472                                 temp.col = region_start;
 473                                 temp.oldCol = col_index-1;
 474                                 temp.row = region_index;
 475
 476                                 trace.push_back(temp);
 477
 478                                 region_index = path[i].row;
 479                                 region_start = col_index;
 480                         }
 481                 }
 482
 483                 // get last one
 484                 trace_struct temp;
 485                 temp.col = region_start;
 486                 temp.oldCol = path[path.size()-1].col;
 487                 temp.row = region_index;
 488                 trace.push_back(temp);
 489
 490                 return trace;
 491
 492         }
 493         catch(exception& e) {
 494                 m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
 495                 exit(1);
 496         }
 497 }
 498
 499 /***************************************************************************************************************
 500
 501 vector<trace_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
 502         try {
 503
 504
 505                 //get matrix dimensions
 506                 int numCols = query->getAligned().length();
 507                 int numRows = ms.size();
 508
 509
 510                 //find highest score scoring matrix
 511                 vector<score_struct> highestStruct;
 512                 int highestScore = 0;
 513
 514                 for (int i = 0; i < numRows; i++) {
 515                         for (int j = 0; j < numCols; j++) {
 516                                 if (ms[i][j].score > highestScore) {
 517                                         highestScore = ms[i][j].score;
 518                                         highestStruct.resize(0);
 519                                         highestStruct.push_back(ms[i][j]);
 520                                 }
 521                                 else if(ms[i][j].score == highestScore){
 522                                         highestStruct.push_back(ms[i][j]);
 523                                 }
 524                         }
 525                 }
 526
 527                 //cout << endl << highestScore << '\t' << highestStruct.size() << '\t' << highestStruct[0].row << endl;
 528
 529                 vector<trace_struct> maxTrace;
 530                 double maxPercentIdenticalQueryAntiChimera = 0;
 531
 532                 for(int i=0;i<highestStruct.size();i++){
 533
 534                         vector<score_struct> path;
 535
 536                         int rowIndex = highestStruct[i].row;
 537                         int pos = highestStruct[i].col;
 538                         int score = highestStruct[i].score;
 539
 540                         while (pos >= 0 && score > 0) {
 541                                 score_struct temp = ms[rowIndex][pos];
 542                                 score = temp.score;
 543
 544                                 if (score > 0) {        path.push_back(temp);   }
 545
 546                                 rowIndex = temp.prev;
 547                                 pos--;
 548                         }
 549
 550                         reverse(path.begin(), path.end());
 551
 552                         vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
 553
 554                         //cout << "traces\n";
 555                         //for(int j=0;j<trace.size();j++){
 556                         //      cout << trace[j].col << '\t' << trace[j].oldCol << '\t' << refSeqs[trace[j].row]->getName() << endl;
 557                         //}
 558
 559                         int traceStart = path[0].col;
 560                         int traceEnd = path[path.size()-1].col;
 561 //                      cout << "traceStart/End\t" << traceStart << '\t' << traceEnd << endl;
 562
 563                         string queryInRange = query->getAligned();
 564                         queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
 565 //                      cout << "here" << endl;
 566                         string chimeraSeq = constructChimericSeq(trace, refSeqs);
 567                         string antiChimeraSeq = constructAntiChimericSeq(trace, refSeqs);
 568
 569                         percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
 570                         double percentIdenticalQueryAntiChimera = computePercentID(queryInRange, antiChimeraSeq);
 571 //                      cout << i << '\t' << percentIdenticalQueryChimera << '\t' << percentIdenticalQueryAntiChimera << endl;
 572
 573                         if(percentIdenticalQueryAntiChimera > maxPercentIdenticalQueryAntiChimera){
 574                                 maxPercentIdenticalQueryAntiChimera = percentIdenticalQueryAntiChimera;
 575                                 maxTrace = trace;
 576                         }
 577                 }
 578 //              cout << maxPercentIdenticalQueryAntiChimera << endl;
 579                 return maxTrace;
 580
 581
 582         }
 583         catch(exception& e) {
 584                 m->errorOut(e, "Maligner", "extractHighestPath");
 585                 exit(1);
 586         }
 587 }
 588
 589 //***************************************************************************************************************
 590
 591 vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path, vector<Sequence*> seqs) {
 592         try {
 593                 vector<trace_struct> trace;
 594
 595                 int region_index = path[0].row;
 596                 int region_start = path[0].col;
 597
 598                 for (int i = 1; i < path.size(); i++) {
 599
 600                         int next_region_index = path[i].row;
 601
 602                         if (next_region_index != region_index) {
 603
 604                                 // add trace region
 605                                 int col_index = path[i].col;
 606                                 trace_struct temp;
 607                                 temp.col = region_start;
 608                                 temp.oldCol = col_index-1;
 609                                 temp.row = region_index;
 610
 611                                 trace.push_back(temp);
 612
 613                                 region_index = path[i].row;
 614                                 region_start = col_index;
 615                         }
 616                 }
 617
 618                 // get last one
 619                 trace_struct temp;
 620                 temp.col = region_start;
 621                 temp.oldCol = path[path.size()-1].col;
 622                 temp.row = region_index;
 623                 trace.push_back(temp);
 624
 625 //              cout << endl;
 626 //              cout << trace.size() << endl;
 627 //              for(int i=0;i<trace.size();i++){
 628 //                      cout << seqs[trace[i].row]->getName() << endl;
 629 //              }
 630 //              cout << endl;
 631
 632                 return trace;
 633
 634         }
 635         catch(exception& e) {
 636                 m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
 637                 exit(1);
 638         }
 639 }
 640 */
 641 //***************************************************************************************************************
 642
 643 string Maligner::constructChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
 644         try {
 645                 string chimera = "";
 646
 647                 for (int i = 0; i < trace.size(); i++) {
 648 //                      cout << i << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
 649
 650                         string seqAlign = seqs[trace[i].row]->getAligned();
 651                         seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
 652                         chimera += seqAlign;
 653                 }
 654
 655                 if (chimera != "") { chimera = chimera.substr(0, (chimera.length()-1)); }
 656                 return chimera;
 657         }
 658         catch(exception& e) {
 659                 m->errorOut(e, "Maligner", "constructChimericSeq");
 660                 exit(1);
 661         }
 662 }
 663
 664 //***************************************************************************************************************
 665
 666 string Maligner::constructAntiChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
 667         try {
 668                 string antiChimera = "";
 669
 670                 for (int i = 0; i < trace.size(); i++) {
 671 //                      cout << i << '\t' << (trace.size() - i - 1) << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
 672
 673                         int oppositeIndex = trace.size() - i - 1;
 674
 675                         string seqAlign = seqs[trace[oppositeIndex].row]->getAligned();
 676                         seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
 677                         antiChimera += seqAlign;
 678                 }
 679
 680                 return antiChimera;
 681         }
 682         catch(exception& e) {
 683                 m->errorOut(e, "Maligner", "constructChimericSeq");
 684                 exit(1);
 685         }
 686 }
 687
 688 //***************************************************************************************************************
 689 float Maligner::computePercentID(string queryAlign, string chimera) {
 690         try {
 691
 692                 if (queryAlign.length() != chimera.length()) {
 693                         m->mothurOut("Error, alignment strings are of different lengths: "); m->mothurOutEndLine();
 694                         m->mothurOut(toString(queryAlign.length())); m->mothurOutEndLine();
 695                         m->mothurOut(toString(chimera.length())); m->mothurOutEndLine();
 696                         return -1.0;
 697                 }
 698
 699                 int numIdentical = 0;
 700                 int countA = 0;
 701                 int countB = 0;
 702                 for (int i = 0; i < queryAlign.length(); i++) {
 703                         if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
 704                                 ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
 705                         else {
 706
 707                                 bool charA = false; bool charB = false;
 708                                 if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
 709                                 if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
 710
 711                                 if (charA || charB) {
 712
 713                                         if (charA) { countA++; }
 714                                         if (charB) { countB++; }
 715
 716                                         if (queryAlign[i] == chimera[i]) {
 717                                                 numIdentical++;
 718                                         }
 719                                 }
 720                         }
 721                 }
 722
 723                 float numBases = (countA + countB) /(float) 2;
 724
 725                 if (numBases == 0) { return 0; }
 726
 727                 float percentIdentical = (numIdentical/(float)numBases) * 100;
 728
 729                 return percentIdentical;
 730
 731         }
 732         catch(exception& e) {
 733                 m->errorOut(e, "Maligner", "computePercentID");
 734                 exit(1);
 735         }
 736 }
 737 //***************************************************************************************************************