ccode.cpp

   1 /*
   2  *  ccode.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 8/24/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "ccode.h"
  11 #include "ignoregaps.h"
  12 #include "eachgapdist.h"
  13
  14
  15 //***************************************************************************************************************
  16 Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int numW, string o) : Chimera() {
  17         fastafile = filename;
  18         outputDir = o;
  19         templateFileName = temp;  templateSeqs = readSeqs(temp);
  20         setMask(mask);
  21         filter = f;
  22         window = win;
  23         numWanted = numW;
  24
  25         distCalc = new eachGapDist();
  26         decalc = new DeCalculator();
  27
  28         mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
  29
  30         #ifdef USE_MPI
  31
  32                 //char* inFileName = new char[mapInfo.length()];
  33                 //memcpy(inFileName, mapInfo.c_str(), mapInfo.length());
  34
  35                 char inFileName[1024];
  36                 strcpy(inFileName, mapInfo.c_str());
  37
  38                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
  39
  40                 MPI_File_open(MPI_COMM_WORLD, inFileName, outMode, MPI_INFO_NULL, &outMap);  //comm, filename, mode, info, filepointer
  41
  42                 //delete inFileName;
  43
  44                 int pid;
  45                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  46
  47                 if (pid == 0) {
  48                         string outString = "Place in masked, filtered and trimmed sequence\tPlace in original alignment\n";
  49
  50                         MPI_Status status;
  51                         int length = outString.length();
  52                         char* buf2 = new char[length];
  53                         memcpy(buf2, outString.c_str(), length);
  54
  55                         MPI_File_write_shared(outMap, buf2, length, MPI_CHAR, &status);
  56                         delete buf2;
  57                 }
  58         #else
  59
  60                 ofstream out2;
  61                 openOutputFile(mapInfo, out2);
  62
  63                 out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
  64                 out2.close();
  65         #endif
  66 }
  67 //***************************************************************************************************************
  68 Ccode::~Ccode() {
  69         delete distCalc;
  70         delete decalc;
  71
  72         #ifdef USE_MPI
  73                 MPI_File_close(&outMap);
  74         #endif
  75 }
  76 //***************************************************************************************************************
  77 int Ccode::print(ostream& out, ostream& outAcc) {
  78         try {
  79
  80                 ofstream out2;
  81                 openOutputFileAppend(mapInfo, out2);
  82
  83                 out2 << querySeq->getName() << endl;
  84                 for (it = spotMap.begin(); it!= spotMap.end(); it++) {
  85                         out2 << it->first << '\t' << it->second << endl;
  86                 }
  87                 out2.close();
  88                 out << querySeq->getName() << endl << endl << "Reference sequences used and distance to query:" << endl;
  89
  90                 for (int j = 0; j < closest.size(); j++) {
  91                         out << closest[j].seq->getName() << '\t' << closest[j].dist << endl;
  92                 }
  93                 out << endl << endl;
  94
  95                 //for each window
  96                 //window mapping info.
  97                 out << "Mapping information: ";
  98                 //you mask and did not filter
  99                 if ((seqMask != "") && (!filter)) { out << "mask and trim."; }
 100
 101                 //you filtered and did not mask
 102                 if ((seqMask == "") && (filter)) { out << "filter and trim."; }
 103
 104                 //you masked and filtered
 105                 if ((seqMask != "") && (filter)) { out << "mask, filter and trim."; }
 106
 107                 out << endl << "Window\tStartPos\tEndPos" << endl;
 108                 it = trim.begin();
 109                 for (int k = 0; k < windows.size()-1; k++) {
 110                         out << k+1 << '\t' << spotMap[windows[k]-it->first] << '\t' << spotMap[windows[k]-it->first+windowSizes] << endl;
 111                 }
 112
 113                 out << windows.size() << '\t' << spotMap[windows[windows.size()-1]-it->first] << '\t' << spotMap[it->second-it->first-1] << endl;
 114                 out << endl;
 115                 out << "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova" << endl;
 116                 for (int k = 0; k < windows.size(); k++) {
 117                         float ds = averageQuery[k] / averageRef[k];
 118                         out << k+1 << '\t' << averageQuery[k] << '\t' << sdQuery[k] << '\t' << averageRef[k] << '\t'<< sdRef[k] << '\t' << ds << '\t' << anova[k] << endl;
 119                 }
 120                 out << endl;
 121
 122                 //varRef
 123                 //varQuery
 124                 /* F test for differences among variances.
 125                 * varQuery is expected to be higher or similar than varRef */
 126                 //float fs = varQuery[query] / varRef[query];   /* F-Snedecor, test for differences of variances */
 127
 128                 bool results = false;
 129
 130                 //confidence limit, t - Student, anova
 131                 out << "Window\tConfidenceLimit\tt-Student\tAnova" << endl;
 132
 133                 for (int k = 0; k < windows.size(); k++) {
 134                         string temp = "";
 135                         if (isChimericConfidence[k]) {  temp += "*\t"; }
 136                         else { temp += "\t"; }
 137
 138                         if (isChimericTStudent[k]) {  temp += "*\t"; }
 139                         else { temp += "\t"; }
 140
 141                         if (isChimericANOVA[k]) {  temp += "*\t"; }
 142                         else { temp += "\t"; }
 143
 144                         out << k+1 << '\t' << temp << endl;
 145
 146                         if (temp == "*\t*\t*\t") {  results = true;  }
 147                 }
 148                 out << endl;
 149
 150                 if (results) {
 151                         m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
 152                         outAcc << querySeq->getName() << endl;
 153                 }
 154
 155                 //free memory
 156                 for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
 157
 158                 return results;
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "Ccode", "print");
 162                 exit(1);
 163         }
 164 }
 165 #ifdef USE_MPI
 166 //***************************************************************************************************************
 167 int Ccode::print(MPI_File& out, MPI_File& outAcc) {
 168         try {
 169
 170                 string outMapString = "";
 171
 172                 outMapString += querySeq->getName() + "\n";
 173                 for (it = spotMap.begin(); it!= spotMap.end(); it++) {
 174                         outMapString += toString(it->first)  + "\t" + toString(it->second)  + "\n";
 175                 }
 176                 printMapping(outMapString);
 177                 outMapString = "";
 178
 179                 string outString = "";
 180                 string outAccString = "";
 181
 182                 outString +=  querySeq->getName() + "\n\nReference sequences used and distance to query:\n";
 183
 184                 for (int j = 0; j < closest.size(); j++) {
 185                         outString += closest[j].seq->getName() + "\t" + toString(closest[j].dist) + "\n";
 186                 }
 187                 outString += "\n\nMapping information: ";
 188
 189                 //for each window
 190                 //window mapping info.
 191                 //you mask and did not filter
 192                 if ((seqMask != "") && (!filter)) { outString += "mask and trim."; }
 193
 194                 //you filtered and did not mask
 195                 if ((seqMask == "") && (filter)) { outString += "filter and trim."; }
 196
 197                 //you masked and filtered
 198                 if ((seqMask != "") && (filter)) { outString += "mask, filter and trim."; }
 199
 200                 outString += "\nWindow\tStartPos\tEndPos\n";
 201                 it = trim.begin();
 202                 for (int k = 0; k < windows.size()-1; k++) {
 203                         outString += toString(k+1) + "\t" + toString(spotMap[windows[k]-it->first]) + "\t" + toString(spotMap[windows[k]-it->first+windowSizes]) + "\n";
 204                 }
 205
 206                 outString += toString(windows.size()) + "\t" + toString(spotMap[windows[windows.size()-1]-it->first]) + "\t" + toString(spotMap[it->second-it->first-1]) + "\n\n";
 207
 208                 outString += "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova\n";
 209                 for (int k = 0; k < windows.size(); k++) {
 210                         float ds = averageQuery[k] / averageRef[k];
 211                         outString += toString(k+1) + "\t" + toString(averageQuery[k]) + "\t" + toString(sdQuery[k]) + "\t" + toString(averageRef[k]) + "\t" + toString(sdRef[k]) + "\t" + toString(ds) + "\t" + toString(anova[k]) + "\n";
 212                 }
 213
 214                 //varRef
 215                 //varQuery
 216                 /* F test for differences among variances.
 217                 * varQuery is expected to be higher or similar than varRef */
 218                 //float fs = varQuery[query] / varRef[query];   /* F-Snedecor, test for differences of variances */
 219
 220                 bool results = false;
 221
 222                 //confidence limit, t - Student, anova
 223                 outString += "\nWindow\tConfidenceLimit\tt-Student\tAnova\n";
 224
 225                 for (int k = 0; k < windows.size(); k++) {
 226                         string temp = "";
 227                         if (isChimericConfidence[k]) {  temp += "*\t"; }
 228                         else { temp += "\t"; }
 229
 230                         if (isChimericTStudent[k]) {  temp += "*\t"; }
 231                         else { temp += "\t"; }
 232
 233                         if (isChimericANOVA[k]) {  temp += "*\t"; }
 234                         else { temp += "\t"; }
 235
 236                         outString += toString(k+1) + "\t" + temp + "\n";
 237
 238                         if (temp == "*\t*\t*\t") {  results = true;  }
 239                 }
 240                 outString += "\n";
 241
 242                 MPI_Status status;
 243                 int length = outString.length();
 244                 char* buf2 = new char[length];
 245                 memcpy(buf2, outString.c_str(), length);
 246
 247                 MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
 248                 delete buf2;
 249
 250                 if (results) {
 251                         m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
 252                         outAccString += querySeq->getName() + "\n";
 253
 254                         MPI_Status statusAcc;
 255                         length = outAccString.length();
 256                         char* buf = new char[length];
 257                         memcpy(buf, outAccString.c_str(), length);
 258
 259                         MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
 260                         delete buf;
 261                 }
 262
 263                 //free memory
 264                 for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
 265
 266                 return results;
 267         }
 268         catch(exception& e) {
 269                 m->errorOut(e, "Ccode", "print");
 270                 exit(1);
 271         }
 272 }
 273 //***************************************************************************************************************
 274 int Ccode::printMapping(string& output) {
 275         try {
 276                         MPI_Status status;
 277                         int length = output.length();
 278                         char* buf = new char[length];
 279                         memcpy(buf, output.c_str(), length);
 280
 281                         MPI_File_write_shared(outMap, buf, length, MPI_CHAR, &status);
 282                         delete buf;
 283
 284         }
 285         catch(exception& e) {
 286                 m->errorOut(e, "Ccode", "printMapping");
 287                 exit(1);
 288         }
 289 }
 290 #endif
 291 //***************************************************************************************************************
 292 int Ccode::getChimeras(Sequence* query) {
 293         try {
 294
 295                 closest.clear();
 296                 refCombo = 0;
 297                 sumRef.clear();
 298                 varRef.clear();
 299                 varQuery.clear();
 300                 sdRef.clear();
 301                 sdQuery.clear();
 302                 sumQuery.clear();
 303                 sumSquaredRef.clear();
 304                 sumSquaredQuery.clear();
 305                 averageRef.clear();
 306                 averageQuery.clear();
 307                 anova.clear();
 308                 isChimericConfidence.clear();
 309                 isChimericTStudent.clear();
 310                 isChimericANOVA.clear();
 311                 trim.clear();
 312                 spotMap.clear();
 313                 windowSizes = window;
 314                 windows.clear();
 315
 316
 317                 querySeq = query;
 318
 319                 //find closest matches to query
 320                 closest = findClosest(query, numWanted);
 321
 322                 if (m->control_pressed) {  return 0;  }
 323
 324                 //initialize spotMap
 325                 for (int i = 0; i < query->getAligned().length(); i++) {        spotMap[i] = i;         }
 326
 327                 //mask sequences if the user wants to
 328                 if (seqMask != "") {
 329                         decalc->setMask(seqMask);
 330
 331                         decalc->runMask(query);
 332
 333                         //mask closest
 334                         for (int i = 0; i < closest.size(); i++) {      decalc->runMask(closest[i].seq);        }
 335
 336                         spotMap = decalc->getMaskMap();
 337                 }
 338
 339                 if (filter) {
 340                         vector<Sequence*> temp;
 341                         for (int i = 0; i < closest.size(); i++) { temp.push_back(closest[i].seq);  }
 342                         temp.push_back(query);
 343
 344                         createFilter(temp, 0.5);
 345
 346                         for (int i = 0; i < temp.size(); i++) {
 347                                 if (m->control_pressed) {  return 0;  }
 348                                 runFilter(temp[i]);
 349                         }
 350
 351                         //update spotMap
 352                         map<int, int> newMap;
 353                         int spot = 0;
 354
 355                         for (int i = 0; i < filterString.length(); i++) {
 356                                 if (filterString[i] == '1') {
 357                                         //add to newMap
 358                                         newMap[spot] = spotMap[i];
 359                                         spot++;
 360                                 }
 361                         }
 362                         spotMap = newMap;
 363                 }
 364
 365                 //trim sequences - this follows ccodes remove_extra_gaps
 366                 trimSequences(query);
 367                 if (m->control_pressed) {  return 0;  }
 368
 369                 //windows are equivalent to words - ccode paper recommends windows are between 5% and 20% on alignment length().
 370                 //Our default will be 10% and we will warn if user tries to use a window above or below these recommendations
 371                 windows = findWindows();
 372                 if (m->control_pressed) {  return 0;  }
 373
 374                 //remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later
 375                 removeBadReferenceSeqs(closest);
 376                 if (m->control_pressed) {  return 0;  }
 377
 378                 //find the averages for each querys references
 379                 getAverageRef(closest);  //fills sumRef, averageRef, sumSquaredRef and refCombo.
 380                 getAverageQuery(closest, query);  //fills sumQuery, averageQuery, sumSquaredQuery.
 381                 if (m->control_pressed) {  return 0;  }
 382
 383                 //find the averages for each querys references
 384                 findVarianceRef();  //fills varRef and sdRef also sets minimum error rate to 0.001 to avoid divide by 0.
 385                 if (m->control_pressed) {  return 0;  }
 386
 387                 //find the averages for the query
 388                 findVarianceQuery();  //fills varQuery and sdQuery also sets minimum error rate to 0.001 to avoid divide by 0.
 389                 if (m->control_pressed) {  return 0;  }
 390
 391                 determineChimeras();  //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA.
 392                 if (m->control_pressed) {  return 0;  }
 393
 394                 return 0;
 395         }
 396         catch(exception& e) {
 397                 m->errorOut(e, "Ccode", "getChimeras");
 398                 exit(1);
 399         }
 400 }
 401 /***************************************************************************************************************/
 402 //ccode algo says it does this to "Removes the initial and final gaps to avoid biases due to incomplete sequences."
 403 void Ccode::trimSequences(Sequence* query) {
 404         try {
 405
 406                 int frontPos = 0;  //should contain first position in all seqs that is not a gap character
 407                 int rearPos = query->getAligned().length();
 408
 409                 //********find first position in closest seqs that is a non gap character***********//
 410                 //find first position all query seqs that is a non gap character
 411                 for (int i = 0; i < closest.size(); i++) {
 412
 413                         string aligned = closest[i].seq->getAligned();
 414                         int pos = 0;
 415
 416                         //find first spot in this seq
 417                         for (int j = 0; j < aligned.length(); j++) {
 418                                 if (isalpha(aligned[j])) {
 419                                         pos = j;
 420                                         break;
 421                                 }
 422                         }
 423
 424                         //save this spot if it is the farthest
 425                         if (pos > frontPos) { frontPos = pos; }
 426                 }
 427
 428                 //find first position all querySeq[query] that is a non gap character
 429                 string aligned = query->getAligned();
 430                 int pos = 0;
 431
 432                 //find first spot in this seq
 433                 for (int j = 0; j < aligned.length(); j++) {
 434                         if (isalpha(aligned[j])) {
 435                                 pos = j;
 436                                 break;
 437                         }
 438                 }
 439
 440                 //save this spot if it is the farthest
 441                 if (pos > frontPos) { frontPos = pos; }
 442
 443
 444                 //********find last position in closest seqs that is a non gap character***********//
 445                 for (int i = 0; i < closest.size(); i++) {
 446
 447                         string aligned = closest[i].seq->getAligned();
 448                         int pos = aligned.length();
 449
 450                         //find first spot in this seq
 451                         for (int j = aligned.length()-1; j >= 0; j--) {
 452                                 if (isalpha(aligned[j])) {
 453                                         pos = j;
 454                                         break;
 455                                 }
 456                         }
 457
 458                         //save this spot if it is the farthest
 459                         if (pos < rearPos) { rearPos = pos; }
 460                 }
 461
 462                 //find last position all querySeqs[query] that is a non gap character
 463                 aligned = query->getAligned();
 464                 pos = aligned.length();
 465
 466                 //find first spot in this seq
 467                 for (int j = aligned.length()-1; j >= 0; j--) {
 468                         if (isalpha(aligned[j])) {
 469                                 pos = j;
 470                                 break;
 471                         }
 472                 }
 473
 474                 //save this spot if it is the farthest
 475                 if (pos < rearPos) { rearPos = pos; }
 476
 477
 478                 //check to make sure that is not whole seq
 479                 if ((rearPos - frontPos - 1) <= 0) {  m->mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine(); exit(1);  }
 480
 481                 map<int, int> tempTrim;
 482                 tempTrim[frontPos] = rearPos;
 483
 484                 //save trimmed locations
 485                 trim = tempTrim;
 486
 487                 //update spotMask
 488                 map<int, int> newMap;
 489                 int spot = 0;
 490
 491                 for (int i = frontPos; i < rearPos; i++) {
 492                         //add to newMap
 493                         newMap[spot] = spotMap[i];
 494                         spot++;
 495                 }
 496                 spotMap = newMap;
 497         }
 498         catch(exception& e) {
 499                 m->errorOut(e, "Ccode", "trimSequences");
 500                 exit(1);
 501         }
 502 }
 503 /***************************************************************************************************************/
 504 vector<int> Ccode::findWindows() {
 505         try {
 506
 507                 vector<int> win;
 508                 it = trim.begin();
 509
 510                 int length = it->second - it->first;
 511
 512                 //default is wanted = 10% of total length
 513                 if (windowSizes > length) {
 514                         m->mothurOut("You have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.");
 515                         windowSizes = length / 10;
 516                 }else if (windowSizes == 0) { windowSizes = length / 10;  }
 517                 else if (windowSizes > (length * 0.20)) {
 518                         m->mothurOut("You have selected a window that is larger than 20% of your sequence length.  This is not recommended, but I will continue anyway."); m->mothurOutEndLine();
 519                 }else if (windowSizes < (length * 0.05)) {
 520                         m->mothurOut("You have selected a window that is smaller than 5% of your sequence length.  This is not recommended, but I will continue anyway."); m->mothurOutEndLine();
 521                 }
 522
 523                 //save starting points of each window
 524                 for (int m = it->first;  m < (it->second-windowSizes); m+=windowSizes) {  win.push_back(m);  }
 525
 526                 //save last window
 527                 if (win[win.size()-1] < (it->first+length)) {
 528                         win.push_back(win[win.size()-1]+windowSizes); // ex. string length is 115, window is 25, without this you would get 0, 25, 50, 75
 529                 }                                                                                                                                                                                                       //with this you would get 1,25,50,75,100
 530
 531                 return win;
 532         }
 533         catch(exception& e) {
 534                 m->errorOut(e, "Ccode", "findWindows");
 535                 exit(1);
 536         }
 537 }
 538 //***************************************************************************************************************
 539 int Ccode::getDiff(string seqA, string seqB) {
 540         try {
 541
 542                 int numDiff = 0;
 543
 544                 for (int i = 0; i < seqA.length(); i++) {
 545                         //if you are both not gaps
 546                         //if (isalpha(seqA[i]) && isalpha(seqA[i])) {
 547                                 //are you different
 548                                 if (seqA[i] != seqB[i]) {
 549                                          int ok; /* ok=1 means equivalent base. Checks for degenerate bases */
 550
 551                                         /* the char in base_a and base_b have been checked and they are different */
 552                                         if ((seqA[i] == 'N') && (seqB[i] != '-')) ok = 1;
 553                                         else if ((seqB[i] == 'N') && (seqA[i] != '-')) ok = 1;
 554                                         else if ((seqA[i] == 'Y') && ((seqB[i] == 'C') || (seqB[i] == 'T'))) ok = 1;
 555                                         else if ((seqB[i] == 'Y') && ((seqA[i] == 'C') || (seqA[i] == 'T'))) ok = 1;
 556                                         else if ((seqA[i] == 'R') && ((seqB[i] == 'G') || (seqB[i] == 'A'))) ok = 1;
 557                                         else if ((seqB[i] == 'R') && ((seqA[i] == 'G') || (seqA[i] == 'A'))) ok = 1;
 558                                         else if ((seqA[i] == 'S') && ((seqB[i] == 'C') || (seqB[i] == 'G'))) ok = 1;
 559                                         else if ((seqB[i] == 'S') && ((seqA[i] == 'C') || (seqA[i] == 'G'))) ok = 1;
 560                                         else if ((seqA[i] == 'W') && ((seqB[i] == 'T') || (seqB[i] == 'A'))) ok = 1;
 561                                         else if ((seqB[i] == 'W') && ((seqA[i] == 'T') || (seqA[i] == 'A'))) ok = 1;
 562                                         else if ((seqA[i] == 'M') && ((seqB[i] == 'A') || (seqB[i] == 'C'))) ok = 1;
 563                                         else if ((seqB[i] == 'M') && ((seqA[i] == 'A') || (seqA[i] == 'C'))) ok = 1;
 564                                         else if ((seqA[i] == 'K') && ((seqB[i] == 'T') || (seqB[i] == 'G'))) ok = 1;
 565                                         else if ((seqB[i] == 'K') && ((seqA[i] == 'T') || (seqA[i] == 'G'))) ok = 1;
 566                                         else if ((seqA[i] == 'V') && ((seqB[i] == 'C') || (seqB[i] == 'A') || (seqB[i] == 'G'))) ok = 1;
 567                                         else if ((seqB[i] == 'V') && ((seqA[i] == 'C') || (seqA[i] == 'A') || (seqA[i] == 'G'))) ok = 1;
 568                                         else if ((seqA[i] == 'H') && ((seqB[i] == 'T') || (seqB[i] == 'A') || (seqB[i] == 'C'))) ok = 1;
 569                                         else if ((seqB[i] == 'H') && ((seqA[i] == 'T') || (seqA[i] == 'A') || (seqA[i] == 'C'))) ok = 1;
 570                                         else if ((seqA[i] == 'D') && ((seqB[i] == 'T') || (seqB[i] == 'A') || (seqB[i] == 'G'))) ok = 1;
 571                                         else if ((seqB[i] == 'D') && ((seqA[i] == 'T') || (seqA[i] == 'A') || (seqA[i] == 'G'))) ok = 1;
 572                                         else if ((seqA[i] == 'B') && ((seqB[i] == 'C') || (seqB[i] == 'T') || (seqB[i] == 'G'))) ok = 1;
 573                                         else if ((seqB[i] == 'B') && ((seqA[i] == 'C') || (seqA[i] == 'T') || (seqA[i] == 'G'))) ok = 1;
 574                                         else ok = 0;  /* the bases are different and not equivalent */
 575
 576                                         //check if they are both blanks
 577                                         if ((seqA[i] == '.') && (seqB[i] == '-')) ok = 1;
 578                                         else if ((seqB[i] == '.') && (seqA[i] == '-')) ok = 1;
 579
 580                                         if (ok == 0) {  numDiff++;  }
 581                                 }
 582                         //}
 583                 }
 584
 585                 return numDiff;
 586
 587         }
 588         catch(exception& e) {
 589                 m->errorOut(e, "Ccode", "getDiff");
 590                 exit(1);
 591         }
 592 }
 593 //***************************************************************************************************************
 594 //tried to make this look most like ccode original implementation
 595 void Ccode::removeBadReferenceSeqs(vector<SeqDist>& seqs) {
 596         try {
 597
 598                 vector< vector<int> > numDiffBases;
 599                 numDiffBases.resize(seqs.size());
 600                 //initialize to 0
 601                 for (int i = 0; i < numDiffBases.size(); i++) { numDiffBases[i].resize(seqs.size(),0); }
 602
 603                 it = trim.begin();
 604                 int length = it->second - it->first;
 605
 606                 //calc differences from each sequence to everyother seq in the set
 607                 for (int i = 0; i < seqs.size(); i++) {
 608
 609                         string seqA = seqs[i].seq->getAligned().substr(it->first, length);
 610
 611                         //so you don't calc i to j and j to i since they are the same
 612                         for (int j = 0; j < i; j++) {
 613
 614                                 string seqB = seqs[j].seq->getAligned().substr(it->first, length);
 615
 616                                 //compare strings
 617                                 int numDiff = getDiff(seqA, seqB);
 618
 619                                 numDiffBases[i][j] = numDiff;
 620                                 numDiffBases[j][i] = numDiff;
 621                         }
 622                 }
 623
 624                 //initailize remove to 0
 625                 vector<int> remove;  remove.resize(seqs.size(), 0);
 626                 float top = ((20*length) / (float) 100);
 627                 float bottom = ((0.5*length) / (float) 100);
 628
 629                 //check each numDiffBases and if any are higher than threshold set remove to 1 so you can remove those seqs from the closest set
 630                 for (int i = 0; i < numDiffBases.size(); i++) {
 631                         for (int j = 0; j < i; j++) {
 632                                 //are you more than 20% different
 633                                 if (numDiffBases[i][j] > top)           {  remove[j] = 1;  }
 634                                 //are you less than 0.5% different
 635                                 if (numDiffBases[i][j] < bottom)        {  remove[j] = 1;  }
 636                         }
 637                 }
 638
 639                 int numSeqsLeft = 0;
 640
 641                 //count seqs that are not going to be removed
 642                 for (int i = 0; i < remove.size(); i++) {
 643                         if (remove[i] == 0)  { numSeqsLeft++;  }
 644                 }
 645
 646                 //if you have enough then remove bad ones
 647                 if (numSeqsLeft >= 3) {
 648                         vector<SeqDist> goodSeqs;
 649                         //remove bad seqs
 650                         for (int i = 0; i < remove.size(); i++) {
 651                                 if (remove[i] == 0) {
 652                                         goodSeqs.push_back(seqs[i]);
 653                                 }
 654                         }
 655
 656                         seqs = goodSeqs;
 657
 658                 }else { //warn, but dont remove any
 659                         m->mothurOut(querySeq->getName() + " does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check."); m->mothurOutEndLine();
 660                 }
 661
 662         }
 663         catch(exception& e) {
 664                 m->errorOut(e, "Ccode", "removeBadReferenceSeqs");
 665                 exit(1);
 666         }
 667 }
 668 //***************************************************************************************************************
 669 //makes copy of templateseq for filter
 670 vector<SeqDist>  Ccode::findClosest(Sequence* q, int numWanted) {
 671         try{
 672
 673                 vector<SeqDist>  topMatches;
 674
 675                 Sequence query = *(q);
 676
 677                 //calc distance to each sequence in template seqs
 678                 for (int i = 0; i < templateSeqs.size(); i++) {
 679
 680                         Sequence ref = *(templateSeqs[i]);
 681
 682                         //find overall dist
 683                         distCalc->calcDist(query, ref);
 684                         float dist = distCalc->getDist();
 685
 686                         //save distance
 687                         SeqDist temp;
 688                         temp.seq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
 689                         temp.dist = dist;
 690
 691                         topMatches.push_back(temp);
 692                 }
 693
 694                 sort(topMatches.begin(), topMatches.end(), compareSeqDist);
 695
 696                 for (int i = numWanted; i < topMatches.size(); i++) {  delete topMatches[i].seq;  }
 697
 698                 topMatches.resize(numWanted);
 699
 700                 return topMatches;
 701
 702         }
 703         catch(exception& e) {
 704                 m->errorOut(e, "Ccode", "findClosestSides");
 705                 exit(1);
 706         }
 707 }
 708 /**************************************************************************************************/
 709 //find the distances from each reference sequence to every other reference sequence for each window for this query
 710 void Ccode::getAverageRef(vector<SeqDist> ref) {
 711         try {
 712
 713                 vector< vector< vector<int> > >  diffs;  //diffs[0][1][2] is the number of differences between ref seq 0 and ref seq 1 at window 2.
 714
 715                 //initialize diffs vector
 716                 diffs.resize(ref.size());
 717                 for (int i = 0; i < diffs.size(); i++) {
 718                         diffs[i].resize(ref.size());
 719                         for (int j = 0; j < diffs[i].size(); j++) {
 720                                 diffs[i][j].resize(windows.size(), 0);
 721                         }
 722                 }
 723
 724                 it = trim.begin();
 725
 726                 //find the distances from each reference sequence to every other reference sequence for each window for this query
 727                 for (int i = 0; i < ref.size(); i++) {
 728
 729                         string refI = ref[i].seq->getAligned();
 730
 731                         //j<i, so you don't find distances from i to j and then j to i.
 732                         for (int j = 0; j < i; j++) {
 733
 734                                 string refJ = ref[j].seq->getAligned();
 735
 736                                 for (int k = 0; k < windows.size(); k++) {
 737
 738                                         string refIWindowk, refJWindowk;
 739
 740                                         if (k < windows.size()-1) {
 741                                                 //get window strings
 742                                                 refIWindowk = refI.substr(windows[k], windowSizes);
 743                                                 refJWindowk = refJ.substr(windows[k], windowSizes);
 744                                         }else { //last window may be smaller than rest - see findwindows
 745                                                 //get window strings
 746                                                 refIWindowk = refI.substr(windows[k], (it->second-windows[k]));
 747                                                 refJWindowk = refJ.substr(windows[k], (it->second-windows[k]));
 748                                         }
 749
 750                                         //find differences
 751                                         int diff = getDiff(refIWindowk, refJWindowk);
 752
 753                                         //save differences in [i][j][k] and [j][i][k] since they are the same
 754                                         diffs[i][j][k] = diff;
 755                                         diffs[j][i][k] = diff;
 756
 757                                 }//k
 758
 759                         }//j
 760
 761                 }//i
 762
 763                 //initialize sumRef for this query
 764                 sumRef.resize(windows.size(), 0);
 765                 sumSquaredRef.resize(windows.size(), 0);
 766                 averageRef.resize(windows.size(), 0);
 767
 768                 //find the sum of the differences for hte reference sequences
 769                 for (int i = 0; i < diffs.size(); i++) {
 770                         for (int j = 0; j < i; j++) {
 771
 772                                 //increment this querys reference sequences combos
 773                                 refCombo++;
 774
 775                                 for (int k = 0; k < diffs[i][j].size(); k++) {
 776                                         sumRef[k] += diffs[i][j][k];
 777                                         sumSquaredRef[k] += (diffs[i][j][k]*diffs[i][j][k]);
 778                                 }//k
 779
 780                         }//j
 781                 }//i
 782
 783
 784                 //find the average of the differences for the references for each window
 785                 for (int i = 0; i < windows.size(); i++) {
 786                         averageRef[i] = sumRef[i] / (float) refCombo;
 787                 }
 788
 789         }
 790         catch(exception& e) {
 791                 m->errorOut(e, "Ccode", "getAverageRef");
 792                 exit(1);
 793         }
 794 }
 795 /**************************************************************************************************/
 796 void Ccode::getAverageQuery (vector<SeqDist> ref, Sequence* query) {
 797         try {
 798
 799                 vector< vector<int> >  diffs;  //diffs[1][2] is the number of differences between querySeqs[query] and ref seq 1 at window 2.
 800
 801                 //initialize diffs vector
 802                 diffs.resize(ref.size());
 803                 for (int j = 0; j < diffs.size(); j++) {
 804                         diffs[j].resize(windows.size(), 0);
 805                 }
 806
 807                 it = trim.begin();
 808
 809                 string refQuery = query->getAligned();
 810
 811                 //j<i, so you don't find distances from i to j and then j to i.
 812                 for (int j = 0; j < ref.size(); j++) {
 813
 814                          string refJ = ref[j].seq->getAligned();
 815
 816                          for (int k = 0; k < windows.size(); k++) {
 817
 818                                         string QueryWindowk, refJWindowk;
 819
 820                                         if (k < windows.size()-1) {
 821                                                 //get window strings
 822                                                 QueryWindowk = refQuery.substr(windows[k], windowSizes);
 823                                                 refJWindowk = refJ.substr(windows[k], windowSizes);
 824                                         }else { //last window may be smaller than rest - see findwindows
 825                                                 //get window strings
 826                                                 QueryWindowk = refQuery.substr(windows[k], (it->second-windows[k]));
 827                                                 refJWindowk = refJ.substr(windows[k], (it->second-windows[k]));
 828                                         }
 829
 830                                         //find differences
 831                                         int diff = getDiff(QueryWindowk, refJWindowk);
 832
 833                                         //save differences
 834                                         diffs[j][k] = diff;
 835
 836                          }//k
 837                 }//j
 838
 839
 840                 //initialize sumRef for this query
 841                 sumQuery.resize(windows.size(), 0);
 842                 sumSquaredQuery.resize(windows.size(), 0);
 843                 averageQuery.resize(windows.size(), 0);
 844
 845                 //find the sum of the differences
 846                 for (int j = 0; j < diffs.size(); j++) {
 847                         for (int k = 0; k < diffs[j].size(); k++) {
 848                                 sumQuery[k] += diffs[j][k];
 849                                 sumSquaredQuery[k] += (diffs[j][k]*diffs[j][k]);
 850                         }//k
 851                 }//j
 852
 853
 854                 //find the average of the differences for the references for each window
 855                 for (int i = 0; i < windows.size(); i++) {
 856                         averageQuery[i] = sumQuery[i] / (float) ref.size();
 857                 }
 858         }
 859         catch(exception& e) {
 860                 m->errorOut(e, "Ccode", "getAverageQuery");
 861                 exit(1);
 862         }
 863 }
 864 /**************************************************************************************************/
 865 void Ccode::findVarianceRef() {
 866         try {
 867
 868                 varRef.resize(windows.size(), 0);
 869                 sdRef.resize(windows.size(), 0);
 870
 871                 //for each window
 872                 for (int i = 0; i < windows.size(); i++) {
 873                         varRef[i] = (sumSquaredRef[i] - ((sumRef[i]*sumRef[i])/(float)refCombo)) / (float)(refCombo-1);
 874                         sdRef[i] = sqrt(varRef[i]);
 875
 876                         //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation
 877                         if (averageRef[i] < 0.001)                      {       averageRef[i] = 0.001;          }
 878                         if (sumRef[i] < 0.001)                          {       sumRef[i] = 0.001;                      }
 879                         if (varRef[i] < 0.001)                          {       varRef[i] = 0.001;                      }
 880                         if (sumSquaredRef[i] < 0.001)           {       sumSquaredRef[i] = 0.001;       }
 881                         if (sdRef[i] < 0.001)                           {       sdRef[i] = 0.001;                       }
 882
 883                 }
 884         }
 885         catch(exception& e) {
 886                 m->errorOut(e, "Ccode", "findVarianceRef");
 887                 exit(1);
 888         }
 889 }
 890 /**************************************************************************************************/
 891 void Ccode::findVarianceQuery() {
 892         try {
 893                 varQuery.resize(windows.size(), 0);
 894                 sdQuery.resize(windows.size(), 0);
 895
 896                 //for each window
 897                 for (int i = 0; i < windows.size(); i++) {
 898                         varQuery[i] = (sumSquaredQuery[i] - ((sumQuery[i]*sumQuery[i])/(float) closest.size())) / (float) (closest.size()-1);
 899                         sdQuery[i] = sqrt(varQuery[i]);
 900
 901                         //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation
 902                         if (averageQuery[i] < 0.001)                    {       averageQuery[i] = 0.001;                }
 903                         if (sumQuery[i] < 0.001)                                {       sumQuery[i] = 0.001;                    }
 904                         if (varQuery[i] < 0.001)                                {       varQuery[i] = 0.001;                    }
 905                         if (sumSquaredQuery[i] < 0.001)         {       sumSquaredQuery[i] = 0.001;     }
 906                         if (sdQuery[i] < 0.001)                         {       sdQuery[i] = 0.001;                     }
 907                 }
 908
 909         }
 910         catch(exception& e) {
 911                 m->errorOut(e, "Ccode", "findVarianceQuery");
 912                 exit(1);
 913         }
 914 }
 915 /**************************************************************************************************/
 916 void Ccode::determineChimeras() {
 917         try {
 918
 919                 isChimericConfidence.resize(windows.size(), false);
 920                 isChimericTStudent.resize(windows.size(), false);
 921                 isChimericANOVA.resize(windows.size(), false);
 922                 anova.resize(windows.size());
 923
 924
 925                 //for each window
 926                 for (int i = 0; i < windows.size(); i++) {
 927
 928                         //get confidence limits
 929                         float t = getT(closest.size()-1);  //how many seqs you are comparing to this querySeq
 930                         float dsUpper = (averageQuery[i] + (t * sdQuery[i])) / averageRef[i];
 931                         float dsLower = (averageQuery[i] - (t * sdQuery[i])) / averageRef[i];
 932
 933                         if ((dsUpper > 1.0) && (dsLower > 1.0) && (averageQuery[i] > averageRef[i])) {  /* range does not include 1 */
 934                                         isChimericConfidence[i] = true;   /* significantly higher at P<0.05 */
 935
 936                         }
 937
 938                         //student t test
 939                         int degreeOfFreedom = refCombo + closest.size() - 2;
 940                         float denomForT = (((refCombo-1) * varQuery[i] + (closest.size() - 1) * varRef[i]) / (float) degreeOfFreedom) * ((refCombo + closest.size()) / (float) (refCombo * closest.size()));    /* denominator, without sqrt(), for ts calculations */
 941
 942                         float ts = fabs((averageQuery[i] - averageRef[i]) / (sqrt(denomForT)));  /* value of ts for t-student test */
 943                         t = getT(degreeOfFreedom);
 944
 945                         if ((ts >= t) && (averageQuery[i] > averageRef[i])) {
 946                                 isChimericTStudent[i] = true;   /* significantly higher at P<0.05 */
 947                         }
 948
 949                         //anova test
 950                         float value1 = sumQuery[i] + sumRef[i];
 951                         float value2 = sumSquaredQuery[i] + sumSquaredRef[i];
 952                         float value3 = ((sumQuery[i]*sumQuery[i]) / (float) (closest.size())) + ((sumRef[i] * sumRef[i]) / (float) refCombo);
 953                         float value4 = (value1 * value1) / ( (float) (closest.size() + refCombo) );
 954                         float value5 = value2 - value4;
 955                         float value6 = value3 - value4;
 956                         float value7 = value5 - value6;
 957                         float value8 = value7 / ((float) degreeOfFreedom);
 958                         float anovaValue = value6 / value8;
 959
 960                         float f = getF(degreeOfFreedom);
 961
 962                          if ((anovaValue >= f) && (averageQuery[i] > averageRef[i]))  {
 963                        isChimericANOVA[i] = true;   /* significant P<0.05 */
 964                 }
 965
 966                         if (isnan(anovaValue) || isinf(anovaValue)) { anovaValue = 0.0; }
 967
 968                         anova[i] = anovaValue;
 969                 }
 970
 971         }
 972         catch(exception& e) {
 973                 m->errorOut(e, "Ccode", "determineChimeras");
 974                 exit(1);
 975         }
 976 }
 977 /**************************************************************************************************/
 978 float Ccode::getT(int numseq) {
 979         try {
 980
 981                 float tvalue = 0;
 982
 983                 /* t-student critical values for different degrees of freedom and alpha 0.1 in one-tail tests (equivalent to 0.05) */
 984                 if (numseq > 120) tvalue = 1.645;
 985                 else if (numseq > 60) tvalue = 1.658;
 986         else if (numseq > 40) tvalue = 1.671;
 987         else if (numseq > 30) tvalue = 1.684;
 988         else if (numseq > 29) tvalue = 1.697;
 989         else if (numseq > 28) tvalue = 1.699;
 990         else if (numseq > 27) tvalue = 1.701;
 991         else if (numseq > 26) tvalue = 1.703;
 992         else if (numseq > 25) tvalue = 1.706;
 993         else if (numseq > 24) tvalue = 1.708;
 994         else if (numseq > 23) tvalue = 1.711;
 995         else if (numseq > 22) tvalue = 1.714;
 996         else if (numseq > 21) tvalue = 1.717;
 997         else if (numseq > 20) tvalue = 1.721;
 998         else if (numseq > 19) tvalue = 1.725;
 999         else if (numseq > 18) tvalue = 1.729;
1000         else if (numseq > 17) tvalue = 1.734;
1001         else if (numseq > 16) tvalue = 1.740;
1002         else if (numseq > 15) tvalue = 1.746;
1003         else if (numseq > 14) tvalue = 1.753;
1004         else if (numseq > 13) tvalue = 1.761;
1005         else if (numseq > 12) tvalue = 1.771;
1006         else if (numseq > 11) tvalue = 1.782;
1007         else if (numseq > 10) tvalue = 1.796;
1008         else if (numseq > 9) tvalue = 1.812;
1009         else if (numseq > 8) tvalue = 1.833;
1010         else if (numseq > 7) tvalue = 1.860;
1011         else if (numseq > 6) tvalue = 1.895;
1012         else if (numseq > 5) tvalue = 1.943;
1013         else if (numseq > 4) tvalue = 2.015;
1014         else if (numseq > 3) tvalue = 2.132;
1015         else if (numseq > 2) tvalue = 2.353;
1016         else if (numseq > 1) tvalue = 2.920;
1017                 else if (numseq <= 1) {
1018                         m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
1019                 }
1020
1021                 return tvalue;
1022         }
1023         catch(exception& e) {
1024                 m->errorOut(e, "Ccode", "getT");
1025                 exit(1);
1026         }
1027 }
1028 /**************************************************************************************************/
1029 float Ccode::getF(int numseq) {
1030         try {
1031
1032                 float fvalue = 0;
1033
1034                  /* F-Snedecor critical values for v1=1 and different degrees of freedom v2 and alpha 0.05 */
1035         if (numseq > 120) fvalue = 3.84;
1036         else if (numseq > 60) fvalue = 3.92;
1037         else if (numseq > 40) fvalue = 4.00;
1038         else if (numseq > 30) fvalue = 4.08;
1039         else if (numseq > 29) fvalue = 4.17;
1040         else if (numseq > 28) fvalue = 4.18;
1041         else if (numseq > 27) fvalue = 4.20;
1042         else if (numseq > 26) fvalue = 4.21;
1043         else if (numseq > 25) fvalue = 4.23;
1044         else if (numseq > 24) fvalue = 4.24;
1045         else if (numseq > 23) fvalue = 4.26;
1046         else if (numseq > 22) fvalue = 4.28;
1047         else if (numseq > 21) fvalue = 4.30;
1048         else if (numseq > 20) fvalue = 4.32;
1049         else if (numseq > 19) fvalue = 4.35;
1050         else if (numseq > 18) fvalue = 4.38;
1051         else if (numseq > 17) fvalue = 4.41;
1052         else if (numseq > 16) fvalue = 4.45;
1053         else if (numseq > 15) fvalue = 4.49;
1054         else if (numseq > 14) fvalue = 4.54;
1055         else if (numseq > 13) fvalue = 4.60;
1056         else if (numseq > 12) fvalue = 4.67;
1057         else if (numseq > 11) fvalue = 4.75;
1058         else if (numseq > 10) fvalue = 4.84;
1059         else if (numseq > 9) fvalue = 4.96;
1060         else if (numseq > 8) fvalue = 5.12;
1061         else if (numseq > 7) fvalue = 5.32;
1062         else if (numseq > 6) fvalue = 5.59;
1063         else if (numseq > 5) fvalue = 5.99;
1064         else if (numseq > 4) fvalue = 6.61;
1065         else if (numseq > 3) fvalue = 7.71;
1066         else if (numseq > 2) fvalue = 10.1;
1067         else if (numseq > 1) fvalue = 18.5;
1068         else if (numseq > 0) fvalue = 161;
1069                 else if (numseq <= 0) {
1070                         m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
1071         }
1072
1073                 return fvalue;
1074         }
1075         catch(exception& e) {
1076                 m->errorOut(e, "Ccode", "getF");
1077                 exit(1);
1078         }
1079 }
1080 //***************************************************************************************************************
1081
1082
1083