5 * Created by westcott on 8/24/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
11 #include "ignoregaps.h"
12 #include "eachgapdist.h"
15 //***************************************************************************************************************
16 Ccode::Ccode(string filename, string temp) { fastafile = filename; templateFile = temp; }
17 //***************************************************************************************************************
21 for (int i = 0; i < querySeqs.size(); i++) { delete querySeqs[i]; }
22 for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; }
25 errorOut(e, "Ccode", "~Ccode");
29 //***************************************************************************************************************
30 void Ccode::print(ostream& out) {
35 string mapInfo = getRootName(fastafile) + "mapinfo";
37 openOutputFile(mapInfo, out2);
39 out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
41 for (int j = 0; j < querySeqs.size(); j++) {
42 out2 << querySeqs[j]->getName() << endl;
43 for (it = spotMap[j].begin(); it!= spotMap[j].end(); it++) {
44 out2 << it->first << '\t' << it->second << endl;
49 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
51 out << "For full window mapping info refer to " << mapInfo << endl << endl;
53 for (int i = 0; i < querySeqs.size(); i++) {
55 out << querySeqs[i]->getName() << endl << endl << "Reference sequences used and distance to query:" << endl;
57 for (int j = 0; j < closest[i].size(); j++) {
58 out << setprecision(3) << closest[i][j].seq->getName() << '\t' << closest[i][j].dist << endl;
63 //window mapping info.
64 out << "Mapping information: ";
65 //you mask and did not filter
66 if ((seqMask != "") && (!filter)) { out << "mask and trim."; }
68 //you filtered and did not mask
69 if ((seqMask == "") && (filter)) { out << "filter and trim."; }
71 //you masked and filtered
72 if ((seqMask != "") && (filter)) { out << "mask, filter and trim."; }
74 out << endl << "Window\tStartPos\tEndPos" << endl;
77 for (int k = 0; k < windows[i].size()-1; k++) {
78 out << k+1 << '\t' << spotMap[i][windows[i][k]-it->first] << '\t' << spotMap[i][windows[i][k]-it->first+windowSizes[i]] << endl;
81 out << windows[i].size() << '\t' << spotMap[i][windows[i][windows[i].size()-1]-it->first] << '\t' << spotMap[i][it->second-it->first-1] << endl;
84 out << "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova" << endl;
85 for (int k = 0; k < windows[i].size(); k++) {
86 float ds = averageQuery[i][k] / averageRef[i][k];
87 out << k+1 << '\t' << averageQuery[i][k] << '\t' << sdQuery[i][k] << '\t' << averageRef[i][k] << '\t'<< sdRef[i][k] << '\t' << ds << '\t' << anova[i][k] << endl;
93 /* F test for differences among variances.
94 * varQuery is expected to be higher or similar than varRef */
95 //float fs = varQuery[query][i] / varRef[query][i]; /* F-Snedecor, test for differences of variances */
99 //confidence limit, t - Student, anova
100 out << "Window\tConfidenceLimit\tt-Student\tAnova" << endl;
102 for (int k = 0; k < windows[i].size(); k++) {
104 if (isChimericConfidence[i][k]) { temp += "*\t"; }
105 else { temp += "\t"; }
107 if (isChimericTStudent[i][k]) { temp += "*\t"; }
108 else { temp += "\t"; }
110 if (isChimericANOVA[i][k]) { temp += "*\t"; }
111 else { temp += "\t"; }
113 out << k+1 << '\t' << temp << endl;
115 if (temp == "*\t*\t*\t") { results = true; }
120 mothurOut(querySeqs[i]->getName() + " was found have at least one chimeric window."); mothurOutEndLine();
124 catch(exception& e) {
125 errorOut(e, "Ccode", "print");
130 //***************************************************************************************************************
131 void Ccode::getChimeras() {
134 //read in query sequences and subject sequences
135 mothurOut("Reading sequences and template file... "); cout.flush();
136 querySeqs = readSeqs(fastafile);
137 templateSeqs = readSeqs(templateFile);
138 mothurOut("Done."); mothurOutEndLine();
140 int numSeqs = querySeqs.size();
142 closest.resize(numSeqs);
144 refCombo.resize(numSeqs, 0);
145 sumRef.resize(numSeqs);
146 varRef.resize(numSeqs);
147 varQuery.resize(numSeqs);
148 sdRef.resize(numSeqs);
149 sdQuery.resize(numSeqs);
150 sumQuery.resize(numSeqs);
151 sumSquaredRef.resize(numSeqs);
152 sumSquaredQuery.resize(numSeqs);
153 averageRef.resize(numSeqs);
154 averageQuery.resize(numSeqs);
155 anova.resize(numSeqs);
156 isChimericConfidence.resize(numSeqs);
157 isChimericTStudent.resize(numSeqs);
158 isChimericANOVA.resize(numSeqs);
159 trim.resize(numSeqs);
160 spotMap.resize(numSeqs);
161 windowSizes.resize(numSeqs, window);
162 windows.resize(numSeqs);
164 //break up file if needed
165 int linesPerProcess = numSeqs / processors ;
167 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
168 //find breakup of sequences for all times we will Parallelize
169 if (processors == 1) { lines.push_back(new linePair(0, numSeqs)); }
172 for (int i = 0; i < (processors-1); i++) {
173 lines.push_back(new linePair((i*linesPerProcess), ((i*linesPerProcess) + linesPerProcess)));
175 //this is necessary to get remainder of processors / numSeqs so you don't miss any lines at the end
176 int i = processors - 1;
177 lines.push_back(new linePair((i*linesPerProcess), numSeqs));
181 lines.push_back(new linePair(0, numSeqs));
184 distCalc = new eachGapDist();
185 decalc = new DeCalculator();
188 if (processors == 1) {
189 mothurOut("Finding top matches for sequences... "); cout.flush();
190 closest = findClosest(lines[0]->start, lines[0]->end, numWanted);
191 mothurOut("Done."); mothurOutEndLine();
192 }else { createProcessesClosest(); }
195 for (int j = 0; j < numSeqs; j++) {
196 for (int i = 0; i < querySeqs[0]->getAligned().length(); i++) {
201 //mask sequences if the user wants to
203 decalc->setMask(seqMask);
206 for (int i = 0; i < querySeqs.size(); i++) {
207 decalc->runMask(querySeqs[i]);
211 for (int i = 0; i < templateSeqs.size(); i++) {
212 decalc->runMask(templateSeqs[i]);
215 for (int i = 0; i < numSeqs; i++) {
216 spotMap[i] = decalc->getMaskMap();
221 vector<Sequence*> temp = templateSeqs;
222 for (int i = 0; i < querySeqs.size(); i++) { temp.push_back(querySeqs[i]); }
226 runFilter(querySeqs);
227 runFilter(templateSeqs);
230 map<int, int> newMap;
234 for (int i = 0; i < filterString.length(); i++) {
235 if (filterString[i] == '1') {
237 newMap[spot] = spotMap[j][i];
242 for (int i = 0; i < numSeqs; i++) {
247 //trim sequences - this follows ccodes remove_extra_gaps
248 for (int i = 0; i < querySeqs.size(); i++) {
252 //windows are equivalent to words - ccode paper recommends windows are between 5% and 20% on alignment length().
253 //Our default will be 10% and we will warn if user tries to use a window above or below these recommendations
254 for (int i = 0; i < querySeqs.size(); i++) {
255 windows[i] = findWindows(i);
258 //remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later
259 if (processors == 1) {
260 for (int i = 0; i < closest.size(); i++) {
261 removeBadReferenceSeqs(closest[i], i);
263 }else { createProcessesRemoveBad(); }
266 if (processors == 1) {
267 //find the averages for each querys references
268 for (int i = 0; i < numSeqs; i++) {
269 getAverageRef(closest[i], i); //fills sumRef[i], averageRef[i], sumSquaredRef[i] and refCombo[i].
272 //find the averages for the query
273 for (int i = 0; i < numSeqs; i++) {
274 getAverageQuery(closest[i], i); //fills sumQuery[i], averageQuery[i], sumSquaredQuery[i].
276 }else { createProcessesAverages(); }
278 if (processors == 1) {
279 //find the averages for each querys references
280 for (int i = 0; i < numSeqs; i++) {
281 findVarianceRef(i); //fills varRef[i] and sdRef[i] also sets minimum error rate to 0.001 to avoid divide by 0.
284 //find the averages for the query
285 for (int i = 0; i < numSeqs; i++) {
286 findVarianceQuery(i); //fills varQuery[i] and sdQuery[i] also sets minimum error rate to 0.001 to avoid divide by 0.
288 }else { createProcessesVariances(); }
290 if (processors == 1) {
291 for (int i = 0; i < numSeqs; i++) {
292 determineChimeras(i); //fills anova, isChimericConfidence[i], isChimericTStudent[i] and isChimericANOVA[i].
294 }else { createProcessesDetermine(); }
297 for (int i = 0; i < lines.size(); i++) { delete lines[i]; }
302 catch(exception& e) {
303 errorOut(e, "Ccode", "getChimeras");
307 /***************************************************************************************************************/
308 //ccode algo says it does this to "Removes the initial and final gaps to avoid biases due to incomplete sequences."
309 void Ccode::trimSequences(int query) {
312 int frontPos = 0; //should contain first position in all seqs that is not a gap character
313 int rearPos = querySeqs[query]->getAligned().length();
315 //********find first position in closest seqs that is a non gap character***********//
316 //find first position all query seqs that is a non gap character
317 for (int i = 0; i < closest[query].size(); i++) {
319 string aligned = closest[query][i].seq->getAligned();
322 //find first spot in this seq
323 for (int j = 0; j < aligned.length(); j++) {
324 if (isalpha(aligned[j])) {
330 //save this spot if it is the farthest
331 if (pos > frontPos) { frontPos = pos; }
334 //find first position all querySeq[query] that is a non gap character
335 string aligned = querySeqs[query]->getAligned();
338 //find first spot in this seq
339 for (int j = 0; j < aligned.length(); j++) {
340 if (isalpha(aligned[j])) {
346 //save this spot if it is the farthest
347 if (pos > frontPos) { frontPos = pos; }
350 //********find last position in closest seqs that is a non gap character***********//
351 for (int i = 0; i < closest[query].size(); i++) {
353 string aligned = closest[query][i].seq->getAligned();
354 int pos = aligned.length();
356 //find first spot in this seq
357 for (int j = aligned.length()-1; j >= 0; j--) {
358 if (isalpha(aligned[j])) {
364 //save this spot if it is the farthest
365 if (pos < rearPos) { rearPos = pos; }
368 //find last position all querySeqs[query] that is a non gap character
369 aligned = querySeqs[query]->getAligned();
370 pos = aligned.length();
372 //find first spot in this seq
373 for (int j = aligned.length()-1; j >= 0; j--) {
374 if (isalpha(aligned[j])) {
380 //save this spot if it is the farthest
381 if (pos < rearPos) { rearPos = pos; }
384 //check to make sure that is not whole seq
385 if ((rearPos - frontPos - 1) <= 0) { mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); mothurOutEndLine(); exit(1); }
387 map<int, int> tempTrim;
388 tempTrim[frontPos] = rearPos;
390 //save trimmed locations
391 trim[query] = tempTrim;
394 map<int, int> newMap;
397 for (int i = frontPos; i < rearPos; i++) {
399 //cout << query << '\t' << i << '\t' << spotMap[query][i] << endl;
400 newMap[spot] = spotMap[query][i];
404 //for (it = newMap.begin(); it!=newMap.end(); it++) {
405 //cout << query << '\t' << it->first << '\t' << it->second << endl;
408 spotMap[query] = newMap;
412 catch(exception& e) {
413 errorOut(e, "Ccode", "trimSequences");
418 /***************************************************************************************************************/
419 vector<int> Ccode::findWindows(int query) {
423 it = trim[query].begin();
425 int length = it->second - it->first;
427 //default is wanted = 10% of total length
428 if (windowSizes[query] > length) {
429 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.");
430 windowSizes[query] = length / 10;
431 }else if (windowSizes[query] == 0) { windowSizes[query] = length / 10; }
432 else if (windowSizes[query] > (length / 20)) {
433 mothurOut("You have selected a window that is larger than 20% of your sequence length. This is not recommended, but I will continue anyway."); mothurOutEndLine();
434 }else if (windowSizes[query] < (length / 5)) {
435 mothurOut("You have selected a window that is smaller than 5% of your sequence length. This is not recommended, but I will continue anyway."); mothurOutEndLine();
438 //save starting points of each window
439 for (int m = it->first; m < (it->second-windowSizes[query]); m+=windowSizes[query]) { win.push_back(m); }
442 if (win[win.size()-1] < (it->first+length)) {
443 win.push_back(win[win.size()-1]+windowSizes[query]); // ex. string length is 115, window is 25, without this you would get 0, 25, 50, 75
444 } //with this you would get 1,25,50,75,100
450 catch(exception& e) {
451 errorOut(e, "Ccode", "findWindows");
455 //***************************************************************************************************************
456 int Ccode::getDiff(string seqA, string seqB) {
461 for (int i = 0; i < seqA.length(); i++) {
462 //if you are both not gaps
463 //if (isalpha(seqA[i]) && isalpha(seqA[i])) {
465 if (seqA[i] != seqB[i]) {
466 int ok; /* ok=1 means equivalent base. Checks for degenerate bases */
468 /* the char in base_a and base_b have been checked and they are different */
469 if ((seqA[i] == 'N') && (seqB[i] != '-')) ok = 1;
470 else if ((seqB[i] == 'N') && (seqA[i] != '-')) ok = 1;
471 else if ((seqA[i] == 'Y') && ((seqB[i] == 'C') || (seqB[i] == 'T'))) ok = 1;
472 else if ((seqB[i] == 'Y') && ((seqA[i] == 'C') || (seqA[i] == 'T'))) ok = 1;
473 else if ((seqA[i] == 'R') && ((seqB[i] == 'G') || (seqB[i] == 'A'))) ok = 1;
474 else if ((seqB[i] == 'R') && ((seqA[i] == 'G') || (seqA[i] == 'A'))) ok = 1;
475 else if ((seqA[i] == 'S') && ((seqB[i] == 'C') || (seqB[i] == 'G'))) ok = 1;
476 else if ((seqB[i] == 'S') && ((seqA[i] == 'C') || (seqA[i] == 'G'))) ok = 1;
477 else if ((seqA[i] == 'W') && ((seqB[i] == 'T') || (seqB[i] == 'A'))) ok = 1;
478 else if ((seqB[i] == 'W') && ((seqA[i] == 'T') || (seqA[i] == 'A'))) ok = 1;
479 else if ((seqA[i] == 'M') && ((seqB[i] == 'A') || (seqB[i] == 'C'))) ok = 1;
480 else if ((seqB[i] == 'M') && ((seqA[i] == 'A') || (seqA[i] == 'C'))) ok = 1;
481 else if ((seqA[i] == 'K') && ((seqB[i] == 'T') || (seqB[i] == 'G'))) ok = 1;
482 else if ((seqB[i] == 'K') && ((seqA[i] == 'T') || (seqA[i] == 'G'))) ok = 1;
483 else if ((seqA[i] == 'V') && ((seqB[i] == 'C') || (seqB[i] == 'A') || (seqB[i] == 'G'))) ok = 1;
484 else if ((seqB[i] == 'V') && ((seqA[i] == 'C') || (seqA[i] == 'A') || (seqA[i] == 'G'))) ok = 1;
485 else if ((seqA[i] == 'H') && ((seqB[i] == 'T') || (seqB[i] == 'A') || (seqB[i] == 'C'))) ok = 1;
486 else if ((seqB[i] == 'H') && ((seqA[i] == 'T') || (seqA[i] == 'A') || (seqA[i] == 'C'))) ok = 1;
487 else if ((seqA[i] == 'D') && ((seqB[i] == 'T') || (seqB[i] == 'A') || (seqB[i] == 'G'))) ok = 1;
488 else if ((seqB[i] == 'D') && ((seqA[i] == 'T') || (seqA[i] == 'A') || (seqA[i] == 'G'))) ok = 1;
489 else if ((seqA[i] == 'B') && ((seqB[i] == 'C') || (seqB[i] == 'T') || (seqB[i] == 'G'))) ok = 1;
490 else if ((seqB[i] == 'B') && ((seqA[i] == 'C') || (seqA[i] == 'T') || (seqA[i] == 'G'))) ok = 1;
491 else ok = 0; /* the bases are different and not equivalent */
493 //check if they are both blanks
494 if ((seqA[i] == '.') && (seqB[i] == '-')) ok = 1;
495 else if ((seqB[i] == '.') && (seqA[i] == '-')) ok = 1;
497 if (ok == 0) { numDiff++; }
505 catch(exception& e) {
506 errorOut(e, "Ccode", "getDiff");
510 //***************************************************************************************************************
511 //tried to make this look most like ccode original implementation
512 void Ccode::removeBadReferenceSeqs(vector<SeqDist>& seqs, int query) {
515 vector< vector<int> > numDiffBases;
516 numDiffBases.resize(seqs.size());
518 for (int i = 0; i < numDiffBases.size(); i++) { numDiffBases[i].resize(seqs.size(),0); }
520 it = trim[query].begin();
521 int length = it->second - it->first;
523 //calc differences from each sequence to everyother seq in the set
524 for (int i = 0; i < seqs.size(); i++) {
526 string seqA = seqs[i].seq->getAligned().substr(it->first, length);
528 //so you don't calc i to j and j to i since they are the same
529 for (int j = 0; j < i; j++) {
531 string seqB = seqs[j].seq->getAligned().substr(it->first, length);
534 int numDiff = getDiff(seqA, seqB);
536 numDiffBases[i][j] = numDiff;
537 numDiffBases[j][i] = numDiff;
541 //initailize remove to 0
542 vector<int> remove; remove.resize(seqs.size(), 0);
543 float top = ((20*length) / (float) 100);
544 float bottom = ((0.5*length) / (float) 100);
546 //check each numDiffBases and if any are higher than threshold set remove to 1 so you can remove those seqs from the closest set
547 for (int i = 0; i < numDiffBases.size(); i++) {
548 for (int j = 0; j < i; j++) {
549 //are you more than 20% different
550 if (numDiffBases[i][j] > top) { remove[j] = 1; }
551 //are you less than 0.5% different
552 if (numDiffBases[i][j] < bottom) { remove[j] = 1; }
558 //count seqs that are not going to be removed
559 for (int i = 0; i < remove.size(); i++) {
560 if (remove[i] == 0) { numSeqsLeft++; }
563 //if you have enough then remove bad ones
564 if (numSeqsLeft >= 3) {
565 vector<SeqDist> goodSeqs;
567 for (int i = 0; i < remove.size(); i++) {
568 if (remove[i] == 0) {
569 goodSeqs.push_back(seqs[i]);
575 }else { //warn, but dont remove any
576 mothurOut(querySeqs[query]->getName() + " does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check."); mothurOutEndLine();
581 catch(exception& e) {
582 errorOut(e, "Ccode", "removeBadReferenceSeqs");
586 //***************************************************************************************************************
587 vector< vector<SeqDist> > Ccode::findClosest(int start, int end, int numWanted) {
590 vector< vector<SeqDist> > topMatches; topMatches.resize(querySeqs.size());
592 float smallestOverall, smallestLeft, smallestRight;
593 smallestOverall = 1000; smallestLeft = 1000; smallestRight = 1000;
595 //for each sequence in querySeqs - find top matches to use as reference
596 for(int j = start; j < end; j++){
598 Sequence query = *(querySeqs[j]);
600 vector<SeqDist> distances;
602 //calc distance to each sequence in template seqs
603 for (int i = 0; i < templateSeqs.size(); i++) {
605 Sequence ref = *(templateSeqs[i]);
608 distCalc->calcDist(query, ref);
609 float dist = distCalc->getDist();
613 temp.seq = templateSeqs[i];
616 distances.push_back(temp);
619 sort(distances.begin(), distances.end(), compareSeqDist);
621 //save the number of top matches wanted
622 for (int h = 0; h < numWanted; h++) {
623 topMatches[j].push_back(distances[h]);
630 catch(exception& e) {
631 errorOut(e, "Ccode", "findClosestSides");
635 /**************************************************************************************************/
636 //find the distances from each reference sequence to every other reference sequence for each window for this query
637 void Ccode::getAverageRef(vector<SeqDist> ref, int query) {
640 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.
642 //initialize diffs vector
643 diffs.resize(ref.size());
644 for (int i = 0; i < diffs.size(); i++) {
645 diffs[i].resize(ref.size());
646 for (int j = 0; j < diffs[i].size(); j++) {
647 diffs[i][j].resize(windows[query].size(), 0);
651 it = trim[query].begin();
653 //find the distances from each reference sequence to every other reference sequence for each window for this query
654 for (int i = 0; i < ref.size(); i++) {
656 string refI = ref[i].seq->getAligned();
658 //j<i, so you don't find distances from i to j and then j to i.
659 for (int j = 0; j < i; j++) {
661 string refJ = ref[j].seq->getAligned();
663 for (int k = 0; k < windows[query].size(); k++) {
665 string refIWindowk, refJWindowk;
667 if (k < windows[query].size()-1) {
669 refIWindowk = refI.substr(windows[query][k], windowSizes[query]);
670 refJWindowk = refJ.substr(windows[query][k], windowSizes[query]);
671 }else { //last window may be smaller than rest - see findwindows
673 refIWindowk = refI.substr(windows[query][k], (it->second-windows[query][k]));
674 refJWindowk = refJ.substr(windows[query][k], (it->second-windows[query][k]));
678 int diff = getDiff(refIWindowk, refJWindowk);
679 //cout << i << '\t' << j << '\t' << k << '\t' << diff << endl;
680 //save differences in [i][j][k] and [j][i][k] since they are the same
681 diffs[i][j][k] = diff;
682 diffs[j][i][k] = diff;
690 //initialize sumRef for this query
691 sumRef[query].resize(windows[query].size(), 0);
692 sumSquaredRef[query].resize(windows[query].size(), 0);
693 averageRef[query].resize(windows[query].size(), 0);
695 //find the sum of the differences for hte reference sequences
696 for (int i = 0; i < diffs.size(); i++) {
697 for (int j = 0; j < i; j++) {
699 //increment this querys reference sequences combos
702 for (int k = 0; k < diffs[i][j].size(); k++) {
703 sumRef[query][k] += diffs[i][j][k];
704 sumSquaredRef[query][k] += (diffs[i][j][k]*diffs[i][j][k]);
711 //find the average of the differences for the references for each window
712 for (int i = 0; i < windows[query].size(); i++) {
713 averageRef[query][i] = sumRef[query][i] / (float) refCombo[query];
717 catch(exception& e) {
718 errorOut(e, "Ccode", "getAverageRef");
722 /**************************************************************************************************/
723 void Ccode::getAverageQuery (vector<SeqDist> ref, int query) {
726 vector< vector<int> > diffs; //diffs[1][2] is the number of differences between querySeqs[query] and ref seq 1 at window 2.
728 //initialize diffs vector
729 diffs.resize(ref.size());
730 for (int j = 0; j < diffs.size(); j++) {
731 diffs[j].resize(windows[query].size(), 0);
734 it = trim[query].begin();
736 string refQuery = querySeqs[query]->getAligned();
738 //j<i, so you don't find distances from i to j and then j to i.
739 for (int j = 0; j < ref.size(); j++) {
741 string refJ = ref[j].seq->getAligned();
743 for (int k = 0; k < windows[query].size(); k++) {
745 string QueryWindowk, refJWindowk;
747 if (k < windows[query].size()-1) {
749 QueryWindowk = refQuery.substr(windows[query][k], windowSizes[query]);
750 refJWindowk = refJ.substr(windows[query][k], windowSizes[query]);
751 }else { //last window may be smaller than rest - see findwindows
753 QueryWindowk = refQuery.substr(windows[query][k], (it->second-windows[query][k]));
754 refJWindowk = refJ.substr(windows[query][k], (it->second-windows[query][k]));
758 int diff = getDiff(QueryWindowk, refJWindowk);
759 //cout << j << '\t' << k << '\t' << diff << endl;
767 //initialize sumRef for this query
768 sumQuery[query].resize(windows[query].size(), 0);
769 sumSquaredQuery[query].resize(windows[query].size(), 0);
770 averageQuery[query].resize(windows[query].size(), 0);
772 //find the sum of the differences
773 for (int j = 0; j < diffs.size(); j++) {
774 for (int k = 0; k < diffs[j].size(); k++) {
775 sumQuery[query][k] += diffs[j][k];
776 sumSquaredQuery[query][k] += (diffs[j][k]*diffs[j][k]);
781 //find the average of the differences for the references for each window
782 for (int i = 0; i < windows[query].size(); i++) {
783 averageQuery[query][i] = sumQuery[query][i] / (float) ref.size();
788 catch(exception& e) {
789 errorOut(e, "Ccode", "getAverageQuery");
793 /**************************************************************************************************/
794 void Ccode::findVarianceRef (int query) {
797 varRef[query].resize(windows[query].size(), 0);
798 sdRef[query].resize(windows[query].size(), 0);
801 for (int i = 0; i < windows[query].size(); i++) {
802 varRef[query][i] = (sumSquaredRef[query][i] - ((sumRef[query][i]*sumRef[query][i])/(float)refCombo[query])) / (float)(refCombo[query]-1);
803 sdRef[query][i] = sqrt(varRef[query][i]);
805 //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation
806 if (averageRef[query][i] < 0.001) { averageRef[query][i] = 0.001; }
807 if (sumRef[query][i] < 0.001) { sumRef[query][i] = 0.001; }
808 if (varRef[query][i] < 0.001) { varRef[query][i] = 0.001; }
809 if (sumSquaredRef[query][i] < 0.001) { sumSquaredRef[query][i] = 0.001; }
810 if (sdRef[query][i] < 0.001) { sdRef[query][i] = 0.001; }
814 catch(exception& e) {
815 errorOut(e, "Ccode", "findVarianceRef");
819 /**************************************************************************************************/
820 void Ccode::findVarianceQuery (int query) {
822 varQuery[query].resize(windows[query].size(), 0);
823 sdQuery[query].resize(windows[query].size(), 0);
826 for (int i = 0; i < windows[query].size(); i++) {
827 varQuery[query][i] = (sumSquaredQuery[query][i] - ((sumQuery[query][i]*sumQuery[query][i])/(float) closest[query].size())) / (float) (closest[query].size()-1);
828 sdQuery[query][i] = sqrt(varQuery[query][i]);
830 //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation
831 if (averageQuery[query][i] < 0.001) { averageQuery[query][i] = 0.001; }
832 if (sumQuery[query][i] < 0.001) { sumQuery[query][i] = 0.001; }
833 if (varQuery[query][i] < 0.001) { varQuery[query][i] = 0.001; }
834 if (sumSquaredQuery[query][i] < 0.001) { sumSquaredQuery[query][i] = 0.001; }
835 if (sdQuery[query][i] < 0.001) { sdQuery[query][i] = 0.001; }
839 catch(exception& e) {
840 errorOut(e, "Ccode", "findVarianceQuery");
844 /**************************************************************************************************/
845 void Ccode::determineChimeras (int query) {
848 isChimericConfidence[query].resize(windows[query].size(), false);
849 isChimericTStudent[query].resize(windows[query].size(), false);
850 isChimericANOVA[query].resize(windows[query].size(), false);
851 anova[query].resize(windows[query].size());
855 for (int i = 0; i < windows[query].size(); i++) {
857 //get confidence limits
858 float t = getT(closest[query].size()-1); //how many seqs you are comparing to this querySeq
859 float dsUpper = (averageQuery[query][i] + (t * sdQuery[query][i])) / averageRef[query][i];
860 float dsLower = (averageQuery[query][i] - (t * sdQuery[query][i])) / averageRef[query][i];
861 //cout << t << '\t' << "ds upper = " << dsUpper << " dsLower = " << dsLower << endl;
862 if ((dsUpper > 1.0) && (dsLower > 1.0) && (averageQuery[query][i] > averageRef[query][i])) { /* range does not include 1 */
863 isChimericConfidence[query][i] = true; /* significantly higher at P<0.05 */
864 //cout << i << " made it here" << endl;
868 int degreeOfFreedom = refCombo[query] + closest[query].size() - 2;
869 float denomForT = (((refCombo[query]-1) * varQuery[query][i] + (closest[query].size() - 1) * varRef[query][i]) / (float) degreeOfFreedom) * ((refCombo[query] + closest[query].size()) / (float) (refCombo[query] * closest[query].size())); /* denominator, without sqrt(), for ts calculations */
871 float ts = fabs((averageQuery[query][i] - averageRef[query][i]) / (sqrt(denomForT))); /* value of ts for t-student test */
872 t = getT(degreeOfFreedom);
873 //cout << i << '\t' << t << '\t' << ts << endl;
874 if ((ts >= t) && (averageQuery[query][i] > averageRef[query][i])) {
875 isChimericTStudent[query][i] = true; /* significantly higher at P<0.05 */
879 float value1 = sumQuery[query][i] + sumRef[query][i];
880 float value2 = sumSquaredQuery[query][i] + sumSquaredRef[query][i];
881 float value3 = ((sumQuery[query][i]*sumQuery[query][i]) / (float) (closest[query].size())) + ((sumRef[query][i] * sumRef[query][i]) / (float) refCombo[query]);
882 float value4 = (value1 * value1) / ( (float) (closest[query].size() + refCombo[query]) );
883 float value5 = value2 - value4;
884 float value6 = value3 - value4;
885 float value7 = value5 - value6;
886 float value8 = value7 / ((float) degreeOfFreedom);
887 float anovaValue = value6 / value8;
889 float f = getF(degreeOfFreedom);
891 if ((anovaValue >= f) && (averageQuery[query][i] > averageRef[query][i])) {
892 isChimericANOVA[query][i] = true; /* significant P<0.05 */
895 if (isnan(anovaValue) || isinf(anovaValue)) { anovaValue = 0.0; }
897 anova[query][i] = anovaValue;
901 catch(exception& e) {
902 errorOut(e, "Ccode", "determineChimeras");
906 /**************************************************************************************************/
907 float Ccode::getT(int numseq) {
912 /* t-student critical values for different degrees of freedom and alpha 0.1 in one-tail tests (equivalent to 0.05) */
913 if (numseq > 120) tvalue = 1.645;
914 else if (numseq > 60) tvalue = 1.658;
915 else if (numseq > 40) tvalue = 1.671;
916 else if (numseq > 30) tvalue = 1.684;
917 else if (numseq > 29) tvalue = 1.697;
918 else if (numseq > 28) tvalue = 1.699;
919 else if (numseq > 27) tvalue = 1.701;
920 else if (numseq > 26) tvalue = 1.703;
921 else if (numseq > 25) tvalue = 1.706;
922 else if (numseq > 24) tvalue = 1.708;
923 else if (numseq > 23) tvalue = 1.711;
924 else if (numseq > 22) tvalue = 1.714;
925 else if (numseq > 21) tvalue = 1.717;
926 else if (numseq > 20) tvalue = 1.721;
927 else if (numseq > 19) tvalue = 1.725;
928 else if (numseq > 18) tvalue = 1.729;
929 else if (numseq > 17) tvalue = 1.734;
930 else if (numseq > 16) tvalue = 1.740;
931 else if (numseq > 15) tvalue = 1.746;
932 else if (numseq > 14) tvalue = 1.753;
933 else if (numseq > 13) tvalue = 1.761;
934 else if (numseq > 12) tvalue = 1.771;
935 else if (numseq > 11) tvalue = 1.782;
936 else if (numseq > 10) tvalue = 1.796;
937 else if (numseq > 9) tvalue = 1.812;
938 else if (numseq > 8) tvalue = 1.833;
939 else if (numseq > 7) tvalue = 1.860;
940 else if (numseq > 6) tvalue = 1.895;
941 else if (numseq > 5) tvalue = 1.943;
942 else if (numseq > 4) tvalue = 2.015;
943 else if (numseq > 3) tvalue = 2.132;
944 else if (numseq > 2) tvalue = 2.353;
945 else if (numseq > 1) tvalue = 2.920;
946 else if (numseq <= 1) {
947 mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine();
952 catch(exception& e) {
953 errorOut(e, "Ccode", "getT");
957 /**************************************************************************************************/
958 float Ccode::getF(int numseq) {
963 /* F-Snedecor critical values for v1=1 and different degrees of freedom v2 and alpha 0.05 */
964 if (numseq > 120) fvalue = 3.84;
965 else if (numseq > 60) fvalue = 3.92;
966 else if (numseq > 40) fvalue = 4.00;
967 else if (numseq > 30) fvalue = 4.08;
968 else if (numseq > 29) fvalue = 4.17;
969 else if (numseq > 28) fvalue = 4.18;
970 else if (numseq > 27) fvalue = 4.20;
971 else if (numseq > 26) fvalue = 4.21;
972 else if (numseq > 25) fvalue = 4.23;
973 else if (numseq > 24) fvalue = 4.24;
974 else if (numseq > 23) fvalue = 4.26;
975 else if (numseq > 22) fvalue = 4.28;
976 else if (numseq > 21) fvalue = 4.30;
977 else if (numseq > 20) fvalue = 4.32;
978 else if (numseq > 19) fvalue = 4.35;
979 else if (numseq > 18) fvalue = 4.38;
980 else if (numseq > 17) fvalue = 4.41;
981 else if (numseq > 16) fvalue = 4.45;
982 else if (numseq > 15) fvalue = 4.49;
983 else if (numseq > 14) fvalue = 4.54;
984 else if (numseq > 13) fvalue = 4.60;
985 else if (numseq > 12) fvalue = 4.67;
986 else if (numseq > 11) fvalue = 4.75;
987 else if (numseq > 10) fvalue = 4.84;
988 else if (numseq > 9) fvalue = 4.96;
989 else if (numseq > 8) fvalue = 5.12;
990 else if (numseq > 7) fvalue = 5.32;
991 else if (numseq > 6) fvalue = 5.59;
992 else if (numseq > 5) fvalue = 5.99;
993 else if (numseq > 4) fvalue = 6.61;
994 else if (numseq > 3) fvalue = 7.71;
995 else if (numseq > 2) fvalue = 10.1;
996 else if (numseq > 1) fvalue = 18.5;
997 else if (numseq > 0) fvalue = 161;
998 else if (numseq <= 0) {
999 mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine();
1004 catch(exception& e) {
1005 errorOut(e, "Ccode", "getF");
1010 /**************************************************************************************************/
1011 void Ccode::createProcessesClosest() {
1013 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1015 vector<int> processIDS;
1017 //loop through and create all the processes you want
1018 while (process != processors) {
1022 processIDS.push_back(pid);
1024 }else if (pid == 0){
1026 mothurOut("Finding top matches for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
1027 closest = findClosest(lines[process]->start, lines[process]->end, numWanted);
1028 mothurOut("Done finding top matches for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
1030 //write out data to file so parent can read it
1032 string s = toString(getpid()) + ".temp";
1033 openOutputFile(s, out);
1036 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1037 for (int j = 0; j < closest[i].size(); j++) {
1038 closest[i][j].seq->printSequence(out);
1041 out << ">" << endl; //to stop sequence read
1043 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1044 for (int j = 0; j < closest[i].size(); j++) {
1045 out << closest[i][j].dist << '\t';
1051 }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
1054 //force parent to wait until all the processes are done
1055 for (int i=0;i<processors;i++) {
1056 int temp = processIDS[i];
1060 //get data created by processes
1061 for (int i=0;i<processors;i++) {
1063 string s = toString(processIDS[i]) + ".temp";
1064 openInputFile(s, in);
1066 vector< vector<Sequence*> > tempClosest; tempClosest.resize(querySeqs.size());
1068 for (int k = lines[i]->start; k < lines[i]->end; k++) {
1069 vector<Sequence*> tempVector;
1071 for (int j = 0; j < numWanted; j++) {
1073 Sequence* temp = new Sequence(in);
1076 tempVector.push_back(temp);
1079 tempClosest[k] = tempVector;
1083 in >> junk; gobble(in); // to get ">"
1085 vector< vector<float> > dists; dists.resize(querySeqs.size());
1087 for (int k = lines[i]->start; k < lines[i]->end; k++) {
1088 dists[k].resize(numWanted);
1089 for (int j = 0; j < numWanted; j++) {
1096 for (int k = lines[i]->start; k < lines[i]->end; k++) {
1097 closest[k].resize(numWanted);
1098 for (int j = 0; j < closest[k].size(); j++) {
1099 closest[k][j].seq = tempClosest[k][j];
1100 closest[k][j].dist = dists[k][j];
1110 closest = findClosest(lines[0]->start, lines[0]->end, numWanted);
1114 catch(exception& e) {
1115 errorOut(e, "Ccode", "createProcessesClosest");
1120 //***************************************************************************************************************
1121 void Ccode::createProcessesRemoveBad() {
1123 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1125 vector<int> processIDS;
1127 //loop through and create all the processes you want
1128 while (process != processors) {
1132 processIDS.push_back(pid);
1134 }else if (pid == 0){
1136 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1137 removeBadReferenceSeqs(closest[i], i);
1140 //write out data to file so parent can read it
1142 string s = toString(getpid()) + ".temp";
1143 openOutputFile(s, out);
1146 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1147 out << closest[i].size() << endl;
1148 for (int j = 0; j < closest[i].size(); j++) {
1149 closest[i][j].seq->printSequence(out);
1151 out << ">" << endl; //to stop sequence read
1154 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1155 for (int j = 0; j < closest[i].size(); j++) {
1156 out << closest[i][j].dist << '\t';
1164 }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
1167 //force parent to wait until all the processes are done
1168 for (int i=0;i<processors;i++) {
1169 int temp = processIDS[i];
1173 //get data created by processes
1174 for (int i=0;i<processors;i++) {
1176 string s = toString(processIDS[i]) + ".temp";
1177 openInputFile(s, in);
1179 vector< vector<Sequence*> > tempClosest; tempClosest.resize(querySeqs.size());
1182 for (int k = lines[i]->start; k < lines[i]->end; k++) {
1186 sizes.push_back(num);
1189 vector<Sequence*> tempVector;
1191 for (int j = 0; j < num; j++) {
1193 Sequence* temp = new Sequence(in);
1196 tempVector.push_back(temp);
1199 in >> junk; gobble(in); // to get ">"
1201 tempClosest[k] = tempVector;
1204 vector< vector<float> > dists; dists.resize(querySeqs.size());
1206 for (int k = lines[i]->start; k < lines[i]->end; k++) {
1207 dists[k].resize(sizes[count]);
1208 for (int j = 0; j < sizes[count]; j++) {
1216 for (int k = lines[i]->start; k < lines[i]->end; k++) {
1217 for (int j = 0; j < sizes[count]; j++) {
1218 closest[k][j].seq = tempClosest[k][j];
1219 closest[k][j].dist = dists[k][j];
1228 for (int i = 0; i < closest.size(); i++) {
1229 removeBadReferenceSeqs(closest[i], i);
1234 catch(exception& e) {
1235 errorOut(e, "Ccode", "createProcessesRemoveBad");
1239 //***************************************************************************************************************
1240 void Ccode::createProcessesAverages() {
1242 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1244 vector<int> processIDS;
1246 //loop through and create all the processes you want
1247 while (process != processors) {
1251 processIDS.push_back(pid);
1253 }else if (pid == 0){
1255 //find the averages for each querys references
1256 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1257 getAverageRef(closest[i], i); //fills sumRef[i], averageRef[i], sumSquaredRef[i] and refCombo[i].
1260 //find the averages for the query
1261 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1262 getAverageQuery(closest[i], i); //fills sumQuery[i], averageQuery[i], sumSquaredQuery[i].
1266 //write out data to file so parent can read it
1268 string s = toString(getpid()) + ".temp";
1269 openOutputFile(s, out);
1272 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1273 for (int j = 0; j < windows[i].size(); j++) {
1274 out << sumRef[i][j] << '\t';
1277 for (int j = 0; j < windows[i].size(); j++) {
1278 out << averageRef[i][j] << '\t';
1281 for (int j = 0; j < windows[i].size(); j++) {
1282 out << sumSquaredRef[i][j] << '\t';
1285 for (int j = 0; j < windows[i].size(); j++) {
1286 out << sumQuery[i][j] << '\t';
1289 for (int j = 0; j < windows[i].size(); j++) {
1290 out << averageQuery[i][j] << '\t';
1293 for (int j = 0; j < windows[i].size(); j++) {
1294 out << sumSquaredQuery[i][j] << '\t';
1297 out << refCombo[i] << endl;
1303 }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
1306 //force parent to wait until all the processes are done
1307 for (int i=0;i<processors;i++) {
1308 int temp = processIDS[i];
1312 //get data created by processes
1313 for (int i=0;i<processors;i++) {
1315 string s = toString(processIDS[i]) + ".temp";
1316 openInputFile(s, in);
1319 for (int k = lines[i]->start; k < lines[i]->end; k++) {
1320 sumRef[k].resize(windows[k].size());
1321 averageRef[k].resize(windows[k].size());
1322 sumSquaredRef[k].resize(windows[k].size());
1323 averageQuery[k].resize(windows[k].size());
1324 sumQuery[k].resize(windows[k].size());
1325 sumSquaredQuery[k].resize(windows[k].size());
1327 for (int j = 0; j < windows[k].size(); j++) {
1331 for (int j = 0; j < windows[k].size(); j++) {
1332 in >> averageRef[k][j];
1335 for (int j = 0; j < windows[k].size(); j++) {
1336 in >> sumSquaredRef[k][j];
1339 for (int j = 0; j < windows[k].size(); j++) {
1340 in >> sumQuery[k][j];
1343 for (int j = 0; j < windows[k].size(); j++) {
1344 in >> averageQuery[k][j];
1347 for (int j = 0; j < windows[k].size(); j++) {
1348 in >> sumSquaredQuery[k][j];
1359 //find the averages for each querys references
1360 for (int i = 0; i < querySeqs.size(); i++) {
1361 getAverageRef(closest[i], i); //fills sumRef[i], averageRef[i], sumSquaredRef[i] and refCombo[i].
1364 //find the averages for the query
1365 for (int i = 0; i < querySeqs.size(); i++) {
1366 getAverageQuery(closest[i], i); //fills sumQuery[i], averageQuery[i], sumSquaredQuery[i].
1372 catch(exception& e) {
1373 errorOut(e, "Ccode", "createProcessesAverages");
1377 //***************************************************************************************************************
1378 void Ccode::createProcessesVariances() {
1380 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1382 vector<int> processIDS;
1384 //loop through and create all the processes you want
1385 while (process != processors) {
1389 processIDS.push_back(pid);
1391 }else if (pid == 0){
1393 //find the averages for each querys references
1394 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1395 findVarianceRef(i); //fills varRef[i] and sdRef[i] also sets minimum error rate to 0.001 to avoid divide by 0.
1398 //find the averages for the query
1399 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1400 findVarianceQuery(i); //fills varQuery[i] and sdQuery[i] also sets minimum error rate to 0.001 to avoid divide by 0.
1404 //write out data to file so parent can read it
1406 string s = toString(getpid()) + ".temp";
1407 openOutputFile(s, out);
1410 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1411 for (int j = 0; j < windows[i].size(); j++) {
1412 out << varRef[i][j] << '\t';
1415 for (int j = 0; j < windows[i].size(); j++) {
1416 out << sdRef[i][j] << '\t';
1419 for (int j = 0; j < windows[i].size(); j++) {
1420 out << varQuery[i][j] << '\t';
1423 for (int j = 0; j < windows[i].size(); j++) {
1424 out << sdQuery[i][j] << '\t';
1432 }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
1435 //force parent to wait until all the processes are done
1436 for (int i=0;i<processors;i++) {
1437 int temp = processIDS[i];
1441 //get data created by processes
1442 for (int i=0;i<processors;i++) {
1444 string s = toString(processIDS[i]) + ".temp";
1445 openInputFile(s, in);
1448 for (int k = lines[i]->start; k < lines[i]->end; k++) {
1449 varRef[k].resize(windows[k].size());
1450 sdRef[k].resize(windows[k].size());
1451 varQuery[k].resize(windows[k].size());
1452 sdQuery[k].resize(windows[k].size());
1454 for (int j = 0; j < windows[k].size(); j++) {
1458 for (int j = 0; j < windows[k].size(); j++) {
1462 for (int j = 0; j < windows[k].size(); j++) {
1463 in >> varQuery[k][j];
1466 for (int j = 0; j < windows[k].size(); j++) {
1467 in >> sdQuery[k][j];
1476 //find the averages for each querys references
1477 for (int i = 0; i < querySeqs.size(); i++) {
1478 findVarianceRef(i); //fills varRef[i] and sdRef[i] also sets minimum error rate to 0.001 to avoid divide by 0.
1481 //find the averages for the query
1482 for (int i = 0; i < querySeqs.size(); i++) {
1483 findVarianceQuery(i); //fills v arQuery[i] and sdQuery[i] also sets minimum error rate to 0.001 to avoid divide by 0.
1487 catch(exception& e) {
1488 errorOut(e, "Ccode", "createProcessesVariances");
1492 //***************************************************************************************************************
1493 void Ccode::createProcessesDetermine() {
1495 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1497 vector<int> processIDS;
1499 //loop through and create all the processes you want
1500 while (process != processors) {
1504 processIDS.push_back(pid);
1506 }else if (pid == 0){
1508 //find the averages for each querys references
1509 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1510 determineChimeras(i); //fills anova, isChimericConfidence[i], isChimericTStudent[i] and isChimericANOVA[i].
1513 //write out data to file so parent can read it
1515 string s = toString(getpid()) + ".temp";
1516 openOutputFile(s, out);
1519 for (int i = lines[process]->start; i < lines[process]->end; i++) {
1520 for (int j = 0; j < windows[i].size(); j++) {
1521 out << anova[i][j] << '\t';
1524 for (int j = 0; j < windows[i].size(); j++) {
1525 out << isChimericConfidence[i][j] << '\t';
1528 for (int j = 0; j < windows[i].size(); j++) {
1529 out << isChimericTStudent[i][j] << '\t';
1532 for (int j = 0; j < windows[i].size(); j++) {
1533 out << isChimericANOVA[i][j] << '\t';
1541 }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
1544 //force parent to wait until all the processes are done
1545 for (int i=0;i<processors;i++) {
1546 int temp = processIDS[i];
1550 //get data created by processes
1551 for (int i=0;i<processors;i++) {
1553 string s = toString(processIDS[i]) + ".temp";
1554 openInputFile(s, in);
1557 for (int k = lines[i]->start; k < lines[i]->end; k++) {
1558 anova[k].resize(windows[k].size());
1559 isChimericConfidence[k].resize(windows[k].size(), false);
1560 isChimericTStudent[k].resize(windows[k].size(), false);
1561 isChimericANOVA[k].resize(windows[k].size(), false);
1564 for (int j = 0; j < windows[k].size(); j++) {
1568 for (int j = 0; j < windows[k].size(); j++) {
1570 if (tempBool == 1) { isChimericConfidence[k][j] = true; }
1573 for (int j = 0; j < windows[k].size(); j++) {
1575 if (tempBool == 1) { isChimericTStudent[k][j] = true; }
1578 for (int j = 0; j < windows[k].size(); j++) {
1580 if (tempBool == 1) { isChimericANOVA[k][j] = true; }
1589 for (int i = 0; i < querySeqs.size(); i++) {
1590 determineChimeras(i); //fills anova, isChimericConfidence[i], isChimericTStudent[i] and isChimericANOVA[i].
1595 catch(exception& e) {
1596 errorOut(e, "Ccode", "createProcessesDetermine");
1600 //***************************************************************************************************************