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 o) {
17 fastafile = filename; outputDir = o;
18 distCalc = new eachGapDist();
19 decalc = new DeCalculator();
21 mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
23 openOutputFile(mapInfo, out2);
25 out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
28 //***************************************************************************************************************
33 //***************************************************************************************************************
34 void Ccode::printHeader(ostream& out) {
35 out << "For full window mapping info refer to " << mapInfo << endl << endl;
37 //***************************************************************************************************************
38 void Ccode::print(ostream& out, ostream& outAcc) {
42 openOutputFileAppend(mapInfo, out2);
44 out2 << querySeq->getName() << endl;
45 for (it = spotMap.begin(); it!= spotMap.end(); it++) {
46 out2 << it->first << '\t' << it->second << endl;
49 out << querySeq->getName() << endl << endl << "Reference sequences used and distance to query:" << endl;
51 for (int j = 0; j < closest.size(); j++) {
52 out << closest[j].seq->getName() << '\t' << closest[j].dist << endl;
57 //window mapping info.
58 out << "Mapping information: ";
59 //you mask and did not filter
60 if ((seqMask != "") && (!filter)) { out << "mask and trim."; }
62 //you filtered and did not mask
63 if ((seqMask == "") && (filter)) { out << "filter and trim."; }
65 //you masked and filtered
66 if ((seqMask != "") && (filter)) { out << "mask, filter and trim."; }
68 out << endl << "Window\tStartPos\tEndPos" << endl;
70 for (int k = 0; k < windows.size()-1; k++) {
71 out << k+1 << '\t' << spotMap[windows[k]-it->first] << '\t' << spotMap[windows[k]-it->first+windowSizes] << endl;
74 out << windows.size() << '\t' << spotMap[windows[windows.size()-1]-it->first] << '\t' << spotMap[it->second-it->first-1] << endl;
76 out << "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova" << endl;
77 for (int k = 0; k < windows.size(); k++) {
78 float ds = averageQuery[k] / averageRef[k];
79 out << k+1 << '\t' << averageQuery[k] << '\t' << sdQuery[k] << '\t' << averageRef[k] << '\t'<< sdRef[k] << '\t' << ds << '\t' << anova[k] << endl;
85 /* F test for differences among variances.
86 * varQuery is expected to be higher or similar than varRef */
87 //float fs = varQuery[query] / varRef[query]; /* F-Snedecor, test for differences of variances */
91 //confidence limit, t - Student, anova
92 out << "Window\tConfidenceLimit\tt-Student\tAnova" << endl;
94 for (int k = 0; k < windows.size(); k++) {
96 if (isChimericConfidence[k]) { temp += "*\t"; }
97 else { temp += "\t"; }
99 if (isChimericTStudent[k]) { temp += "*\t"; }
100 else { temp += "\t"; }
102 if (isChimericANOVA[k]) { temp += "*\t"; }
103 else { temp += "\t"; }
105 out << k+1 << '\t' << temp << endl;
107 if (temp == "*\t*\t*\t") { results = true; }
112 m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
113 outAcc << querySeq->getName() << endl;
117 for (int i = 0; i < closest.size(); i++) { delete closest[i].seq; }
121 catch(exception& e) {
122 m->errorOut(e, "Ccode", "print");
126 //***************************************************************************************************************
127 int Ccode::getChimeras(Sequence* query) {
138 sumSquaredRef.clear();
139 sumSquaredQuery.clear();
141 averageQuery.clear();
143 isChimericConfidence.clear();
144 isChimericTStudent.clear();
145 isChimericANOVA.clear();
148 windowSizes = window;
154 //find closest matches to query
155 closest = findClosest(query, numWanted);
158 for (int i = 0; i < query->getAligned().length(); i++) { spotMap[i] = i; }
160 //mask sequences if the user wants to
162 decalc->setMask(seqMask);
164 decalc->runMask(query);
167 for (int i = 0; i < closest.size(); i++) { decalc->runMask(closest[i].seq); }
169 spotMap = decalc->getMaskMap();
173 vector<Sequence*> temp;
174 for (int i = 0; i < closest.size(); i++) { temp.push_back(closest[i].seq); }
175 temp.push_back(query);
177 createFilter(temp, 0.5);
179 for (int i = 0; i < temp.size(); i++) { runFilter(temp[i]); }
182 map<int, int> newMap;
185 for (int i = 0; i < filterString.length(); i++) {
186 if (filterString[i] == '1') {
188 newMap[spot] = spotMap[i];
195 //trim sequences - this follows ccodes remove_extra_gaps
196 trimSequences(query);
199 //windows are equivalent to words - ccode paper recommends windows are between 5% and 20% on alignment length().
200 //Our default will be 10% and we will warn if user tries to use a window above or below these recommendations
201 windows = findWindows();
204 //remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later
205 removeBadReferenceSeqs(closest);
208 //find the averages for each querys references
209 getAverageRef(closest); //fills sumRef, averageRef, sumSquaredRef and refCombo.
210 getAverageQuery(closest, query); //fills sumQuery, averageQuery, sumSquaredQuery.
213 //find the averages for each querys references
214 findVarianceRef(); //fills varRef and sdRef also sets minimum error rate to 0.001 to avoid divide by 0.
217 //find the averages for the query
218 findVarianceQuery(); //fills varQuery and sdQuery also sets minimum error rate to 0.001 to avoid divide by 0.
220 determineChimeras(); //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA.
224 catch(exception& e) {
225 m->errorOut(e, "Ccode", "getChimeras");
229 /***************************************************************************************************************/
230 //ccode algo says it does this to "Removes the initial and final gaps to avoid biases due to incomplete sequences."
231 void Ccode::trimSequences(Sequence* query) {
234 int frontPos = 0; //should contain first position in all seqs that is not a gap character
235 int rearPos = query->getAligned().length();
237 //********find first position in closest seqs that is a non gap character***********//
238 //find first position all query seqs that is a non gap character
239 for (int i = 0; i < closest.size(); i++) {
241 string aligned = closest[i].seq->getAligned();
244 //find first spot in this seq
245 for (int j = 0; j < aligned.length(); j++) {
246 if (isalpha(aligned[j])) {
252 //save this spot if it is the farthest
253 if (pos > frontPos) { frontPos = pos; }
256 //find first position all querySeq[query] that is a non gap character
257 string aligned = query->getAligned();
260 //find first spot in this seq
261 for (int j = 0; j < aligned.length(); j++) {
262 if (isalpha(aligned[j])) {
268 //save this spot if it is the farthest
269 if (pos > frontPos) { frontPos = pos; }
272 //********find last position in closest seqs that is a non gap character***********//
273 for (int i = 0; i < closest.size(); i++) {
275 string aligned = closest[i].seq->getAligned();
276 int pos = aligned.length();
278 //find first spot in this seq
279 for (int j = aligned.length()-1; j >= 0; j--) {
280 if (isalpha(aligned[j])) {
286 //save this spot if it is the farthest
287 if (pos < rearPos) { rearPos = pos; }
290 //find last position all querySeqs[query] that is a non gap character
291 aligned = query->getAligned();
292 pos = aligned.length();
294 //find first spot in this seq
295 for (int j = aligned.length()-1; j >= 0; j--) {
296 if (isalpha(aligned[j])) {
302 //save this spot if it is the farthest
303 if (pos < rearPos) { rearPos = pos; }
306 //check to make sure that is not whole seq
307 if ((rearPos - frontPos - 1) <= 0) { m->mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine(); exit(1); }
309 map<int, int> tempTrim;
310 tempTrim[frontPos] = rearPos;
312 //save trimmed locations
316 map<int, int> newMap;
319 for (int i = frontPos; i < rearPos; i++) {
321 newMap[spot] = spotMap[i];
326 catch(exception& e) {
327 m->errorOut(e, "Ccode", "trimSequences");
331 /***************************************************************************************************************/
332 vector<int> Ccode::findWindows() {
338 int length = it->second - it->first;
340 //default is wanted = 10% of total length
341 if (windowSizes > length) {
342 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.");
343 windowSizes = length / 10;
344 }else if (windowSizes == 0) { windowSizes = length / 10; }
345 else if (windowSizes > (length * 0.20)) {
346 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();
347 }else if (windowSizes < (length * 0.05)) {
348 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();
351 //save starting points of each window
352 for (int m = it->first; m < (it->second-windowSizes); m+=windowSizes) { win.push_back(m); }
355 if (win[win.size()-1] < (it->first+length)) {
356 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
357 } //with this you would get 1,25,50,75,100
361 catch(exception& e) {
362 m->errorOut(e, "Ccode", "findWindows");
366 //***************************************************************************************************************
367 int Ccode::getDiff(string seqA, string seqB) {
372 for (int i = 0; i < seqA.length(); i++) {
373 //if you are both not gaps
374 //if (isalpha(seqA[i]) && isalpha(seqA[i])) {
376 if (seqA[i] != seqB[i]) {
377 int ok; /* ok=1 means equivalent base. Checks for degenerate bases */
379 /* the char in base_a and base_b have been checked and they are different */
380 if ((seqA[i] == 'N') && (seqB[i] != '-')) ok = 1;
381 else if ((seqB[i] == 'N') && (seqA[i] != '-')) ok = 1;
382 else if ((seqA[i] == 'Y') && ((seqB[i] == 'C') || (seqB[i] == 'T'))) ok = 1;
383 else if ((seqB[i] == 'Y') && ((seqA[i] == 'C') || (seqA[i] == 'T'))) ok = 1;
384 else if ((seqA[i] == 'R') && ((seqB[i] == 'G') || (seqB[i] == 'A'))) ok = 1;
385 else if ((seqB[i] == 'R') && ((seqA[i] == 'G') || (seqA[i] == 'A'))) ok = 1;
386 else if ((seqA[i] == 'S') && ((seqB[i] == 'C') || (seqB[i] == 'G'))) ok = 1;
387 else if ((seqB[i] == 'S') && ((seqA[i] == 'C') || (seqA[i] == 'G'))) ok = 1;
388 else if ((seqA[i] == 'W') && ((seqB[i] == 'T') || (seqB[i] == 'A'))) ok = 1;
389 else if ((seqB[i] == 'W') && ((seqA[i] == 'T') || (seqA[i] == 'A'))) ok = 1;
390 else if ((seqA[i] == 'M') && ((seqB[i] == 'A') || (seqB[i] == 'C'))) ok = 1;
391 else if ((seqB[i] == 'M') && ((seqA[i] == 'A') || (seqA[i] == 'C'))) ok = 1;
392 else if ((seqA[i] == 'K') && ((seqB[i] == 'T') || (seqB[i] == 'G'))) ok = 1;
393 else if ((seqB[i] == 'K') && ((seqA[i] == 'T') || (seqA[i] == 'G'))) ok = 1;
394 else if ((seqA[i] == 'V') && ((seqB[i] == 'C') || (seqB[i] == 'A') || (seqB[i] == 'G'))) ok = 1;
395 else if ((seqB[i] == 'V') && ((seqA[i] == 'C') || (seqA[i] == 'A') || (seqA[i] == 'G'))) ok = 1;
396 else if ((seqA[i] == 'H') && ((seqB[i] == 'T') || (seqB[i] == 'A') || (seqB[i] == 'C'))) ok = 1;
397 else if ((seqB[i] == 'H') && ((seqA[i] == 'T') || (seqA[i] == 'A') || (seqA[i] == 'C'))) ok = 1;
398 else if ((seqA[i] == 'D') && ((seqB[i] == 'T') || (seqB[i] == 'A') || (seqB[i] == 'G'))) ok = 1;
399 else if ((seqB[i] == 'D') && ((seqA[i] == 'T') || (seqA[i] == 'A') || (seqA[i] == 'G'))) ok = 1;
400 else if ((seqA[i] == 'B') && ((seqB[i] == 'C') || (seqB[i] == 'T') || (seqB[i] == 'G'))) ok = 1;
401 else if ((seqB[i] == 'B') && ((seqA[i] == 'C') || (seqA[i] == 'T') || (seqA[i] == 'G'))) ok = 1;
402 else ok = 0; /* the bases are different and not equivalent */
404 //check if they are both blanks
405 if ((seqA[i] == '.') && (seqB[i] == '-')) ok = 1;
406 else if ((seqB[i] == '.') && (seqA[i] == '-')) ok = 1;
408 if (ok == 0) { numDiff++; }
416 catch(exception& e) {
417 m->errorOut(e, "Ccode", "getDiff");
421 //***************************************************************************************************************
422 //tried to make this look most like ccode original implementation
423 void Ccode::removeBadReferenceSeqs(vector<SeqDist>& seqs) {
426 vector< vector<int> > numDiffBases;
427 numDiffBases.resize(seqs.size());
429 for (int i = 0; i < numDiffBases.size(); i++) { numDiffBases[i].resize(seqs.size(),0); }
432 int length = it->second - it->first;
434 //calc differences from each sequence to everyother seq in the set
435 for (int i = 0; i < seqs.size(); i++) {
437 string seqA = seqs[i].seq->getAligned().substr(it->first, length);
439 //so you don't calc i to j and j to i since they are the same
440 for (int j = 0; j < i; j++) {
442 string seqB = seqs[j].seq->getAligned().substr(it->first, length);
445 int numDiff = getDiff(seqA, seqB);
447 numDiffBases[i][j] = numDiff;
448 numDiffBases[j][i] = numDiff;
452 //initailize remove to 0
453 vector<int> remove; remove.resize(seqs.size(), 0);
454 float top = ((20*length) / (float) 100);
455 float bottom = ((0.5*length) / (float) 100);
457 //check each numDiffBases and if any are higher than threshold set remove to 1 so you can remove those seqs from the closest set
458 for (int i = 0; i < numDiffBases.size(); i++) {
459 for (int j = 0; j < i; j++) {
460 //are you more than 20% different
461 if (numDiffBases[i][j] > top) { remove[j] = 1; }
462 //are you less than 0.5% different
463 if (numDiffBases[i][j] < bottom) { remove[j] = 1; }
469 //count seqs that are not going to be removed
470 for (int i = 0; i < remove.size(); i++) {
471 if (remove[i] == 0) { numSeqsLeft++; }
474 //if you have enough then remove bad ones
475 if (numSeqsLeft >= 3) {
476 vector<SeqDist> goodSeqs;
478 for (int i = 0; i < remove.size(); i++) {
479 if (remove[i] == 0) {
480 goodSeqs.push_back(seqs[i]);
486 }else { //warn, but dont remove any
487 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();
491 catch(exception& e) {
492 m->errorOut(e, "Ccode", "removeBadReferenceSeqs");
496 //***************************************************************************************************************
497 //makes copy of templateseq for filter
498 vector<SeqDist> Ccode::findClosest(Sequence* q, int numWanted) {
501 vector<SeqDist> topMatches;
503 Sequence query = *(q);
505 //calc distance to each sequence in template seqs
506 for (int i = 0; i < templateSeqs.size(); i++) {
508 Sequence ref = *(templateSeqs[i]);
511 distCalc->calcDist(query, ref);
512 float dist = distCalc->getDist();
516 temp.seq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
519 topMatches.push_back(temp);
522 sort(topMatches.begin(), topMatches.end(), compareSeqDist);
524 for (int i = numWanted; i < topMatches.size(); i++) { delete topMatches[i].seq; }
526 topMatches.resize(numWanted);
531 catch(exception& e) {
532 m->errorOut(e, "Ccode", "findClosestSides");
536 /**************************************************************************************************/
537 //find the distances from each reference sequence to every other reference sequence for each window for this query
538 void Ccode::getAverageRef(vector<SeqDist> ref) {
541 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.
543 //initialize diffs vector
544 diffs.resize(ref.size());
545 for (int i = 0; i < diffs.size(); i++) {
546 diffs[i].resize(ref.size());
547 for (int j = 0; j < diffs[i].size(); j++) {
548 diffs[i][j].resize(windows.size(), 0);
554 //find the distances from each reference sequence to every other reference sequence for each window for this query
555 for (int i = 0; i < ref.size(); i++) {
557 string refI = ref[i].seq->getAligned();
559 //j<i, so you don't find distances from i to j and then j to i.
560 for (int j = 0; j < i; j++) {
562 string refJ = ref[j].seq->getAligned();
564 for (int k = 0; k < windows.size(); k++) {
566 string refIWindowk, refJWindowk;
568 if (k < windows.size()-1) {
570 refIWindowk = refI.substr(windows[k], windowSizes);
571 refJWindowk = refJ.substr(windows[k], windowSizes);
572 }else { //last window may be smaller than rest - see findwindows
574 refIWindowk = refI.substr(windows[k], (it->second-windows[k]));
575 refJWindowk = refJ.substr(windows[k], (it->second-windows[k]));
579 int diff = getDiff(refIWindowk, refJWindowk);
581 //save differences in [i][j][k] and [j][i][k] since they are the same
582 diffs[i][j][k] = diff;
583 diffs[j][i][k] = diff;
591 //initialize sumRef for this query
592 sumRef.resize(windows.size(), 0);
593 sumSquaredRef.resize(windows.size(), 0);
594 averageRef.resize(windows.size(), 0);
596 //find the sum of the differences for hte reference sequences
597 for (int i = 0; i < diffs.size(); i++) {
598 for (int j = 0; j < i; j++) {
600 //increment this querys reference sequences combos
603 for (int k = 0; k < diffs[i][j].size(); k++) {
604 sumRef[k] += diffs[i][j][k];
605 sumSquaredRef[k] += (diffs[i][j][k]*diffs[i][j][k]);
612 //find the average of the differences for the references for each window
613 for (int i = 0; i < windows.size(); i++) {
614 averageRef[i] = sumRef[i] / (float) refCombo;
618 catch(exception& e) {
619 m->errorOut(e, "Ccode", "getAverageRef");
623 /**************************************************************************************************/
624 void Ccode::getAverageQuery (vector<SeqDist> ref, Sequence* query) {
627 vector< vector<int> > diffs; //diffs[1][2] is the number of differences between querySeqs[query] and ref seq 1 at window 2.
629 //initialize diffs vector
630 diffs.resize(ref.size());
631 for (int j = 0; j < diffs.size(); j++) {
632 diffs[j].resize(windows.size(), 0);
637 string refQuery = query->getAligned();
639 //j<i, so you don't find distances from i to j and then j to i.
640 for (int j = 0; j < ref.size(); j++) {
642 string refJ = ref[j].seq->getAligned();
644 for (int k = 0; k < windows.size(); k++) {
646 string QueryWindowk, refJWindowk;
648 if (k < windows.size()-1) {
650 QueryWindowk = refQuery.substr(windows[k], windowSizes);
651 refJWindowk = refJ.substr(windows[k], windowSizes);
652 }else { //last window may be smaller than rest - see findwindows
654 QueryWindowk = refQuery.substr(windows[k], (it->second-windows[k]));
655 refJWindowk = refJ.substr(windows[k], (it->second-windows[k]));
659 int diff = getDiff(QueryWindowk, refJWindowk);
668 //initialize sumRef for this query
669 sumQuery.resize(windows.size(), 0);
670 sumSquaredQuery.resize(windows.size(), 0);
671 averageQuery.resize(windows.size(), 0);
673 //find the sum of the differences
674 for (int j = 0; j < diffs.size(); j++) {
675 for (int k = 0; k < diffs[j].size(); k++) {
676 sumQuery[k] += diffs[j][k];
677 sumSquaredQuery[k] += (diffs[j][k]*diffs[j][k]);
682 //find the average of the differences for the references for each window
683 for (int i = 0; i < windows.size(); i++) {
684 averageQuery[i] = sumQuery[i] / (float) ref.size();
687 catch(exception& e) {
688 m->errorOut(e, "Ccode", "getAverageQuery");
692 /**************************************************************************************************/
693 void Ccode::findVarianceRef() {
696 varRef.resize(windows.size(), 0);
697 sdRef.resize(windows.size(), 0);
700 for (int i = 0; i < windows.size(); i++) {
701 varRef[i] = (sumSquaredRef[i] - ((sumRef[i]*sumRef[i])/(float)refCombo)) / (float)(refCombo-1);
702 sdRef[i] = sqrt(varRef[i]);
704 //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation
705 if (averageRef[i] < 0.001) { averageRef[i] = 0.001; }
706 if (sumRef[i] < 0.001) { sumRef[i] = 0.001; }
707 if (varRef[i] < 0.001) { varRef[i] = 0.001; }
708 if (sumSquaredRef[i] < 0.001) { sumSquaredRef[i] = 0.001; }
709 if (sdRef[i] < 0.001) { sdRef[i] = 0.001; }
713 catch(exception& e) {
714 m->errorOut(e, "Ccode", "findVarianceRef");
718 /**************************************************************************************************/
719 void Ccode::findVarianceQuery() {
721 varQuery.resize(windows.size(), 0);
722 sdQuery.resize(windows.size(), 0);
725 for (int i = 0; i < windows.size(); i++) {
726 varQuery[i] = (sumSquaredQuery[i] - ((sumQuery[i]*sumQuery[i])/(float) closest.size())) / (float) (closest.size()-1);
727 sdQuery[i] = sqrt(varQuery[i]);
729 //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation
730 if (averageQuery[i] < 0.001) { averageQuery[i] = 0.001; }
731 if (sumQuery[i] < 0.001) { sumQuery[i] = 0.001; }
732 if (varQuery[i] < 0.001) { varQuery[i] = 0.001; }
733 if (sumSquaredQuery[i] < 0.001) { sumSquaredQuery[i] = 0.001; }
734 if (sdQuery[i] < 0.001) { sdQuery[i] = 0.001; }
738 catch(exception& e) {
739 m->errorOut(e, "Ccode", "findVarianceQuery");
743 /**************************************************************************************************/
744 void Ccode::determineChimeras() {
747 isChimericConfidence.resize(windows.size(), false);
748 isChimericTStudent.resize(windows.size(), false);
749 isChimericANOVA.resize(windows.size(), false);
750 anova.resize(windows.size());
754 for (int i = 0; i < windows.size(); i++) {
756 //get confidence limits
757 float t = getT(closest.size()-1); //how many seqs you are comparing to this querySeq
758 float dsUpper = (averageQuery[i] + (t * sdQuery[i])) / averageRef[i];
759 float dsLower = (averageQuery[i] - (t * sdQuery[i])) / averageRef[i];
761 if ((dsUpper > 1.0) && (dsLower > 1.0) && (averageQuery[i] > averageRef[i])) { /* range does not include 1 */
762 isChimericConfidence[i] = true; /* significantly higher at P<0.05 */
767 int degreeOfFreedom = refCombo + closest.size() - 2;
768 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 */
770 float ts = fabs((averageQuery[i] - averageRef[i]) / (sqrt(denomForT))); /* value of ts for t-student test */
771 t = getT(degreeOfFreedom);
773 if ((ts >= t) && (averageQuery[i] > averageRef[i])) {
774 isChimericTStudent[i] = true; /* significantly higher at P<0.05 */
778 float value1 = sumQuery[i] + sumRef[i];
779 float value2 = sumSquaredQuery[i] + sumSquaredRef[i];
780 float value3 = ((sumQuery[i]*sumQuery[i]) / (float) (closest.size())) + ((sumRef[i] * sumRef[i]) / (float) refCombo);
781 float value4 = (value1 * value1) / ( (float) (closest.size() + refCombo) );
782 float value5 = value2 - value4;
783 float value6 = value3 - value4;
784 float value7 = value5 - value6;
785 float value8 = value7 / ((float) degreeOfFreedom);
786 float anovaValue = value6 / value8;
788 float f = getF(degreeOfFreedom);
790 if ((anovaValue >= f) && (averageQuery[i] > averageRef[i])) {
791 isChimericANOVA[i] = true; /* significant P<0.05 */
794 if (isnan(anovaValue) || isinf(anovaValue)) { anovaValue = 0.0; }
796 anova[i] = anovaValue;
800 catch(exception& e) {
801 m->errorOut(e, "Ccode", "determineChimeras");
805 /**************************************************************************************************/
806 float Ccode::getT(int numseq) {
811 /* t-student critical values for different degrees of freedom and alpha 0.1 in one-tail tests (equivalent to 0.05) */
812 if (numseq > 120) tvalue = 1.645;
813 else if (numseq > 60) tvalue = 1.658;
814 else if (numseq > 40) tvalue = 1.671;
815 else if (numseq > 30) tvalue = 1.684;
816 else if (numseq > 29) tvalue = 1.697;
817 else if (numseq > 28) tvalue = 1.699;
818 else if (numseq > 27) tvalue = 1.701;
819 else if (numseq > 26) tvalue = 1.703;
820 else if (numseq > 25) tvalue = 1.706;
821 else if (numseq > 24) tvalue = 1.708;
822 else if (numseq > 23) tvalue = 1.711;
823 else if (numseq > 22) tvalue = 1.714;
824 else if (numseq > 21) tvalue = 1.717;
825 else if (numseq > 20) tvalue = 1.721;
826 else if (numseq > 19) tvalue = 1.725;
827 else if (numseq > 18) tvalue = 1.729;
828 else if (numseq > 17) tvalue = 1.734;
829 else if (numseq > 16) tvalue = 1.740;
830 else if (numseq > 15) tvalue = 1.746;
831 else if (numseq > 14) tvalue = 1.753;
832 else if (numseq > 13) tvalue = 1.761;
833 else if (numseq > 12) tvalue = 1.771;
834 else if (numseq > 11) tvalue = 1.782;
835 else if (numseq > 10) tvalue = 1.796;
836 else if (numseq > 9) tvalue = 1.812;
837 else if (numseq > 8) tvalue = 1.833;
838 else if (numseq > 7) tvalue = 1.860;
839 else if (numseq > 6) tvalue = 1.895;
840 else if (numseq > 5) tvalue = 1.943;
841 else if (numseq > 4) tvalue = 2.015;
842 else if (numseq > 3) tvalue = 2.132;
843 else if (numseq > 2) tvalue = 2.353;
844 else if (numseq > 1) tvalue = 2.920;
845 else if (numseq <= 1) {
846 m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
851 catch(exception& e) {
852 m->errorOut(e, "Ccode", "getT");
856 /**************************************************************************************************/
857 float Ccode::getF(int numseq) {
862 /* F-Snedecor critical values for v1=1 and different degrees of freedom v2 and alpha 0.05 */
863 if (numseq > 120) fvalue = 3.84;
864 else if (numseq > 60) fvalue = 3.92;
865 else if (numseq > 40) fvalue = 4.00;
866 else if (numseq > 30) fvalue = 4.08;
867 else if (numseq > 29) fvalue = 4.17;
868 else if (numseq > 28) fvalue = 4.18;
869 else if (numseq > 27) fvalue = 4.20;
870 else if (numseq > 26) fvalue = 4.21;
871 else if (numseq > 25) fvalue = 4.23;
872 else if (numseq > 24) fvalue = 4.24;
873 else if (numseq > 23) fvalue = 4.26;
874 else if (numseq > 22) fvalue = 4.28;
875 else if (numseq > 21) fvalue = 4.30;
876 else if (numseq > 20) fvalue = 4.32;
877 else if (numseq > 19) fvalue = 4.35;
878 else if (numseq > 18) fvalue = 4.38;
879 else if (numseq > 17) fvalue = 4.41;
880 else if (numseq > 16) fvalue = 4.45;
881 else if (numseq > 15) fvalue = 4.49;
882 else if (numseq > 14) fvalue = 4.54;
883 else if (numseq > 13) fvalue = 4.60;
884 else if (numseq > 12) fvalue = 4.67;
885 else if (numseq > 11) fvalue = 4.75;
886 else if (numseq > 10) fvalue = 4.84;
887 else if (numseq > 9) fvalue = 4.96;
888 else if (numseq > 8) fvalue = 5.12;
889 else if (numseq > 7) fvalue = 5.32;
890 else if (numseq > 6) fvalue = 5.59;
891 else if (numseq > 5) fvalue = 5.99;
892 else if (numseq > 4) fvalue = 6.61;
893 else if (numseq > 3) fvalue = 7.71;
894 else if (numseq > 2) fvalue = 10.1;
895 else if (numseq > 1) fvalue = 18.5;
896 else if (numseq > 0) fvalue = 161;
897 else if (numseq <= 0) {
898 m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
903 catch(exception& e) {
904 m->errorOut(e, "Ccode", "getF");
908 //***************************************************************************************************************