X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=slayer.cpp;h=a787f2727dd8290b89bffeb382bae6c15001110d;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=4987d4170337f6d4e172c395c137be71832759ed;hpb=d945488119ad368b180537f36ed40298ff170f39;p=mothur.git diff --git a/slayer.cpp b/slayer.cpp index 4987d41..a787f27 100644 --- a/slayer.cpp +++ b/slayer.cpp @@ -13,10 +13,10 @@ Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp, int mi) : minBS(mi), windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); } /***********************************************************************/ -string Slayer::getResults(Sequence* query, vector refSeqs) { +string Slayer::getResults(Sequence query, vector refSeqs) { try { vector all; all.clear(); - myQuery = *query; + myQuery = query; for (int i = 0; i < refSeqs.size(); i++) { @@ -25,19 +25,21 @@ string Slayer::getResults(Sequence* query, vector refSeqs) { if (m->control_pressed) { return "no"; } //make copies of query and each parent because runBellerophon removes gaps and messes them up - Sequence* q = new Sequence(query->getName(), query->getAligned()); - Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned()); - Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned()); + Sequence q(query.getName(), query.getAligned()); + Sequence leftParent(refSeqs[i].getName(), refSeqs[i].getAligned()); + Sequence rightParent(refSeqs[j].getName(), refSeqs[j].getAligned()); //cout << q->getName() << endl << q->getAligned() << endl << endl; - //cout << leftParent->getName() << endl << leftParent->getAligned() << endl << endl; + //cout << leftParent.getName() << '\t' << leftParent.getAligned().length() << endl << endl; + //cout << rightParent.getName() << '\t' << rightParent.getAligned().length() << endl << endl; + //cout << q.getName() << '\t' << q.getAligned().length() << endl << endl; //cout << rightParent->getName() << endl << rightParent->getAligned() << endl << endl; //cout << " length = " << rightParent->getAligned().length() << endl; map spots; //map from spot in original sequence to spot in filtered sequence for query and both parents vector divs = runBellerophon(q, leftParent, rightParent, spots); - if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; } + if (m->control_pressed) { return "no"; } // cout << "examining:\t" << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << endl; vector selectedDivs; for (int k = 0; k < divs.size(); k++) { @@ -45,7 +47,7 @@ string Slayer::getResults(Sequence* query, vector refSeqs) { vector snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd); vector snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd); - if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; } + if (m->control_pressed) { return "no"; } int numSNPSLeft = snpsLeft.size(); int numSNPSRight = snpsRight.size(); @@ -57,7 +59,7 @@ string Slayer::getResults(Sequence* query, vector refSeqs) { float BS_A, BS_B; bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters); - if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; } + if (m->control_pressed) { return "no"; } divs[k].bsa = BS_A; divs[k].bsb = BS_B; @@ -89,10 +91,6 @@ string Slayer::getResults(Sequence* query, vector refSeqs) { //save selected for (int mi = 0; mi < selectedDivs.size(); mi++) { all.push_back(selectedDivs[mi]); } - - delete q; - delete leftParent; - delete rightParent; } } @@ -116,26 +114,27 @@ string Slayer::getResults(Sequence* query, vector refSeqs) { } } /***********************************************************************/ -vector Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map& spots) { +vector Slayer::runBellerophon(Sequence q, Sequence pA, Sequence pB, map& spots) { try{ vector data; //vertical filter - vector temp; - temp.push_back(q); temp.push_back(pA); temp.push_back(pB); + //cout << q.getName() << endl << q.getAligned() << endl << endl; + //cout << pA.getName() << endl << pA.getUnaligned() << endl << endl; + //cout << pB.getName() << endl << pB.getUnaligned() << endl << endl; //maps spot in new alignment to spot in alignment before filter - spots = verticalFilter(temp); //fills baseSpots + spots = verticalFilter(q, pA, pB); //fills baseSpots //get these to avoid numerous function calls - string query = q->getAligned(); - string parentA = pA->getAligned(); - string parentB = pB->getAligned(); + string query = q.getAligned(); + string parentA = pA.getAligned(); + string parentB = pB.getAligned(); int length = query.length(); -//cout << q->getName() << endl << q->getAligned() << endl << endl; -//cout << pA->getName() << endl << pA->getUnaligned() << endl << endl; -//cout << pB->getName() << endl << pB->getUnaligned() << endl << endl; +//cout << q.getName() << endl << q.getAligned() << endl << endl; +//cout << pA.getName() << endl << pA.getUnaligned() << endl << endl; +//cout << pB.getName() << endl << pB.getUnaligned() << endl << endl; //cout << " length = " << length << endl; //check window size @@ -209,9 +208,9 @@ vector Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* member.winLEnd = breakpoint; member.winRStart = breakpoint+1; member.winREnd = length-1; - member.querySeq = *(q); - member.parentA = *(pA); - member.parentB = *(pB); + member.querySeq = q; + member.parentA = pA; + member.parentB = pB; member.bsa = 0; member.bsb = 0; member.bsMax = 0; @@ -478,33 +477,41 @@ float Slayer::computePercentID(string queryAlign, string chimera, int left, int } /***********************************************************************/ //remove columns that contain any gaps -map Slayer::verticalFilter(vector seqs) { +map Slayer::verticalFilter(Sequence& q, Sequence& pA, Sequence& pB) { try { //find baseSpots baseSpots.clear(); baseSpots.resize(3); //query, parentA, parentB - vector gaps; gaps.resize(seqs[0]->getAligned().length(), 0); + vector gaps; gaps.resize(q.getAligned().length(), 0); - string filterString = (string(seqs[0]->getAligned().length(), '1')); + string filterString = (string(q.getAligned().length(), '1')); - //for each sequence - for (int i = 0; i < seqs.size(); i++) { + string seqAligned = q.getAligned(); + for (int j = 0; j < seqAligned.length(); j++) { + //if this spot is a gap + if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } + } - string seqAligned = seqs[i]->getAligned(); - - for (int j = 0; j < seqAligned.length(); j++) { - //if this spot is a gap - if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } - } + seqAligned = pA.getAligned(); + for (int j = 0; j < seqAligned.length(); j++) { + //if this spot is a gap + if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } } + seqAligned = pB.getAligned(); + for (int j = 0; j < seqAligned.length(); j++) { + //if this spot is a gap + if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } + } + + //zero out spot where any sequences have blanks int numColRemoved = 0; int count = 0; map maskMap; maskMap.clear(); - for(int i = 0; i < seqs[0]->getAligned().length(); i++){ + for(int i = 0; i < q.getAligned().length(); i++){ if(gaps[i] != 0) { filterString[i] = '0'; numColRemoved++; } else { maskMap[count] = i; @@ -512,29 +519,64 @@ map Slayer::verticalFilter(vector seqs) { } } - //for each sequence - for (int i = 0; i < seqs.size(); i++) { - - string seqAligned = seqs[i]->getAligned(); - string newAligned = ""; + seqAligned = q.getAligned(); + string newAligned = ""; - int baseCount = 0; - int count = 0; - for (int j = 0; j < seqAligned.length(); j++) { - //are you a base - if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; } + int baseCount = 0; + count = 0; + for (int j = 0; j < seqAligned.length(); j++) { + //are you a base + if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; } - //if this spot is not a gap - if (filterString[j] == '1') { - newAligned += seqAligned[j]; - baseSpots[i][count] = baseCount; - count++; - } + //if this spot is not a gap + if (filterString[j] == '1') { + newAligned += seqAligned[j]; + baseSpots[0][count] = baseCount; + count++; } + } - seqs[i]->setAligned(newAligned); + q.setAligned(newAligned); + + seqAligned = pA.getAligned(); + newAligned = ""; + + baseCount = 0; + count = 0; + for (int j = 0; j < seqAligned.length(); j++) { + //are you a base + if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; } + + //if this spot is not a gap + if (filterString[j] == '1') { + newAligned += seqAligned[j]; + baseSpots[1][count] = baseCount; + count++; + } + } + + pA.setAligned(newAligned); + + seqAligned = pB.getAligned(); + newAligned = ""; + + baseCount = 0; + count = 0; + for (int j = 0; j < seqAligned.length(); j++) { + //are you a base + if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; } + + //if this spot is not a gap + if (filterString[j] == '1') { + newAligned += seqAligned[j]; + baseSpots[2][count] = baseCount; + count++; + } } + pB.setAligned(newAligned); + + return maskMap; } catch(exception& e) {