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<Sequence*> refSeqs) {
+string Slayer::getResults(Sequence query, vector<Sequence> refSeqs) {
try {
vector<data_struct> all; all.clear();
- myQuery = *query;
-
-
+ myQuery = query;
+
for (int i = 0; i < refSeqs.size(); i++) {
for (int j = i+1; j < refSeqs.size(); j++) {
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() << '\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<int, int> spots; //map from spot in original sequence to spot in filtered sequence for query and both parents
vector<data_struct> 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<data_struct> selectedDivs;
for (int k = 0; k < divs.size(); k++) {
vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
vector<snps> 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();
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;
//save selected
for (int mi = 0; mi < selectedDivs.size(); mi++) { all.push_back(selectedDivs[mi]); }
-
- delete q;
- delete leftParent;
- delete rightParent;
}
}
}
}
/***********************************************************************/
-vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map<int, int>& spots) {
+vector<data_struct> Slayer::runBellerophon(Sequence q, Sequence pA, Sequence pB, map<int, int>& spots) {
try{
vector<data_struct> data;
//vertical filter
- vector<Sequence*> 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
int rightLength = length - leftLength;
float QLA = computePercentID(query, parentA, 0, breakpoint);
- float QRB = computePercentID(query, parentB, breakpoint+1, length);
+ float QRB = computePercentID(query, parentB, breakpoint+1, length-1);
float QLB = computePercentID(query, parentB, 0, breakpoint);
- float QRA = computePercentID(query, parentA, breakpoint+1, length);
+ float QRA = computePercentID(query, parentA, breakpoint+1, length-1);
float LAB = computePercentID(parentA, parentB, 0, breakpoint);
- float RAB = computePercentID(parentA, parentB, breakpoint+1, length);
+ float RAB = computePercentID(parentA, parentB, breakpoint+1, length-1);
float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
//cout << q->getName() << '\t';
//cout << pA->getName() << '\t';
//cout << pB->getName() << '\t';
- // cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
+ //cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
//cout << "\tCHIM_TYPE_B\t" << divR_QLB_QRA << "\tQLB: " << QLB << "\tQRA: " << QRA << "\tQLB_QRA: " << QLB_QRA << endl;
//cout << leftLength << '\t' << rightLength << '\t' << QLA << '\t' << QRB << '\t' << QLB << '\t' << QRA << '\t' << LAB << '\t' << RAB << '\t' << AB << '\t' << QA << '\t' << QB << '\t' << QLA_QRB << '\t' << QLB_QRA << endl;
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;
}
/***********************************************************************/
//remove columns that contain any gaps
-map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
+map<int, int> Slayer::verticalFilter(Sequence& q, Sequence& pA, Sequence& pB) {
try {
//find baseSpots
baseSpots.clear();
baseSpots.resize(3); //query, parentA, parentB
- vector<int> gaps; gaps.resize(seqs[0]->getAligned().length(), 0);
+ vector<int> 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<int, int> 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;
}
}
- //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) {
projects / mothur.git / blobdiff