A7E9B68512D37EC400DA6239 /* chimerarealigner.h */,
A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */,
A7E9B68912D37EC400DA6239 /* chimeraslayer.h */,
+ A7E9B6C212D37EC400DA6239 /* decalc.h */,
A7E9B6C112D37EC400DA6239 /* decalc.cpp */,
A7E9B74612D37EC400DA6239 /* maligner.h */,
- A7E9B6C212D37EC400DA6239 /* decalc.h */,
A7E9B74512D37EC400DA6239 /* maligner.cpp */,
A7E9B79312D37EC400DA6239 /* pintail.cpp */,
A7E9B79412D37EC400DA6239 /* pintail.h */,
Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
+ vector<float> leftScores = databaseLeft->getMegaBlastSearchScores();
vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
+ vector<float> rightScores = databaseLeft->getMegaBlastSearchScores();
//if ((tempIndexesRight.size() == 0) && (tempIndexesLeft.size() == 0)) { m->mothurOut("megablast returned " + toString(tempIndexesRight.size()) + " results for the right end, and " + toString(tempIndexesLeft.size()) + " for the left end. Needed " + toString(num+1) + ". Unable to process sequence " + q->getName()); m->mothurOutEndLine(); return refResults; }
vector<int> smaller;
+ vector<float> smallerScores;
vector<int> larger;
+ vector<float> largerScores;
- if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight; larger = tempIndexesLeft; }
- else { smaller = tempIndexesLeft; larger = tempIndexesRight; }
+ if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight; smallerScores = rightScores; larger = tempIndexesLeft; largerScores = leftScores; }
+ else { smaller = tempIndexesLeft; smallerScores = leftScores; larger = tempIndexesRight; largerScores = rightScores; }
+
+ //for (int i = 0; i < smaller.size(); i++) { cout << "smaller = " << smaller[i] << '\t' << smallerScores[i] << endl; }
+ //cout << endl;
+ //for (int i = 0; i < larger.size(); i++) { cout << "larger = " << larger[i] << '\t' << largerScores[i] << endl; }
//merge results
map<int, int> seen;
map<int, int>::iterator it;
-
+ float lastSmaller = smallerScores[0];
+ float lastLarger = largerScores[0];
+ int lasti = 0;
vector<int> mergedResults;
for (int i = 0; i < smaller.size(); i++) {
//add left if you havent already
if (it == seen.end()) {
mergedResults.push_back(smaller[i]);
seen[smaller[i]] = smaller[i];
+ lastSmaller = smallerScores[i];
}
//add right if you havent already
if (it == seen.end()) {
mergedResults.push_back(larger[i]);
seen[larger[i]] = larger[i];
+ lastLarger = largerScores[i];
}
+
+ lasti = i;
+ if (mergedResults.size() > num) { break; }
}
- for (int i = smaller.size(); i < larger.size(); i++) {
- it = seen.find(larger[i]);
- if (it == seen.end()) {
- mergedResults.push_back(larger[i]);
- seen[larger[i]] = larger[i];
+ //save lasti for smaller ties below
+ lasti++;
+ int iSmaller = lasti;
+
+ if (!(mergedResults.size() > num)) { //if we still need more results.
+ for (int i = smaller.size(); i < larger.size(); i++) {
+ it = seen.find(larger[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(larger[i]);
+ seen[larger[i]] = larger[i];
+ lastLarger = largerScores[i];
+ }
+
+ lasti = i;
+ if (mergedResults.size() > num) { break; }
}
}
+
+ //add in any ties from smaller
+ while (iSmaller < smaller.size()) {
+ if (smallerScores[iSmaller] == lastSmaller) {
+ it = seen.find(smaller[iSmaller]);
+
+ if (it == seen.end()) {
+ mergedResults.push_back(smaller[iSmaller]);
+ seen[smaller[iSmaller]] = smaller[iSmaller];
+ }
+ }
+ else { break; }
+ iSmaller++;
+ }
+
+ lasti++;
+ //add in any ties from larger
+ while (lasti < larger.size()) {
+ if (largerScores[lasti] == lastLarger) { //is it a tie
+ it = seen.find(larger[lasti]);
+
+ if (it == seen.end()) { //we haven't already seen it
+ mergedResults.push_back(larger[lasti]);
+ seen[larger[lasti]] = larger[lasti];
+ }
+ }
+ else { break; }
+ lasti++;
+ }
+
+ numWanted = seen.size();
+
if (mergedResults.size() < numWanted) { numWanted = mergedResults.size(); }
//cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted << endl;
for (int i = 0; i < numWanted; i++) {