vector<int> topMatches;
bool templateSameLength = true;
string sequence = query->getAligned();
- vector<seqDist> dists;
+ vector<seqDist> dists;
searchScore = -1.0;
if (sequence.length() != templateSeqsLength) { templateSameLength = false; }
if (templateSameLength && templateAligned) {
- //calc distance from this sequence to every sequence in the template
- for (int i = 0; i < data.size(); i++) {
- distCalculator->calcDist(*query, data[i]);
- float dist = distCalculator->getDist();
+ if (numWanted != 1) {
- //save distance to each template sequence
- seqDist temp(-1, i, dist);
- dists.push_back(temp);
- }
-
- sort(dists.begin(), dists.end(), compareSequenceDistance); //sorts by distance lowest to highest
-
- //save distance of best match
- searchScore = dists[0].dist;
-
- //fill topmatches with numwanted closest sequences indexes
- for (int i = 0; i < numWanted; i++) {
- topMatches.push_back(dists[i].seq2);
+ dists.resize(data.size());
+
+ //calc distance from this sequence to every sequence in the template
+ for (int i = 0; i < data.size(); i++) {
+ distCalculator->calcDist(*query, data[i]);
+ float dist = distCalculator->getDist();
+
+ //save distance to each template sequence
+ dists[i].seq1 = -1;
+ dists[i].seq2 = i;
+ dists[i].dist = dist;
+ }
+
+ sort(dists.begin(), dists.end(), compareSequenceDistance); //sorts by distance lowest to highest
+
+ //save distance of best match
+ searchScore = dists[0].dist;
+
+ //fill topmatches with numwanted closest sequences indexes
+ for (int i = 0; i < numWanted; i++) {
+ topMatches.push_back(dists[i].seq2);
+ }
+ }else {
+ int bestIndex = 0;
+ float smallDist = 100000;
+ for (int i = 0; i < data.size(); i++) {
+ distCalculator->calcDist(*query, data[i]);
+ float dist = distCalculator->getDist();
+
+ //are you smaller?
+ if (dist < smallDist) {
+ bestIndex = i;
+ smallDist = dist;
+ }
+ }
+
+ searchScore = smallDist;
+ topMatches.push_back(bestIndex);
}
}else{