+ if (numWanted > data.size()){
+ m->mothurOut("numwanted is larger than the number of template sequences, using "+ toString(data.size()) + ".");
+ m->mothurOutEndLine();
+ numWanted = data.size();
+ }
+
+ if (sequence.length() != templateSeqsLength) { templateSameLength = false; }
+
+ if (templateSameLength && templateAligned) {
+ if (numWanted != 1) {
+
+ 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);
+ Scores.push_back(dists[i].dist);
+ }
+ }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);
+ Scores.push_back(smallDist);
+ }
+
+ }else{
+ m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length.");
+ m->mothurOutEndLine();
+ exit(1);
+ }
+
+ return topMatches;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceDB", "findClosestSequence");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+bool DistanceDB::isAligned(string seq){
+ try {
+ bool aligned;
+
+ int pos = seq.find_first_of(".-");
+
+ if (pos != seq.npos) {
+ aligned = true;
+ }else { aligned = false; }
+
+
+ return aligned;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceDB", "isAligned");
+ exit(1);
+ }