#include "database.hpp"
#include "sequence.hpp"
#include "distancedb.hpp"
-#include "eachgapdist.h"
+#include "onegapignore.h"
+
/**************************************************************************************************/
-DistanceDB::DistanceDB() {
+DistanceDB::DistanceDB() : Database() {
try {
templateAligned = true;
templateSeqsLength = 0;
- distCalculator = new eachGapDist();
+ distCalculator = new oneGapIgnoreTermGapDist();
}
catch(exception& e) {
m->errorOut(e, "DistanceDB", "DistanceDB");
void DistanceDB::addSequence(Sequence seq) {
try {
//are the template sequences aligned
- if (!isAligned(seq.getAligned())) { templateAligned = false; m->mothurOut(seq.getName() + " is not aligned. Sequences must be aligned to use the distance method."); m->mothurOutEndLine(); }
+ if (!isAligned(seq.getAligned())) {
+ templateAligned = false;
+ m->mothurOut(seq.getName() + " is not aligned. Sequences must be aligned to use the distance method.");
+ m->mothurOutEndLine();
+ }
if (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); }
vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
try {
vector<int> topMatches;
+ Scores.clear();
bool templateSameLength = true;
string sequence = query->getAligned();
- vector<seqDist> dists;
+ vector<seqDist> dists;
+
+ searchScore = -1.0;
- 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 (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) {
- //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
-
- //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);
+ 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();
+ m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length.");
+ m->mothurOutEndLine();
exit(1);
}