indexes.clear();
vector<Sequence*> seqsMatches;
+
vector<SeqDist> distsLeft;
vector<SeqDist> distsRight;
float distRight = distcalculator->getDist();
SeqDist subjectLeft;
- subjectLeft.seq = db[j];
+ subjectLeft.seq = NULL;
subjectLeft.dist = distLeft;
subjectLeft.index = j;
distsLeft.push_back(subjectLeft);
SeqDist subjectRight;
- subjectRight.seq = db[j];
+ subjectRight.seq = NULL;
subjectRight.dist = distRight;
subjectRight.index = j;
int lasti = 0;
for (int i = 0; i < distsLeft.size(); i++) {
//add left if you havent already
- it = seen.find(distsLeft[i].seq->getName());
+ it = seen.find(db[distsLeft[i].index]->getName());
if (it == seen.end()) {
dists.push_back(distsLeft[i]);
- seen[distsLeft[i].seq->getName()] = distsLeft[i].seq->getName();
+ seen[db[distsLeft[i].index]->getName()] = db[distsLeft[i].index]->getName();
lastLeft = distsLeft[i].dist;
}
//add right if you havent already
- it = seen.find(distsRight[i].seq->getName());
+ it = seen.find(db[distsRight[i].index]->getName());
if (it == seen.end()) {
dists.push_back(distsRight[i]);
- seen[distsRight[i].seq->getName()] = distsRight[i].seq->getName();
+ seen[db[distsRight[i].index]->getName()] = db[distsRight[i].index]->getName();
lastRight = distsRight[i].dist;
}
//cout << numWanted << endl;
for (int i = 0; i < numWanted; i++) {
//cout << dists[i].seq->getName() << '\t' << dists[i].dist << endl;
- Sequence* temp = new Sequence(dists[i].seq->getName(), dists[i].seq->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
+ Sequence* temp = new Sequence(db[dists[i].index]->getName(), db[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
seqsMatches.push_back(temp);
indexes.push_back(dists[i].index);
}
map<int, int> trimmedPos;
//check to make sure that is not whole seq
if ((rearPos - frontPos - 1) <= 0) {
- m->mothurOut("[ERROR]: when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine();
+ m->mothurOut("[ERROR]: when I trim " + query->getName() + ", the entire sequence is trimmed. Skipping."); m->mothurOutEndLine();
query->setAligned("");
//trim topMatches
for (int i = 0; i < topMatches.size(); i++) {