DeCalculator() {};
~DeCalculator() {};
- vector<Sequence*> findClosest(Sequence*, vector<Sequence*>, int); //takes querySeq, a reference db and numWanted - returns indexes to closest seqs in db
+ vector<Sequence*> findClosest(Sequence*, vector<Sequence*>, int&, vector<int>&); //takes querySeq, a reference db, numWanted and indexes
+ Sequence* findClosest(Sequence*, vector<Sequence*>);
set<int> getPos() { return h; }
void setMask(string);
void setAlignmentLength(int l) { alignLength = l; }