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