- vector<Sequence> findPairs(int, int);
- vector<int> findWindows(Sequence*, int, int, int&);
- vector<float> calcObserved(Sequence*, Sequence, vector<int>, int);
+ DeCalculator() { m = MothurOut::getInstance(); }
+ ~DeCalculator() {};
+
+ vector<Sequence> findClosest(Sequence, vector<Sequence*>&, vector<Sequence*>&, int, int); //takes querySeq, a reference db, filteredRefDB, numWanted, minSim
+ Sequence* findClosest(Sequence*, vector<Sequence*>);
+ set<int> getPos() { return h; }
+ void setMask(string);
+ void setAlignmentLength(int l) { alignLength = l; }
+ void runMask(Sequence*);
+ void trimSeqs(Sequence*, Sequence*, map<int, int>&);
+ map<int, int> trimSeqs(Sequence&, vector<Sequence>&);
+ void removeObviousOutliers(vector< vector<float> >&, int);
+ vector<float> calcFreq(vector<Sequence*>, string);
+ vector<int> findWindows(Sequence*, int, int, int&, int);
+ vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);