- vector<Sequence> findPairs(int, int);
- vector<int> findWindows(Sequence*, int, int, int&);
- vector<float> calcObserved(Sequence*, Sequence, vector<int>, int);
+ DeCalculator() {};
+ ~DeCalculator() {};
+
+ set<int> getPos() { return h; }
+ void setMask(string m);
+ void runMask(Sequence*);
+ void trimSeqs(Sequence*, Sequence*, map<int, int>&);
+ vector<float> calcFreq(vector<Sequence*>, string);
+ vector<int> findWindows(Sequence*, int, int, int&, int);
+ vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);