public:
- DeCalculator() {};
+ DeCalculator() { m = MothurOut::getInstance(); }
~DeCalculator() {};
+ 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; }
void runMask(Sequence*);
void trimSeqs(Sequence*, Sequence*, map<int, int>&);
- vector< vector<float> > removeObviousOutliers(vector< vector<quanMember> >&, int);
+ map<int, int> trimSeqs(Sequence*, vector<Sequence*>);
+ void removeObviousOutliers(vector< vector<quanMember> >&, int);
vector<float> calcFreq(vector<Sequence*>, string);
vector<int> findWindows(Sequence*, int, int, int&, int);
vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
vector<int> returnObviousOutliers(vector< vector<quanMember> >, int);
+ map<int, int> getMaskMap() { return maskMap; }
+
private:
//vector<quanMember> sortContrib(map<quanMember*, float>); //used by mallard
float findAverage(vector<float>);
string seqMask;
set<int> h;
int alignLength;
+ map<int, int> maskMap;
+ MothurOut* m;
};