public:
- DeCalculator() {};
+ 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>&);
- vector< vector<float> > removeObviousOutliers(vector< vector<quanMember> >&, 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);
float calcDE(vector<float>, vector<float>);
float calcDist(Sequence*, Sequence*, int, int);
float getCoef(vector<float>, vector<float>);
- vector< vector<quanMember> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int, vector<float>&);
+ vector< vector<float> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, 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
+ //vector<quanMember> sortContrib(map<quanMember*, float>); //used by mallard
float findAverage(vector<float>);
//int findLargestContrib(vector<int>);
//void removeContrib(int, vector<quanMember>&);
string seqMask;
set<int> h;
int alignLength;
+ map<int, int> maskMap;
+ MothurOut* m;
};