DeCalculator() { m = MothurOut::getInstance(); }
~DeCalculator() {};
- vector<Sequence*> findClosest(Sequence*, vector<Sequence*>&, vector<Sequence*>&, int, int); //takes querySeq, a reference db, filteredRefDB, numWanted, minSim
+ 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*>);
+ 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);