/***********************************************************************/
-//This class was created using the algorythms described in the
+//This class was created using the algorithms described in the
// "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" paper
//by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.
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);