added modify names parameter to set.dir

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index 42e14416004efbea78edb36e19bf6a799d3ab523..d6cca182e81937dd5a494d57c2c8221b6039ad45 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -39,14 +39,14 @@ class DeCalculator {
                DeCalculator() { m = MothurOut::getInstance(); }
                ~DeCalculator() {};
                
-               vector<Sequence*> findClosest(Sequence*, vector<Sequence*>&, vector<Sequence*>&, int);  //takes querySeq, a reference db, filteredRefDB, numWanted 
+               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);