changes while testing

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index 2d0d529dfb7136e22894ecc46a0f36be01eef353..d1daf050e004333228e39fb5aaa7621dd1b0bcf6 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -14,7 +14,7 @@
 
 /***********************************************************************/
 
-//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.
 
@@ -39,14 +39,14 @@ class DeCalculator {
                DeCalculator() { m = MothurOut::getInstance(); }
                ~DeCalculator() {};
                
-               vector<Sequence*> findClosest(Sequence*, vector<Sequence*>, int&, vector<int>&);  //takes querySeq, a reference db, numWanted and indexes 
+               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);