X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=decalc.h;h=d1daf050e004333228e39fb5aaa7621dd1b0bcf6;hp=2d0d529dfb7136e22894ecc46a0f36be01eef353;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=2f17ce987b15dca9a309116d9df5131a1d3a35ee

diff --git a/decalc.h b/decalc.h
index 2d0d529..d1daf05 100644
--- 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);