X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=decalc.h;h=d1daf050e004333228e39fb5aaa7621dd1b0bcf6;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=5f0a82025c557a75c3adc4715526fa17bd5fe5a5;hpb=05a0195e07c42c996592ee1c8abb63adedb7f493;p=mothur.git

diff --git a/decalc.h b/decalc.h
index 5f0a820..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.
 
@@ -36,17 +36,18 @@ class DeCalculator {
 
 	public:
 		
-		DeCalculator() {};
+		DeCalculator() { m = MothurOut::getInstance(); }
 		~DeCalculator() {};
 		
-		vector<Sequence*> findClosest(Sequence*, vector<Sequence*>, int);  //takes querySeq, a reference db and numWanted - returns indexes to closest seqs in db
+		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>&);
-		void trimSeqs(Sequence*, vector<Sequence*>);
-		void removeObviousOutliers(vector< vector<quanMember> >&, int);
+		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);
 		vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
@@ -55,7 +56,7 @@ class DeCalculator {
 		float calcDE(vector<float>, vector<float>);
 		float calcDist(Sequence*, Sequence*, int, int);
 		float getCoef(vector<float>, vector<float>);
-		vector< vector<quanMember> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int);
+		vector< vector<float> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int);
 		
 		vector<int> returnObviousOutliers(vector< vector<quanMember> >, int);
 		
@@ -70,6 +71,7 @@ class DeCalculator {
 		set<int> h;
 		int alignLength;
 		map<int, int> maskMap;
+		MothurOut* m;
 
 };