X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=decalc.h;h=d1daf050e004333228e39fb5aaa7621dd1b0bcf6;hp=da0f96cd72b69acf3350a1565f66e7586644ff12;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=f7fbd74ffedcf62217109c22e828453eaefa1458

diff --git a/decalc.h b/decalc.h
index da0f96c..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.
 
@@ -36,15 +36,18 @@ class DeCalculator {
 
 	public:
 		
-		DeCalculator() {};
+		DeCalculator() { m = MothurOut::getInstance(); }
 		~DeCalculator() {};
 		
+		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 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);
@@ -53,10 +56,12 @@ 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);
 		
+		map<int, int> getMaskMap() { return maskMap; }
+		
 	private:
 		//vector<quanMember> sortContrib(map<quanMember*, float>);  //used by mallard
 		float findAverage(vector<float>);
@@ -65,6 +70,8 @@ class DeCalculator {
 		string seqMask;
 		set<int> h;
 		int alignLength;
+		map<int, int> maskMap;
+		MothurOut* m;
 
 };