X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=decalc.h;h=d1daf050e004333228e39fb5aaa7621dd1b0bcf6;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=5818539dd8db0c94f19c62bfa942eb499368149b;hpb=dbd5da8043df1cb9f5ff7c6ddb5f550ea49b52c2;p=mothur.git

diff --git a/decalc.h b/decalc.h
index 5818539..d1daf05 100644
--- a/decalc.h
+++ b/decalc.h
@@ -14,31 +14,64 @@
 
 /***********************************************************************/
 
-//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.
 
 /***********************************************************************/
 
+//this structure is necessary to determine the sequence that contributed to the outliers when we remove them
+//this way we can remove all scores that are contributed by outlier sequences.
+struct quanMember {
+	float score;
+	int member1;
+	int member2;
+	quanMember (float s, int m, int n) : score(s), member1(m),  member2(n) {}
+	quanMember() {}
+	
+};
+		
+//********************************************************************************************************************
 class DeCalculator {
 
 	public:
-	
-		void trimSeqs(Sequence*, Sequence, map<int, int>&);
-		vector<float> readFreq();
-		vector<float> calcFreq(vector<Sequence*>);
 		
-		vector<Sequence> findPairs(int, int);
-		vector<int> findWindows(Sequence*, int, int, int&);
-		vector<float> calcObserved(Sequence*, Sequence, vector<int>, int);
+		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>&);
+		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);
 		vector<float>  calcExpected(vector<float>, float);
-		vector<float>  findQav(vector<int>, int);  
+		vector<float>  findQav(vector<int>, int, vector<float>);  
 		float calcDE(vector<float>, vector<float>);
-		float calcDist(Sequence*, Sequence, int, int);
+		float calcDist(Sequence*, Sequence*, int, int);
 		float getCoef(vector<float>, vector<float>);
+		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>);
+		//int findLargestContrib(vector<int>);
+		//void removeContrib(int, vector<quanMember>&);
+		string seqMask;
+		set<int> h;
+		int alignLength;
+		map<int, int> maskMap;
+		MothurOut* m;
 
 };