X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=decalc.h;h=d6cca182e81937dd5a494d57c2c8221b6039ad45;hp=dbdf31650235f5b0d5074923d8495591380ec30b;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=7597c66c08bac938fedcacc1f760186bc077b3f1

diff --git a/decalc.h b/decalc.h
index dbdf316..d6cca18 100644
--- a/decalc.h
+++ b/decalc.h
@@ -20,29 +20,58 @@
 
 /***********************************************************************/
 
+//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:
 		
-		DeCalculator() {};
+		DeCalculator() { m = MothurOut::getInstance(); }
 		~DeCalculator() {};
 		
-		void setMask(string m); 
+		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*, 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> calcObserved(Sequence*, Sequence*, vector<int>, int);
 		vector<float>  calcExpected(vector<float>, float);
 		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;
 
 };