X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=decalc.h;fp=decalc.h;h=d6cca182e81937dd5a494d57c2c8221b6039ad45;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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+#ifndef DECALC_H
+#define DECALC_H
+/*
+ *  decalc.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 7/22/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "sequence.hpp"
+
+/***********************************************************************/
+
+//This class was created using the algorythms 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:
+		
+		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>);  
+		float calcDE(vector<float>, vector<float>);
+		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;
+
+};
+
+/***********************************************************************/
+
+#endif