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[mothur.git] / decalc.h

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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