7 * Created by Sarah Westcott on 7/22/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "sequence.hpp"
15 /***********************************************************************/
17 //This class was created using the algorythms described in the
18 // "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" paper
19 //by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.
21 /***********************************************************************/
30 set<int> getPos() { return h; }
31 void setMask(string m);
32 void runMask(Sequence*);
33 void trimSeqs(Sequence*, Sequence*, map<int, int>&);
34 vector<float> calcFreq(vector<Sequence*>, string);
35 vector<int> findWindows(Sequence*, int, int, int&, int);
36 vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
37 vector<float> calcExpected(vector<float>, float);
38 vector<float> findQav(vector<int>, int, vector<float>);
39 float calcDE(vector<float>, vector<float>);
40 float calcDist(Sequence*, Sequence*, int, int);
41 float getCoef(vector<float>, vector<float>);
42 vector< vector<float> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int);
50 /***********************************************************************/