8 * Created by Sarah Westcott on 8/11/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
17 //This class was created using the algorythms described in the
18 // "New Screening Software Shows that Most Recent Large 16SrRNA Gene Clone Libraries Contain Chimeras" paper
19 //by Kevin E. Ashelford 1, Nadia A. Chuzhanova 2, John C. Fry 1, Antonia J. Jones 3 and Andrew J. Weightman 1.
21 /***********************************************************/
23 class Mallard : public Chimera {
32 void setCons(string c) {};
33 void setQuantiles(string q) {};
40 linePair(int i, int j) : start(i), end(j) {}
48 vector<linePair*> lines;
49 vector<Sequence*> querySeqs;
50 vector<int> windowSizes; //windowSizes[0] = window size of querySeqs[0]
52 vector<float> highestDE;
54 vector<float> probabilityProfile;
55 vector< vector<quanMember> > quantilesMembers; //quantiles[0] is the vector of deviations with ceiling score of 1, quantiles[1] is the vector of deviations with ceiling score of 2...
57 void createProcessesQuan();
61 /***********************************************************/