chimeracheckrdp.h

   1 #ifndef CHIMERACHECK_H
   2 #define CHIMERACHECK_H
   3
   4 /*
   5  *  chimeracheckrdp.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/8/09.
   9  *  Copyright 2009 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "chimera.h"
  15 #include "kmer.hpp"
  16 #include "kmerdb.hpp"
  17 #include "database.hpp"
  18
  19 /***********************************************************/
  20 //This class was created using the algorythms described in
  21 //CHIMERA_CHECK version 2.7 written by Niels Larsen.
  22
  23 /***********************************************************/
  24
  25 class ChimeraCheckRDP : public Chimera {
  26
  27         public:
  28                 ChimeraCheckRDP(string, string);
  29                 ~ChimeraCheckRDP();
  30
  31                 void getChimeras();
  32                 void print(ostream&);
  33
  34                 void setCons(string){};
  35                 void setQuantiles(string q) {};
  36
  37
  38         private:
  39
  40                 vector<linePair*> lines;
  41                 vector<Sequence*> querySeqs;
  42                 Database* templateDB;
  43                 Kmer* kmer;
  44
  45                 vector< vector<sim> > IS;  //IS[0] is the vector of IS values for each window for querySeqs[0]
  46                 float chimeraCutoff;
  47
  48
  49                 //map<string, vector< map<int, int> > >:: iterator it;
  50                 //map<int, int>::iterator it2;
  51
  52                 vector<Sequence> closest;               //closest[0] is the closest overall seq to querySeqs[0].
  53
  54                 string fastafile, templateFile;
  55                 map<string, string> names;
  56
  57                 vector<sim> findIS(int);
  58                 int calcKmers(map<int, int>, map<int, int>);
  59                 void getCutoff();
  60                 void makeSVGpic(vector<sim>, int);
  61                 void readName(string);
  62
  63                 void createProcessesIS();
  64
  65 };
  66
  67 /***********************************************************/
  68
  69 #endif
  70