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 //This class was created using the algorythms described in
  20 //CHIMERA_CHECK version 2.7 written by Niels Larsen.
  21
  22 /***********************************************************/
  23
  24 class ChimeraCheckRDP : public Chimera {
  25
  26         public:
  27                 ChimeraCheckRDP(string, string);
  28                 ~ChimeraCheckRDP();
  29
  30                 void getChimeras();
  31                 void print(ostream&);
  32
  33                 void setCons(string){};
  34                 void setQuantiles(string q) {};
  35
  36
  37         private:
  38
  39                 vector<linePair*> lines;
  40                 vector<Sequence*> querySeqs;
  41                 Database* templateDB;
  42                 Kmer* kmer;
  43
  44                 vector< vector<sim> > IS;  //IS[0] is the vector of IS values for each window for querySeqs[0]
  45                 float chimeraCutoff;
  46
  47
  48                 //map<string, vector< map<int, int> > >:: iterator it;
  49                 //map<int, int>::iterator it2;
  50
  51                 vector<Sequence> closest;               //closest[0] is the closest overall seq to querySeqs[0].
  52
  53                 string fastafile, templateFile;
  54                 map<string, string> names;
  55
  56                 vector<sim> findIS(int);
  57                 int calcKmers(map<int, int>, map<int, int>);
  58                 void getCutoff();
  59                 void makeSVGpic(vector<sim>, int);
  60                 void readName(string);
  61
  62                 void createProcessesIS();
  63
  64 };
  65
  66 /***********************************************************/
  67
  68 #endif
  69