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
  46                 //map of vector of maps- I know its a little convaluted but I am trying to save time
  47                 //I think that since the window is only sliding 10 bases there is a good probability that the closest seq to each fragment
  48                 //will be the same for several windows so I want to save the vector of maps containing its kmer info rather than regenerating it.
  49                 //So...
  50                 map<string, vector< map<int, int> > > seqKmerInfo;  // outer map - sequence name -> kmer info
  51                                                                                                                         // kmer info: inner vector of maps - each entry in the vector is a map of the kmers up to that spot in the unaligned seq
  52                                                                                                                         //example:  seqKmerInfo["ecoli"][50] = map containing the kmers found in the first 50 + kmersize characters of ecoli.
  53                                                                                                                         //i chose to store the kmers numbers in a map so you wouldn't have to check for dupilcate entries and could easily find the
  54                                                                                                                         //kmers 2 seqs had in common.  There may be a better way to do this thats why I am leaving so many comments...
  55                 map<string, vector< map<int, int> > >:: iterator it;
  56                 map<int, int>::iterator it2;
  57
  58                 vector<Sequence> closest;               //closest[0] is the closest overall seq to querySeqs[0].
  59
  60                 string fastafile, templateFile;
  61
  62
  63                 vector<sim> findIS(int);
  64                 int calcKmers(map<int, int>, map<int, int>);
  65                 vector< vector<sim> > createProcessesIS(vector<Sequence*>, vector<linePair*>);
  66
  67 };
  68
  69 /***********************************************************/
  70
  71 #endif
  72