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 "alignmentdb.h"
  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, string, bool, int, int, string); //fasta, template, name, svg, increment, ksize, outputDir
  29                 ~ChimeraCheckRDP();
  30
  31                 int getChimeras(Sequence*);
  32                 Sequence print(ostream&, ostream&);
  33
  34                 #ifdef USE_MPI
  35                 Sequence print(MPI_File&, MPI_File&);
  36                 #endif
  37
  38         private:
  39
  40                 Sequence* querySeq;
  41                 AlignmentDB* templateDB;
  42                 Kmer* kmer;
  43                 Sequence closest;               //closest is the closest overall seq to query
  44
  45                 vector<sim>  IS;  //IS is the vector of IS values for each window for query
  46                 string fastafile;
  47                 map<string, string> names;
  48                 string name;
  49                 bool svg;
  50                 int kmerSize, increment;
  51
  52                 vector<sim> findIS();
  53                 int calcKmers(map<int, int>, map<int, int>);
  54                 void makeSVGpic(vector<sim>);
  55                 void readName(string);
  56 };
  57 /***********************************************************/
  58
  59 #endif
  60