maligner.h

   1 #ifndef MALIGNER_H
   2 #define MALIGNER_H
   3 /*
   4  *  maligner.h
   5  *  Mothur
   6  *
   7  *  Created by westcott on 9/23/09.
   8  *  Copyright 2009 Schloss Lab. All rights reserved.
   9  *
  10  */
  11
  12 #include "decalc.h"
  13 #include "chimera.h"
  14 #include "database.hpp"
  15
  16 /***********************************************************************/
  17 //This class was modeled after the chimeraMaligner written by the Broad Institute
  18 /**********************************************************************/
  19 class Maligner {
  20
  21         public:
  22
  23                 Maligner(vector<Sequence*>, int, int, int, float, int, int, string, Database*, Database*);
  24                 ~Maligner() {};
  25
  26                 string getResults(Sequence*, DeCalculator*);
  27                 float getPercentID() {  return percentIdenticalQueryChimera;    }
  28                 vector<results> getOutput()  {  return outputResults;                   }
  29
  30
  31         private:
  32                 Sequence* query;
  33                 vector<Sequence*> refSeqs;
  34                 vector<Sequence*> db;
  35                 int numWanted, matchScore, misMatchPenalty, minCoverage, minSimilarity;
  36                 string searchMethod;
  37                 float minDivR, percentIdenticalQueryChimera;
  38                 vector<results> outputResults;
  39                 vector<int> indexes;  //stores index into template seqs of the refSeqs, so we can return the whole sequence rather than the trimmed and filtered one
  40                 map<int, int> spotMap;
  41                 Database* databaseLeft;
  42                 Database* databaseRight;
  43
  44                 vector<Sequence*> minCoverageFilter(vector<Sequence*>);  //removes top matches that do not have minimum coverage with query.
  45                 int computeChimeraPenalty();
  46                 void verticalFilter(vector<Sequence*>);
  47
  48                 vector< vector<score_struct> > buildScoreMatrix(int, int);
  49                 void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
  50                 vector<trace_struct> extractHighestPath(vector<vector<score_struct> >);
  51                 vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
  52                 string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
  53                 string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence*>);
  54                 float computePercentID(string, string);
  55                 string chimeraMaligner(int, DeCalculator*);
  56                 vector<Sequence*> getBlastSeqs(Sequence*, int);
  57                 vector<Sequence*> getKmerSeqs(Sequence*, int);
  58                 MothurOut* m;
  59
  60 };
  61
  62 /***********************************************************************/
  63
  64 #endif
  65