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
  14 /***********************************************************************/
  15 //This class was modeled after the chimeraMaligner written by the Broad Institute
  16 /***********************************************************************/
  17 struct score_struct {
  18         int prev;
  19         int score;
  20         int row;
  21         int col;
  22 };
  23 /***********************************************************************/
  24 struct trace_struct {
  25         int col;
  26         int oldCol;
  27         int row;
  28 };
  29 /***********************************************************************/
  30 struct results {
  31         int regionStart;
  32         int regionEnd;
  33         string parent;
  34         float queryToParent;
  35         float queryToParentLocal;
  36         float divR;
  37 };
  38
  39 /**********************************************************************/
  40 class Maligner {
  41
  42         public:
  43
  44                 Maligner(vector<Sequence*>, int, int, int, float, int);
  45                 ~Maligner() {};
  46
  47                 string getResults(Sequence*);
  48                 float getPercentID() {  return percentIdenticalQueryChimera;    }
  49                 vector<results> getOutput()  {  return outputResults;                   }
  50
  51
  52         private:
  53                 DeCalculator* decalc;
  54                 Sequence* query;
  55                 vector<Sequence*> refSeqs;
  56                 vector<Sequence*> db;
  57                 int numWanted, matchScore, misMatchPenalty, minCoverage;
  58                 float minDivR, percentIdenticalQueryChimera;
  59                 vector<results> outputResults;
  60
  61                 vector<Sequence*> minCoverageFilter(vector<Sequence*>);  //removes top matches that do not have minimum coverage with query.
  62                 int computeChimeraPenalty();
  63                 void verticalFilter(vector<Sequence*>);
  64
  65                 vector< vector<score_struct> > buildScoreMatrix(int, int);
  66                 void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
  67                 vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
  68                 vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
  69                 string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
  70                 float computePercentID(string, string);
  71
  72 };
  73
  74 /***********************************************************************/
  75
  76 #endif
  77