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
  15 /***********************************************************************/
  16 //This class was modeled after the chimeraMaligner written by the Broad Institute
  17 /**********************************************************************/
  18 class Maligner {
  19
  20         public:
  21
  22                 Maligner(vector<Sequence*>, int, int, int, float, int, int, string);
  23                 ~Maligner() {};
  24
  25                 string getResults(Sequence*, DeCalculator*);
  26                 float getPercentID() {  return percentIdenticalQueryChimera;    }
  27                 vector<results> getOutput()  {  return outputResults;                   }
  28
  29
  30         private:
  31                 Sequence* query;
  32                 vector<Sequence*> refSeqs;
  33                 vector<Sequence*> db;
  34                 int numWanted, matchScore, misMatchPenalty, minCoverage, minSimilarity;
  35                 string searchMethod;
  36                 float minDivR, percentIdenticalQueryChimera;
  37                 vector<results> outputResults;
  38                 map<int, int> spotMap;
  39
  40                 vector<Sequence*> minCoverageFilter(vector<Sequence*>);  //removes top matches that do not have minimum coverage with query.
  41                 int computeChimeraPenalty();
  42                 void verticalFilter(vector<Sequence*>);
  43
  44                 vector< vector<score_struct> > buildScoreMatrix(int, int);
  45                 void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
  46                 vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
  47                 vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
  48                 string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
  49                 float computePercentID(string, string);
  50                 string chimeraMaligner(int, DeCalculator*);
  51                 vector<Sequence*> getBlastSeqs(Sequence*, int);
  52
  53 };
  54
  55 /***********************************************************************/
  56
  57 #endif
  58