gotohoverlap.cpp

   1 /*
   2  *  gotohoverlap.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 12/15/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  *      This class is an Alignment child class that implements the Gotoh pairwise alignment algorithm as described in:
   9  *
  10  *              Gotoh O. 1982.  An improved algorithm for matching biological sequences.  J. Mol. Biol.  162:705-8.
  11  *              Myers, EW & Miller, W.  1988.  Optimal alignments in linear space.  Comput Appl Biosci. 4:11-7.
  12  *
  13  *      This method is nice because it allows for an affine gap penalty to be assessed, which is analogous to what is used
  14  *      in blast and is an alternative to Needleman-Wunsch, which only charges the same penalty for each gap position.
  15  *      Because this method typically has problems at the ends when two sequences do not full overlap, we employ a separate
  16  *      method to fix the ends (see Overlap class documentation)
  17  *
  18  */
  19
  20
  21 #include "alignmentcell.hpp"
  22 #include "overlap.hpp"
  23 #include "alignment.hpp"
  24 #include "gotohoverlap.hpp"
  25
  26 /**************************************************************************************************/
  27
  28 GotohOverlap::GotohOverlap(float gO, float gE, float m, float mm, int r) :
  29         gapOpen(gO), gapExtend(gE), match(m), mismatch(mm), Alignment(r) {
  30
  31         for(int i=1;i<nCols;i++){                               //      we initialize the dynamic programming matrix by setting the pointers in
  32                 alignment[0][i].prevCell = 'l';         //      the first row to the left
  33                 alignment[0][i].cValue = 0;
  34                 alignment[0][i].dValue = 0;
  35         }
  36
  37         for(int i=1;i<nRows;i++){                               //      we initialize the dynamic programming matrix by setting the pointers in
  38                 alignment[i][0].prevCell = 'u';         //      the first column upward
  39                 alignment[i][0].cValue = 0;
  40                 alignment[i][0].iValue = 0;
  41         }
  42 }
  43
  44 /**************************************************************************************************/
  45
  46 void GotohOverlap::align(string A, string B){
  47
  48         seqA = ' ' + A; lA = seqA.length();             //      the algorithm requires that the first character be a dummy value
  49         seqB = ' ' + B; lB = seqB.length();             //      the algorithm requires that the first character be a dummy value
  50
  51         for(int i=1;i<lB;i++){                                  //      the recursion here is shown in Webb and Miller, Fig. 1A.  Note that
  52                 for(int j=1;j<lA;j++){                          //      if we need to conserve on space we should see Fig. 1B, which is linear
  53                                                                                         //      in space, which I think is unnecessary
  54                         float diagonal;
  55                         if(seqB[i] == seqA[j])  {       diagonal = alignment[i-1][j-1].cValue + match;          }
  56                         else                                    {       diagonal = alignment[i-1][j-1].cValue + mismatch;       }
  57
  58                         alignment[i][j].iValue = max(alignment[i][j-1].iValue, alignment[i][j-1].cValue + gapOpen) + gapExtend;
  59                         alignment[i][j].dValue = max(alignment[i-1][j].dValue, alignment[i-1][j].cValue + gapOpen) + gapExtend;
  60
  61                         if(alignment[i][j].iValue > alignment[i][j].dValue){
  62                                 if(alignment[i][j].iValue > diagonal){
  63                                         alignment[i][j].cValue = alignment[i][j].iValue;
  64                                         alignment[i][j].prevCell = 'l';
  65                                 }
  66                                 else{
  67                                         alignment[i][j].cValue = diagonal;
  68                                         alignment[i][j].prevCell = 'd';
  69                                 }
  70                         }
  71                         else{
  72                                 if(alignment[i][j].dValue > diagonal){
  73                                         alignment[i][j].cValue = alignment[i][j].dValue;
  74                                         alignment[i][j].prevCell = 'u';
  75                                 }
  76                                 else{
  77                                         alignment[i][j].cValue = diagonal;
  78                                         alignment[i][j].prevCell = 'd';
  79                                 }
  80                         }
  81
  82                 }
  83         }
  84         Overlap over;
  85         over.setOverlap(alignment, lA, lB, 0);  //      Fix the gaps at the ends of the sequences
  86         traceBack();                                                    //      Construct the alignment and set seqAaln and seqBaln
  87 }
  88
  89 /**************************************************************************************************/