-/*
- * gotohoverlap.cpp
- *
- *
- * Created by Pat Schloss on 12/15/08.
- * Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- * This class is an Alignment child class that implements the Gotoh pairwise alignment algorithm as described in:
- *
- * Gotoh O. 1982. An improved algorithm for matching biological sequences. J. Mol. Biol. 162:705-8.
- * Myers, EW & Miller, W. 1988. Optimal alignments in linear space. Comput Appl Biosci. 4:11-7.
- *
- * This method is nice because it allows for an affine gap penalty to be assessed, which is analogous to what is used
- * in blast and is an alternative to Needleman-Wunsch, which only charges the same penalty for each gap position.
- * Because this method typically has problems at the ends when two sequences do not full overlap, we employ a separate
- * method to fix the ends (see Overlap class documentation)
- *
- */
-
-
-#include "alignmentcell.hpp"
-#include "overlap.hpp"
-#include "alignment.hpp"
-#include "gotohoverlap.hpp"
-
-/**************************************************************************************************/
-
-GotohOverlap::GotohOverlap(float gO, float gE, float f, float mm, int r) :
- gapOpen(gO), gapExtend(gE), match(f), mismatch(mm), Alignment(r) {
-
- try {
- for(int i=1;i<nCols;i++){ // we initialize the dynamic programming matrix by setting the pointers in
- alignment[0][i].prevCell = 'l'; // the first row to the left
- alignment[0][i].cValue = 0;
- alignment[0][i].dValue = 0;
- }
-
- for(int i=1;i<nRows;i++){ // we initialize the dynamic programming matrix by setting the pointers in
- alignment[i][0].prevCell = 'u'; // the first column upward
- alignment[i][0].cValue = 0;
- alignment[i][0].iValue = 0;
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "GotohOverlap", "GotohOverlap");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-void GotohOverlap::align(string A, string B){
- try {
- seqA = ' ' + A; lA = seqA.length(); // the algorithm requires that the first character be a dummy value
- seqB = ' ' + B; lB = seqB.length(); // the algorithm requires that the first character be a dummy value
-
- for(int i=1;i<lB;i++){ // the recursion here is shown in Webb and Miller, Fig. 1A. Note that
- for(int j=1;j<lA;j++){ // if we need to conserve on space we should see Fig. 1B, which is linear
- // in space, which I think is unnecessary
- float diagonal;
- if(seqB[i] == seqA[j]) { diagonal = alignment[i-1][j-1].cValue + match; }
- else { diagonal = alignment[i-1][j-1].cValue + mismatch; }
-
- alignment[i][j].iValue = max(alignment[i][j-1].iValue, alignment[i][j-1].cValue + gapOpen) + gapExtend;
- alignment[i][j].dValue = max(alignment[i-1][j].dValue, alignment[i-1][j].cValue + gapOpen) + gapExtend;
-
- if(alignment[i][j].iValue > alignment[i][j].dValue){
- if(alignment[i][j].iValue > diagonal){
- alignment[i][j].cValue = alignment[i][j].iValue;
- alignment[i][j].prevCell = 'l';
- }
- else{
- alignment[i][j].cValue = diagonal;
- alignment[i][j].prevCell = 'd';
- }
- }
- else{
- if(alignment[i][j].dValue > diagonal){
- alignment[i][j].cValue = alignment[i][j].dValue;
- alignment[i][j].prevCell = 'u';
- }
- else{
- alignment[i][j].cValue = diagonal;
- alignment[i][j].prevCell = 'd';
- }
- }
-
- }
- }
- Overlap over;
- over.setOverlap(alignment, lA, lB, 0); // Fix the gaps at the ends of the sequences
- traceBack(); // Construct the alignment and set seqAaln and seqBaln
-
- }
- catch(exception& e) {
- m->errorOut(e, "GotohOverlap", "align");
- exit(1);
- }
-}
-
-/**************************************************************************************************/