--- /dev/null
+/*
+ * 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)
+ *
+ */
+
+using namespace std;
+
+#include "alignmentcell.hpp"
+#include "overlap.hpp"
+#include "alignment.hpp"
+#include "gotohoverlap.hpp"
+
+/**************************************************************************************************/
+
+GotohOverlap::GotohOverlap(float gO, float gE, float m, float mm, int r) :
+ gapOpen(gO), gapExtend(gE), match(m), mismatch(mm), Alignment(r) {
+
+ 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;
+ }
+}
+
+/**************************************************************************************************/
+
+void GotohOverlap::align(string A, string B){
+
+ 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
+}
+
+/**************************************************************************************************/