--- /dev/null
+/*
+ * needleman.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 "alignment.hpp"
+#include "overlap.hpp"
+#include "needlemanoverlap.hpp"
+
+/**************************************************************************************************/
+
+NeedlemanOverlap::NeedlemanOverlap(float gO, float f, float mm, int r) :// note that we don't have a gap extend
+gap(gO), match(f), mismatch(mm), Alignment(r) { // the gap openning penalty is assessed for
+ try { // every gapped position
+ for(int i=1;i<nCols;i++){
+ alignment[0][i].prevCell = 'l'; // initialize first row by pointing all poiters to the left
+ alignment[0][i].cValue = 0; // and the score to zero
+ }
+
+ for(int i=1;i<nRows;i++){
+ alignment[i][0].prevCell = 'u'; // initialize first column by pointing all poiters upwards
+ alignment[i][0].cValue = 0; // and the score to zero
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NeedlemanOverlap", "NeedlemanOverlap");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+NeedlemanOverlap::~NeedlemanOverlap(){ /* do nothing */ }
+
+/**************************************************************************************************/
+
+void NeedlemanOverlap::align(string A, string B){
+ try {
+
+ seqA = ' ' + A; lA = seqA.length(); // algorithm requires a dummy space at the beginning of each string
+ seqB = ' ' + B; lB = seqB.length(); // algorithm requires a dummy space at the beginning of each string
+
+ if (lA > nRows) { m->mothurOut("One of your candidate sequences is longer than you longest template sequence. Your longest template sequence is " + toString(nRows) + ". Your candidate is " + toString(lA) + "."); m->mothurOutEndLine(); }
+
+ for(int i=1;i<lB;i++){ // This code was largely translated from Perl code provided in Ex 3.1
+
+ for(int j=1;j<lA;j++){ // of the O'Reilly BLAST book. I found that the example output had a
+
+ // number of errors
+ float diagonal;
+ if(seqB[i] == seqA[j]) { diagonal = alignment[i-1][j-1].cValue + match; }
+ else { diagonal = alignment[i-1][j-1].cValue + mismatch; }
+
+ float up = alignment[i-1][j].cValue + gap;
+ float left = alignment[i][j-1].cValue + gap;
+
+ if(diagonal >= up){
+ if(diagonal >= left){
+ alignment[i][j].cValue = diagonal;
+ alignment[i][j].prevCell = 'd';
+ }
+ else{
+ alignment[i][j].cValue = left;
+ alignment[i][j].prevCell = 'l';
+ }
+ }
+ else{
+ if(up >= left){
+ alignment[i][j].cValue = up;
+ alignment[i][j].prevCell = 'u';
+ }
+ else{
+ alignment[i][j].cValue = left;
+ alignment[i][j].prevCell = 'l';
+ }
+ }
+ }
+ }
+
+ Overlap over;
+ over.setOverlap(alignment, lA, lB, 0); // Fix gaps at the beginning and end of the sequences
+ traceBack(); // Traceback the alignment to populate seqAaln and seqBaln
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NeedlemanOverlap", "align");
+ exit(1);
+ }
+
+}
+
+/**************************************************************************************************/
+
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