+++ /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);
- }
-
-}
-
-/**************************************************************************************************/
-