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/*
* 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, bool createBaseMap){
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) + ".\n"); }
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(createBaseMap); // Traceback the alignment to populate seqAaln and seqBaln
}
catch(exception& e) {
m->errorOut(e, "NeedlemanOverlap", "align");
exit(1);
}
}
/**************************************************************************************************/
//A is dna, B is protein
void NeedlemanOverlap::align(Sequence A, Protein B){
try {
string seq = A.getUnaligned();
vector<string> seqA; seqA.push_back(" ");
int extentionSize = 3 - (seq.length() % 3);
for (int i = 0; i < extentionSize; i++) { seq += "."; } //add gaps
for(int j = 0; j<seq.length();){
string temp = ""; temp += seq[j]; j++; temp += seq[j]; j++; temp += seq[j]; j++;
seqA.push_back(temp);
}
lA = seqA.size();
vector<AminoAcid> seqB = B.getAligned();
AminoAcid dummy('.');
seqB.insert(seqB.begin(), dummy); lB = seqB.size();
if (lA > nRows) { m->mothurOut("One of your unaligned sequence is longer than your protein sequence. Your longest protein sequence is " + toString(nRows) + ". Your candidate is " + toString(lA) + ".\n"); }
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;
AminoAcid codon(seqA[j]);
if(seqB[i].getNum() == codon.getNum()) { 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
proteinTraceBack(seqA, seqB);
}
catch(exception& e) {
m->errorOut(e, "NeedlemanOverlap", "align");
exit(1);
}
}
/**************************************************************************************************/
void NeedlemanOverlap::alignPrimer(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) + ".\n"); }
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(isEquivalent(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(false); // Traceback the alignment to populate seqAaln and seqBaln
}
catch(exception& e) {
m->errorOut(e, "NeedlemanOverlap", "alignPrimer");
exit(1);
}
}
//********************************************************************/
bool NeedlemanOverlap::isEquivalent(char oligo, char seq){
try {
bool same = true;
oligo = toupper(oligo);
seq = toupper(seq);
if(oligo != seq){
if(oligo == 'A' && (seq != 'A' && seq != 'M' && seq != 'R' && seq != 'W' && seq != 'D' && seq != 'H' && seq != 'V')) { same = false; }
else if(oligo == 'C' && (seq != 'C' && seq != 'Y' && seq != 'M' && seq != 'S' && seq != 'B' && seq != 'H' && seq != 'V')) { same = false; }
else if(oligo == 'G' && (seq != 'G' && seq != 'R' && seq != 'K' && seq != 'S' && seq != 'B' && seq != 'D' && seq != 'V')) { same = false; }
else if(oligo == 'T' && (seq != 'T' && seq != 'Y' && seq != 'K' && seq != 'W' && seq != 'B' && seq != 'D' && seq != 'H')) { same = false; }
else if((oligo == '.' || oligo == '-')) { same = false; }
else if((oligo == 'N' || oligo == 'I') && (seq == 'N')) { same = false; }
else if(oligo == 'R' && (seq != 'A' && seq != 'G')) { same = false; }
else if(oligo == 'Y' && (seq != 'C' && seq != 'T')) { same = false; }
else if(oligo == 'M' && (seq != 'C' && seq != 'A')) { same = false; }
else if(oligo == 'K' && (seq != 'T' && seq != 'G')) { same = false; }
else if(oligo == 'W' && (seq != 'T' && seq != 'A')) { same = false; }
else if(oligo == 'S' && (seq != 'C' && seq != 'G')) { same = false; }
else if(oligo == 'B' && (seq != 'C' && seq != 'T' && seq != 'G')) { same = false; }
else if(oligo == 'D' && (seq != 'A' && seq != 'T' && seq != 'G')) { same = false; }
else if(oligo == 'H' && (seq != 'A' && seq != 'T' && seq != 'C')) { same = false; }
else if(oligo == 'V' && (seq != 'A' && seq != 'C' && seq != 'G')) { same = false; }
}
return same;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "countDiffs");
exit(1);
}
}
/**************************************************************************************************/
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