4 * Created by Pat Schloss on 12/15/08.
5 * Copyright 2008 Patrick D. Schloss. All rights reserved.
7 * This is a class for an abstract datatype for classes that implement various types of alignment algorithms.
8 * As of 12/18/08 these included alignments based on blastn, needleman-wunsch, and the Gotoh algorithms
12 #include "alignmentcell.hpp"
13 #include "alignment.hpp"
16 /**************************************************************************************************/
18 Alignment::Alignment() { /* do nothing */ }
20 /**************************************************************************************************/
22 Alignment::Alignment(int A) : nCols(A), nRows(A) {
24 alignment.resize(nRows); // For the Gotoh and Needleman-Wunsch we initialize the dynamic programming
25 for(int i=0;i<nRows;i++){ // matrix by initializing a matrix that is A x A. By default we will set A
26 alignment[i].resize(nCols); // at 2000 for 16S rRNA gene sequences
30 errorOut(e, "Alignment", "Alignment");
35 /**************************************************************************************************/
37 void Alignment::traceBack(){ // This traceback routine is used by the dynamic programming algorithms
39 // to fill the values of seqAaln and seqBaln
47 AlignmentCell currentCell = alignment[row][column]; // Start the traceback from the bottom-right corner of the
50 if(currentCell.prevCell == 'x'){ seqAaln = seqBaln = "NOALIGNMENT"; }//If there's an 'x' in the bottom-
51 else{ // right corner bail out because it means nothing got aligned
52 while(currentCell.prevCell != 'x'){ // while the previous cell isn't an 'x', keep going...
54 if(currentCell.prevCell == 'u'){ // if the pointer to the previous cell is 'u', go up in the
55 seqAaln = '-' + seqAaln; // matrix. this indicates that we need to insert a gap in
56 seqBaln = seqB[row] + seqBaln; // seqA and a base in seqB
57 currentCell = alignment[--row][column];
59 else if(currentCell.prevCell == 'l'){ // if the pointer to the previous cell is 'l', go to the left
60 seqBaln = '-' + seqBaln; // in the matrix. this indicates that we need to insert a gap
61 seqAaln = seqA[column] + seqAaln; // in seqB and a base in seqA
62 currentCell = alignment[row][--column];
65 seqAaln = seqA[column] + seqAaln; // otherwise we need to go diagonally up and to the left,
66 seqBaln = seqB[row] + seqBaln; // here we add a base to both alignments
67 currentCell = alignment[--row][--column];
72 pairwiseLength = seqAaln.length();
73 seqAstart = 1; seqAend = 0;
74 seqBstart = 1; seqBend = 0;
76 for(int i=0;i<seqAaln.length();i++){
77 if(seqAaln[i] != '-' && seqBaln[i] == '-') { seqAstart++; }
78 else if(seqAaln[i] == '-' && seqBaln[i] != '-') { seqBstart++; }
82 pairwiseLength -= (seqAstart + seqBstart - 2);
84 for(int i=seqAaln.length()-1; i>=0;i--){
85 if(seqAaln[i] != '-' && seqBaln[i] == '-') { seqAend++; }
86 else if(seqAaln[i] == '-' && seqBaln[i] != '-') { seqBend++; }
89 pairwiseLength -= (seqAend + seqBend);
91 seqAend = seqA.length() - seqAend - 1;
92 seqBend = seqB.length() - seqBend - 1;
95 errorOut(e, "Alignment", "traceBack");
99 /**************************************************************************************************/
101 Alignment::~Alignment(){
103 for (int i = 0; i < alignment.size(); i++) {
104 for (int j = (alignment[i].size()-1); j >= 0; j--) { alignment[i].pop_back(); }
107 catch(exception& e) {
108 errorOut(e, "Alignment", "~Alignment");
113 /**************************************************************************************************/
115 string Alignment::getSeqAAln(){
116 return seqAaln; // this is called to get the alignment of seqA
119 /**************************************************************************************************/
121 string Alignment::getSeqBAln(){
122 return seqBaln; // this is called to get the alignment of seqB
125 /**************************************************************************************************/
127 int Alignment::getCandidateStartPos(){
128 return seqAstart; // this is called to report the quality of the alignment
131 /**************************************************************************************************/
133 int Alignment::getCandidateEndPos(){
134 return seqAend; // this is called to report the quality of the alignment
137 /**************************************************************************************************/
139 int Alignment::getTemplateStartPos(){
140 return seqBstart; // this is called to report the quality of the alignment
143 /**************************************************************************************************/
145 int Alignment::getTemplateEndPos(){
146 return seqBend; // this is called to report the quality of the alignment
149 /**************************************************************************************************/
151 int Alignment::getPairwiseLength(){
152 return pairwiseLength; // this is the pairwise alignment length
155 /**************************************************************************************************/
157 //int Alignment::getLongestTemplateGap(){
159 // int length = seqBaln.length();
161 // int gapLength = 0;
163 // int start = seqAstart;
164 // if(seqAstart < seqBstart){ start = seqBstart; }
165 // for(int i=seqAstart;i<length;i++){
166 // if(seqBaln[i] == '-'){
170 // if(gapLength > 0){
171 // if(gapLength > longGap){ longGap = gapLength; }
179 /**************************************************************************************************/