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
31 /**************************************************************************************************/
33 void Alignment::traceBack(){ // This traceback routine is used by the dynamic programming algorithms
34 // to fill the values of seqAaln and seqBaln
42 AlignmentCell currentCell = alignment[row][column]; // Start the traceback from the bottom-right corner of the
45 if(currentCell.prevCell == 'x'){ seqAaln = seqBaln = "NOALIGNMENT"; }//If there's an 'x' in the bottom-
46 else{ // right corner bail out because it means nothing got aligned
47 while(currentCell.prevCell != 'x'){ // while the previous cell isn't an 'x', keep going...
49 if(currentCell.prevCell == 'u'){ // if the pointer to the previous cell is 'u', go up in the
50 seqAaln = '-' + seqAaln; // matrix. this indicates that we need to insert a gap in
51 seqBaln = seqB[row] + seqBaln; // seqA and a base in seqB
52 currentCell = alignment[--row][column];
54 else if(currentCell.prevCell == 'l'){ // if the pointer to the previous cell is 'l', go to the left
55 seqBaln = '-' + seqBaln; // in the matrix. this indicates that we need to insert a gap
56 seqAaln = seqA[column] + seqAaln; // in seqB and a base in seqA
57 currentCell = alignment[row][--column];
60 seqAaln = seqA[column] + seqAaln; // otherwise we need to go diagonally up and to the left,
61 seqBaln = seqB[row] + seqBaln; // here we add a base to both alignments
62 currentCell = alignment[--row][--column];
67 pairwiseLength = seqAaln.length();
68 seqAstart = 1; seqAend = 0;
69 seqBstart = 1; seqBend = 0;
71 for(int i=0;i<seqAaln.length();i++){
72 if(seqAaln[i] != '-' && seqBaln[i] == '-') { seqAstart++; }
73 else if(seqAaln[i] == '-' && seqBaln[i] != '-') { seqBstart++; }
77 pairwiseLength -= (seqAstart + seqBstart - 2);
79 for(int i=seqAaln.length()-1; i>=0;i--){
80 if(seqAaln[i] != '-' && seqBaln[i] == '-') { seqAend++; }
81 else if(seqAaln[i] == '-' && seqBaln[i] != '-') { seqBend++; }
84 pairwiseLength -= (seqAend + seqBend);
86 seqAend = seqA.length() - seqAend - 1;
87 seqBend = seqB.length() - seqBend - 1;
91 /**************************************************************************************************/
93 string Alignment::getSeqAAln(){
94 return seqAaln; // this is called to get the alignment of seqA
97 /**************************************************************************************************/
99 string Alignment::getSeqBAln(){
100 return seqBaln; // this is called to get the alignment of seqB
103 /**************************************************************************************************/
105 int Alignment::getCandidateStartPos(){
106 return seqAstart; // this is called to report the quality of the alignment
109 /**************************************************************************************************/
111 int Alignment::getCandidateEndPos(){
112 return seqAend; // this is called to report the quality of the alignment
115 /**************************************************************************************************/
117 int Alignment::getTemplateStartPos(){
118 return seqBstart; // this is called to report the quality of the alignment
121 /**************************************************************************************************/
123 int Alignment::getTemplateEndPos(){
124 return seqBend; // this is called to report the quality of the alignment
127 /**************************************************************************************************/
129 int Alignment::getPairwiseLength(){
130 return pairwiseLength; // this is the pairwise alignment length
133 /**************************************************************************************************/
135 //int Alignment::getLongestTemplateGap(){
137 // int length = seqBaln.length();
139 // int gapLength = 0;
141 // int start = seqAstart;
142 // if(seqAstart < seqBstart){ start = seqBstart; }
143 // for(int i=seqAstart;i<length;i++){
144 // if(seqBaln[i] == '-'){
148 // if(gapLength > 0){
149 // if(gapLength > longGap){ longGap = gapLength; }
157 /**************************************************************************************************/