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");
34 /**************************************************************************************************/
35 void Alignment::resize(int A) {
40 alignment.resize(nRows);
41 for(int i=0;i<nRows;i++){
42 alignment[i].resize(nCols);
46 errorOut(e, "Alignment", "resize");
50 /**************************************************************************************************/
52 void Alignment::traceBack(){ // This traceback routine is used by the dynamic programming algorithms
54 // to fill the values of seqAaln and seqBaln
62 AlignmentCell currentCell = alignment[row][column]; // Start the traceback from the bottom-right corner of the
65 if(currentCell.prevCell == 'x'){ seqAaln = seqBaln = "NOALIGNMENT"; }//If there's an 'x' in the bottom-
66 else{ // right corner bail out because it means nothing got aligned
67 while(currentCell.prevCell != 'x'){ // while the previous cell isn't an 'x', keep going...
69 if(currentCell.prevCell == 'u'){ // if the pointer to the previous cell is 'u', go up in the
70 seqAaln = '-' + seqAaln; // matrix. this indicates that we need to insert a gap in
71 seqBaln = seqB[row] + seqBaln; // seqA and a base in seqB
72 currentCell = alignment[--row][column];
74 else if(currentCell.prevCell == 'l'){ // if the pointer to the previous cell is 'l', go to the left
75 seqBaln = '-' + seqBaln; // in the matrix. this indicates that we need to insert a gap
76 seqAaln = seqA[column] + seqAaln; // in seqB and a base in seqA
77 currentCell = alignment[row][--column];
80 seqAaln = seqA[column] + seqAaln; // otherwise we need to go diagonally up and to the left,
81 seqBaln = seqB[row] + seqBaln; // here we add a base to both alignments
82 currentCell = alignment[--row][--column];
87 pairwiseLength = seqAaln.length();
88 seqAstart = 1; seqAend = 0;
89 seqBstart = 1; seqBend = 0;
91 for(int i=0;i<seqAaln.length();i++){
92 if(seqAaln[i] != '-' && seqBaln[i] == '-') { seqAstart++; }
93 else if(seqAaln[i] == '-' && seqBaln[i] != '-') { seqBstart++; }
97 pairwiseLength -= (seqAstart + seqBstart - 2);
99 for(int i=seqAaln.length()-1; i>=0;i--){
100 if(seqAaln[i] != '-' && seqBaln[i] == '-') { seqAend++; }
101 else if(seqAaln[i] == '-' && seqBaln[i] != '-') { seqBend++; }
104 pairwiseLength -= (seqAend + seqBend);
106 seqAend = seqA.length() - seqAend - 1;
107 seqBend = seqB.length() - seqBend - 1;
109 catch(exception& e) {
110 errorOut(e, "Alignment", "traceBack");
114 /**************************************************************************************************/
116 Alignment::~Alignment(){
118 for (int i = 0; i < alignment.size(); i++) {
119 for (int j = (alignment[i].size()-1); j >= 0; j--) { alignment[i].pop_back(); }
122 catch(exception& e) {
123 errorOut(e, "Alignment", "~Alignment");
128 /**************************************************************************************************/
130 string Alignment::getSeqAAln(){
131 return seqAaln; // this is called to get the alignment of seqA
134 /**************************************************************************************************/
136 string Alignment::getSeqBAln(){
137 return seqBaln; // this is called to get the alignment of seqB
140 /**************************************************************************************************/
142 int Alignment::getCandidateStartPos(){
143 return seqAstart; // this is called to report the quality of the alignment
146 /**************************************************************************************************/
148 int Alignment::getCandidateEndPos(){
149 return seqAend; // this is called to report the quality of the alignment
152 /**************************************************************************************************/
154 int Alignment::getTemplateStartPos(){
155 return seqBstart; // this is called to report the quality of the alignment
158 /**************************************************************************************************/
160 int Alignment::getTemplateEndPos(){
161 return seqBend; // this is called to report the quality of the alignment
164 /**************************************************************************************************/
166 int Alignment::getPairwiseLength(){
167 return pairwiseLength; // this is the pairwise alignment length
170 /**************************************************************************************************/
172 //int Alignment::getLongestTemplateGap(){
174 // int length = seqBaln.length();
176 // int gapLength = 0;
178 // int start = seqAstart;
179 // if(seqAstart < seqBstart){ start = seqBstart; }
180 // for(int i=seqAstart;i<length;i++){
181 // if(seqBaln[i] == '-'){
185 // if(gapLength > 0){
186 // if(gapLength > longGap){ longGap = gapLength; }
194 /**************************************************************************************************/