forked from mothur/mothur
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathneedlemanoverlap.cpp
executable file
·200 lines (164 loc) · 7.99 KB
/
needlemanoverlap.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
/*
* 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);
}
}
/**************************************************************************************************/
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) + "."); 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(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(); // 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);
}
}
/**************************************************************************************************/