2368 |
11 Dec 10 |
peter |
// $Id$ |
2368 |
11 Dec 10 |
peter |
2 |
|
2368 |
11 Dec 10 |
peter |
3 |
/* |
4089 |
07 Sep 21 |
peter |
Copyright (C) 2010, 2011, 2012, 2014, 2016, 2021 Peter Johansson |
2368 |
11 Dec 10 |
peter |
5 |
|
2368 |
11 Dec 10 |
peter |
This file is part of the yat library, http://dev.thep.lu.se/yat |
2368 |
11 Dec 10 |
peter |
7 |
|
2368 |
11 Dec 10 |
peter |
The yat library is free software; you can redistribute it and/or |
2368 |
11 Dec 10 |
peter |
modify it under the terms of the GNU General Public License as |
2368 |
11 Dec 10 |
peter |
published by the Free Software Foundation; either version 3 of the |
2368 |
11 Dec 10 |
peter |
License, or (at your option) any later version. |
2368 |
11 Dec 10 |
peter |
12 |
|
2368 |
11 Dec 10 |
peter |
The yat library is distributed in the hope that it will be useful, |
2368 |
11 Dec 10 |
peter |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
2368 |
11 Dec 10 |
peter |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
2368 |
11 Dec 10 |
peter |
General Public License for more details. |
2368 |
11 Dec 10 |
peter |
17 |
|
2368 |
11 Dec 10 |
peter |
You should have received a copy of the GNU General Public License |
2368 |
11 Dec 10 |
peter |
along with yat. If not, see <http://www.gnu.org/licenses/>. |
2368 |
11 Dec 10 |
peter |
20 |
*/ |
2368 |
11 Dec 10 |
peter |
21 |
|
2881 |
18 Nov 12 |
peter |
22 |
#include <config.h> |
2881 |
18 Nov 12 |
peter |
23 |
|
2368 |
11 Dec 10 |
peter |
24 |
#include "Codon.h" |
2368 |
11 Dec 10 |
peter |
25 |
|
2368 |
11 Dec 10 |
peter |
26 |
#include <cassert> |
2369 |
11 Dec 10 |
peter |
27 |
#include <sstream> |
2368 |
11 Dec 10 |
peter |
28 |
#include <stdexcept> |
2368 |
11 Dec 10 |
peter |
29 |
|
2368 |
11 Dec 10 |
peter |
30 |
namespace theplu { |
2368 |
11 Dec 10 |
peter |
31 |
namespace yat { |
2368 |
11 Dec 10 |
peter |
32 |
namespace omic { |
2368 |
11 Dec 10 |
peter |
33 |
|
2368 |
11 Dec 10 |
peter |
34 |
Codon::Map_ Codon::map_; |
2368 |
11 Dec 10 |
peter |
35 |
|
2900 |
13 Dec 12 |
peter |
36 |
Codon::Codon(void) |
2368 |
11 Dec 10 |
peter |
37 |
{ |
2368 |
11 Dec 10 |
peter |
38 |
create_map(); |
2369 |
11 Dec 10 |
peter |
39 |
iter_ = map_.end(); |
2368 |
11 Dec 10 |
peter |
40 |
} |
2368 |
11 Dec 10 |
peter |
41 |
|
2368 |
11 Dec 10 |
peter |
42 |
|
2368 |
11 Dec 10 |
peter |
43 |
Codon::Codon(const std::string& str) |
2368 |
11 Dec 10 |
peter |
44 |
{ |
2368 |
11 Dec 10 |
peter |
45 |
assert(str.size()==3); |
2368 |
11 Dec 10 |
peter |
46 |
std::vector<DNA> vec; |
2368 |
11 Dec 10 |
peter |
47 |
vec.reserve(str.size()); |
2369 |
11 Dec 10 |
peter |
48 |
try { |
2369 |
11 Dec 10 |
peter |
49 |
for (size_t i(0), size(str.size()); i<size; ++i) |
2369 |
11 Dec 10 |
peter |
50 |
vec.push_back(DNA(str[i])); |
2369 |
11 Dec 10 |
peter |
51 |
init(vec); |
2369 |
11 Dec 10 |
peter |
52 |
} |
2369 |
11 Dec 10 |
peter |
53 |
catch (std::invalid_argument& e) { |
2369 |
11 Dec 10 |
peter |
54 |
std::stringstream ss; |
2369 |
11 Dec 10 |
peter |
55 |
ss << e.what() << "\n" |
2369 |
11 Dec 10 |
peter |
56 |
<< "Codon::Codon(1) invalid argument: " << str; |
4060 |
10 May 21 |
peter |
57 |
std::throw_with_nested(std::invalid_argument(ss.str())); |
2369 |
11 Dec 10 |
peter |
58 |
} |
2368 |
11 Dec 10 |
peter |
59 |
} |
2368 |
11 Dec 10 |
peter |
60 |
|
2368 |
11 Dec 10 |
peter |
61 |
|
2368 |
11 Dec 10 |
peter |
62 |
Codon::Codon(const DNA& first, const DNA& second, const DNA& third) |
2368 |
11 Dec 10 |
peter |
63 |
{ |
2368 |
11 Dec 10 |
peter |
64 |
std::vector<DNA> vec; |
2368 |
11 Dec 10 |
peter |
65 |
vec.reserve(3); |
2368 |
11 Dec 10 |
peter |
66 |
vec.push_back(first); |
2368 |
11 Dec 10 |
peter |
67 |
vec.push_back(second); |
2368 |
11 Dec 10 |
peter |
68 |
vec.push_back(third); |
2369 |
11 Dec 10 |
peter |
69 |
try { |
2369 |
11 Dec 10 |
peter |
70 |
init(vec); |
2369 |
11 Dec 10 |
peter |
71 |
} |
2369 |
11 Dec 10 |
peter |
72 |
catch (std::invalid_argument& e) { |
2369 |
11 Dec 10 |
peter |
73 |
std::stringstream ss; |
2369 |
11 Dec 10 |
peter |
74 |
ss << e.what() << "\n" |
2900 |
13 Dec 12 |
peter |
75 |
<< "invalid argument Codon::Codon" |
2369 |
11 Dec 10 |
peter |
76 |
<< "(" << vec[0] << ", " << vec[1] << ", " << vec[2] << ")"; |
2369 |
11 Dec 10 |
peter |
77 |
throw std::invalid_argument(ss.str()); |
2369 |
11 Dec 10 |
peter |
78 |
} |
2368 |
11 Dec 10 |
peter |
79 |
} |
2368 |
11 Dec 10 |
peter |
80 |
|
2368 |
11 Dec 10 |
peter |
81 |
|
3252 |
04 Jun 14 |
peter |
82 |
void Codon::add_to_map(char aa, const std::string& codon) |
2368 |
11 Dec 10 |
peter |
83 |
{ |
3252 |
04 Jun 14 |
peter |
84 |
assert(codon.size()==3); |
3252 |
04 Jun 14 |
peter |
85 |
std::pair<std::vector<DNA>, char> val; |
3252 |
04 Jun 14 |
peter |
86 |
val.second = aa; |
3252 |
04 Jun 14 |
peter |
87 |
val.first.reserve(3); |
3252 |
04 Jun 14 |
peter |
88 |
for (size_t i=0; i<3; ++i) |
3252 |
04 Jun 14 |
peter |
89 |
val.first.push_back(DNA(codon[i])); |
3252 |
04 Jun 14 |
peter |
90 |
map_.insert(map_.end(), val); |
2368 |
11 Dec 10 |
peter |
91 |
} |
2368 |
11 Dec 10 |
peter |
92 |
|
2900 |
13 Dec 12 |
peter |
93 |
|
2369 |
11 Dec 10 |
peter |
94 |
char Codon::amino_acid(void) const |
2369 |
11 Dec 10 |
peter |
95 |
{ |
2369 |
11 Dec 10 |
peter |
96 |
assert(iter_!=map_.end()); |
2369 |
11 Dec 10 |
peter |
97 |
return iter_->second; |
2369 |
11 Dec 10 |
peter |
98 |
} |
2368 |
11 Dec 10 |
peter |
99 |
|
2369 |
11 Dec 10 |
peter |
100 |
|
3487 |
24 Mar 16 |
peter |
101 |
std::string Codon::amino_acid_long(void) const |
3487 |
24 Mar 16 |
peter |
102 |
{ |
3487 |
24 Mar 16 |
peter |
103 |
switch (iter_->second) { |
3487 |
24 Mar 16 |
peter |
104 |
case('A'): return "Ala"; |
3487 |
24 Mar 16 |
peter |
105 |
case('L'): return "Leu"; |
3487 |
24 Mar 16 |
peter |
106 |
case('R'): return "Arg"; |
3487 |
24 Mar 16 |
peter |
107 |
case('K'): return "Lys"; |
3487 |
24 Mar 16 |
peter |
108 |
case('N'): return "Asn"; |
3487 |
24 Mar 16 |
peter |
109 |
case('M'): return "Met"; |
3516 |
26 Jul 16 |
peter |
110 |
case('D'): return "Asp"; |
3487 |
24 Mar 16 |
peter |
111 |
case('F'): return "Phe"; |
3487 |
24 Mar 16 |
peter |
112 |
case('C'): return "Cys"; |
3487 |
24 Mar 16 |
peter |
113 |
case('P'): return "Pro"; |
3487 |
24 Mar 16 |
peter |
114 |
case('Q'): return "Gln"; |
3487 |
24 Mar 16 |
peter |
115 |
case('S'): return "Ser"; |
3487 |
24 Mar 16 |
peter |
116 |
case('E'): return "Glu"; |
3487 |
24 Mar 16 |
peter |
117 |
case('T'): return "Thr"; |
3487 |
24 Mar 16 |
peter |
118 |
case('G'): return "Gly"; |
3487 |
24 Mar 16 |
peter |
119 |
case('W'): return "Trp"; |
3487 |
24 Mar 16 |
peter |
120 |
case('H'): return "His"; |
3487 |
24 Mar 16 |
peter |
121 |
case('Y'): return "Tyr"; |
3487 |
24 Mar 16 |
peter |
122 |
case('I'): return "Ile"; |
3487 |
24 Mar 16 |
peter |
123 |
case('V'): return "Val"; |
3487 |
24 Mar 16 |
peter |
124 |
case('*'): return "Ter"; |
3487 |
24 Mar 16 |
peter |
125 |
default: |
3487 |
24 Mar 16 |
peter |
126 |
assert(0); |
3487 |
24 Mar 16 |
peter |
127 |
} |
3487 |
24 Mar 16 |
peter |
128 |
return ""; |
3487 |
24 Mar 16 |
peter |
129 |
} |
3487 |
24 Mar 16 |
peter |
130 |
|
3487 |
24 Mar 16 |
peter |
131 |
|
2368 |
11 Dec 10 |
peter |
132 |
void Codon::init(const std::vector<DNA>& vec) |
2368 |
11 Dec 10 |
peter |
133 |
{ |
2369 |
11 Dec 10 |
peter |
134 |
assert(vec.size()==3); |
2368 |
11 Dec 10 |
peter |
135 |
create_map(); |
2369 |
11 Dec 10 |
peter |
136 |
iter_ = map_.find(vec); |
2368 |
11 Dec 10 |
peter |
137 |
if (iter_==map_.end()) |
2369 |
11 Dec 10 |
peter |
138 |
throw std::invalid_argument("Codon: invalid codon:"); |
2368 |
11 Dec 10 |
peter |
139 |
} |
2368 |
11 Dec 10 |
peter |
140 |
|
2368 |
11 Dec 10 |
peter |
141 |
|
2368 |
11 Dec 10 |
peter |
142 |
void Codon::create_map(void) |
2368 |
11 Dec 10 |
peter |
143 |
{ |
2368 |
11 Dec 10 |
peter |
144 |
if (!map_.empty()) |
2368 |
11 Dec 10 |
peter |
145 |
return; |
3252 |
04 Jun 14 |
peter |
146 |
add_to_map('K', "AAA"); |
3252 |
04 Jun 14 |
peter |
147 |
add_to_map('N', "AAC"); |
3252 |
04 Jun 14 |
peter |
148 |
add_to_map('K', "AAG"); |
3252 |
04 Jun 14 |
peter |
149 |
add_to_map('N', "AAT"); |
3252 |
04 Jun 14 |
peter |
150 |
add_to_map('T', "ACA"); |
3252 |
04 Jun 14 |
peter |
151 |
add_to_map('T', "ACC"); |
3252 |
04 Jun 14 |
peter |
152 |
add_to_map('T', "ACG"); |
3252 |
04 Jun 14 |
peter |
153 |
add_to_map('T', "ACT"); |
3252 |
04 Jun 14 |
peter |
154 |
add_to_map('R', "AGA"); |
3252 |
04 Jun 14 |
peter |
155 |
add_to_map('S', "AGC"); |
3252 |
04 Jun 14 |
peter |
156 |
add_to_map('R', "AGG"); |
3252 |
04 Jun 14 |
peter |
157 |
add_to_map('S', "AGT"); |
3252 |
04 Jun 14 |
peter |
158 |
add_to_map('I', "ATA"); |
3252 |
04 Jun 14 |
peter |
159 |
add_to_map('I', "ATC"); |
3252 |
04 Jun 14 |
peter |
160 |
add_to_map('M', "ATG"); |
3252 |
04 Jun 14 |
peter |
161 |
add_to_map('I', "ATT"); |
3252 |
04 Jun 14 |
peter |
162 |
add_to_map('Q', "CAA"); |
3252 |
04 Jun 14 |
peter |
163 |
add_to_map('H', "CAC"); |
3252 |
04 Jun 14 |
peter |
164 |
add_to_map('Q', "CAG"); |
3252 |
04 Jun 14 |
peter |
165 |
add_to_map('H', "CAT"); |
3252 |
04 Jun 14 |
peter |
166 |
add_to_map('P', "CCA"); |
3252 |
04 Jun 14 |
peter |
167 |
add_to_map('P', "CCC"); |
3252 |
04 Jun 14 |
peter |
168 |
add_to_map('P', "CCG"); |
3252 |
04 Jun 14 |
peter |
169 |
add_to_map('P', "CCT"); |
3252 |
04 Jun 14 |
peter |
170 |
add_to_map('R', "CGA"); |
3252 |
04 Jun 14 |
peter |
171 |
add_to_map('R', "CGC"); |
3252 |
04 Jun 14 |
peter |
172 |
add_to_map('R', "CGG"); |
3252 |
04 Jun 14 |
peter |
173 |
add_to_map('R', "CGT"); |
3252 |
04 Jun 14 |
peter |
174 |
add_to_map('L', "CTA"); |
3252 |
04 Jun 14 |
peter |
175 |
add_to_map('L', "CTC"); |
3252 |
04 Jun 14 |
peter |
176 |
add_to_map('L', "CTG"); |
3252 |
04 Jun 14 |
peter |
177 |
add_to_map('L', "CTT"); |
3252 |
04 Jun 14 |
peter |
178 |
add_to_map('E', "GAA"); |
3252 |
04 Jun 14 |
peter |
179 |
add_to_map('D', "GAC"); |
3252 |
04 Jun 14 |
peter |
180 |
add_to_map('E', "GAG"); |
3252 |
04 Jun 14 |
peter |
181 |
add_to_map('D', "GAT"); |
3252 |
04 Jun 14 |
peter |
182 |
add_to_map('A', "GCA"); |
3252 |
04 Jun 14 |
peter |
183 |
add_to_map('A', "GCC"); |
3252 |
04 Jun 14 |
peter |
184 |
add_to_map('A', "GCG"); |
3252 |
04 Jun 14 |
peter |
185 |
add_to_map('A', "GCT"); |
3252 |
04 Jun 14 |
peter |
186 |
add_to_map('G', "GGA"); |
3252 |
04 Jun 14 |
peter |
187 |
add_to_map('G', "GGC"); |
3252 |
04 Jun 14 |
peter |
188 |
add_to_map('G', "GGG"); |
3252 |
04 Jun 14 |
peter |
189 |
add_to_map('G', "GGT"); |
3252 |
04 Jun 14 |
peter |
190 |
add_to_map('V', "GTA"); |
3252 |
04 Jun 14 |
peter |
191 |
add_to_map('V', "GTC"); |
3252 |
04 Jun 14 |
peter |
192 |
add_to_map('V', "GTG"); |
3252 |
04 Jun 14 |
peter |
193 |
add_to_map('V', "GTT"); |
3252 |
04 Jun 14 |
peter |
194 |
add_to_map('*', "TAA"); |
3252 |
04 Jun 14 |
peter |
195 |
add_to_map('Y', "TAC"); |
3252 |
04 Jun 14 |
peter |
196 |
add_to_map('*', "TAG"); |
3252 |
04 Jun 14 |
peter |
197 |
add_to_map('Y', "TAT"); |
3252 |
04 Jun 14 |
peter |
198 |
add_to_map('S', "TCA"); |
3252 |
04 Jun 14 |
peter |
199 |
add_to_map('S', "TCC"); |
3252 |
04 Jun 14 |
peter |
200 |
add_to_map('S', "TCG"); |
3252 |
04 Jun 14 |
peter |
201 |
add_to_map('S', "TCT"); |
3252 |
04 Jun 14 |
peter |
202 |
add_to_map('*', "TGA"); |
3252 |
04 Jun 14 |
peter |
203 |
add_to_map('C', "TGC"); |
3252 |
04 Jun 14 |
peter |
204 |
add_to_map('W', "TGG"); |
3252 |
04 Jun 14 |
peter |
205 |
add_to_map('C', "TGT"); |
3252 |
04 Jun 14 |
peter |
206 |
add_to_map('L', "TTA"); |
3252 |
04 Jun 14 |
peter |
207 |
add_to_map('F', "TTC"); |
3252 |
04 Jun 14 |
peter |
208 |
add_to_map('L', "TTG"); |
3252 |
04 Jun 14 |
peter |
209 |
add_to_map('F', "TTT"); |
3252 |
04 Jun 14 |
peter |
210 |
assert(map_.size()==64); |
2368 |
11 Dec 10 |
peter |
211 |
} |
2368 |
11 Dec 10 |
peter |
212 |
|
2368 |
11 Dec 10 |
peter |
213 |
|
2368 |
11 Dec 10 |
peter |
214 |
bool Codon::start(void) const |
2368 |
11 Dec 10 |
peter |
215 |
{ |
2470 |
12 Apr 11 |
peter |
216 |
return iter_->second=='M'; |
2368 |
11 Dec 10 |
peter |
217 |
} |
2368 |
11 Dec 10 |
peter |
218 |
|
2368 |
11 Dec 10 |
peter |
219 |
|
2368 |
11 Dec 10 |
peter |
220 |
bool Codon::stop(void) const |
2368 |
11 Dec 10 |
peter |
221 |
{ |
2368 |
11 Dec 10 |
peter |
222 |
return iter_->second=='*'; |
2368 |
11 Dec 10 |
peter |
223 |
} |
2368 |
11 Dec 10 |
peter |
224 |
|
2368 |
11 Dec 10 |
peter |
225 |
|
2369 |
11 Dec 10 |
peter |
226 |
const DNA& Codon::operator()(size_t i) const |
2369 |
11 Dec 10 |
peter |
227 |
{ |
2369 |
11 Dec 10 |
peter |
228 |
assert(i < iter_->first.size()); |
2369 |
11 Dec 10 |
peter |
229 |
return iter_->first[i]; |
2369 |
11 Dec 10 |
peter |
230 |
} |
2369 |
11 Dec 10 |
peter |
231 |
|
3252 |
04 Jun 14 |
peter |
232 |
|
2900 |
13 Dec 12 |
peter |
233 |
bool Codon::Compare_::operator()(const std::vector<DNA>& lhs, |
2368 |
11 Dec 10 |
peter |
234 |
const std::vector<DNA>& rhs) const |
2368 |
11 Dec 10 |
peter |
235 |
{ |
2368 |
11 Dec 10 |
peter |
236 |
assert(lhs.size()==3); |
2368 |
11 Dec 10 |
peter |
237 |
assert(rhs.size()==3); |
2368 |
11 Dec 10 |
peter |
238 |
for (size_t i=0; i<3; ++i) |
2368 |
11 Dec 10 |
peter |
239 |
if (lhs[i].get()!=rhs[i].get()) |
2368 |
11 Dec 10 |
peter |
240 |
return lhs[i].get() < rhs[i].get(); |
2368 |
11 Dec 10 |
peter |
241 |
return false; |
2368 |
11 Dec 10 |
peter |
242 |
} |
2368 |
11 Dec 10 |
peter |
243 |
|
2368 |
11 Dec 10 |
peter |
244 |
}}} |