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
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
|
/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2012, 2013 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "KeyEncoder.h"
#include <code/Mock/constants.h>
#include <string.h>
#include <iostream>
using namespace std;
#ifdef CONFIG_ASSERT
#include <assert.h>
#endif
// #define DEBUG_ENCODER
//#define DEBUG_GO_ENCODING
PhysicalKmerColor KeyEncoder::getEncoded_EMBL_CDS(const char*identifier){
populateMap();
PhysicalKmerColor value=encode_EMBL_CDS(identifier);
#ifdef DEBUG_ENCODER
cout<<"[encoder] Input: "<<identifier<<" Output: "<<value<<endl;
#endif
return value;
}
/*
encoding identifiers for EMBL_CDS
an identifier is 3 letters and 5 numbers, such as EMBL_CDS:CAA00003
the color namespace mask is 10000000000000000
therefore, the 5 last number can be stored directly as the 5 last numbers
each of the 3 letter can hold 26 values
so basically, convert the 3-letter code to base 10, multiply it by 100000 and add the 5 last numbers.
for the 3-letter code, each letter is valued from 0 to 25. 26^3 = 17576
namespace multiplier 10000000000000000
3-letter code multiplier 100000
the 3-letter code goes from 0 to 17575 and the 5-digit code goes from 0 to 99999
EMBL-CDS can store at most 1 757 582 424 proteins. (uint32_t)
[edit] encoding identifiers for GO
GO:0000001 to are valued from 0 to 9999999 (use uint32_t)
*/
PhysicalKmerColor KeyEncoder::encode_EMBL_CDS(const char*identifier){
/* >EMBL_CDS:CBW26015 CBW26015.1 */
PhysicalKmerColor returnValue=0;
#ifdef CONFIG_ASSERT
assert(strlen(identifier)==3+5);
#endif
PhysicalKmerColor rightPartValue=0;
for(int exponent=0;exponent<5;exponent++){
char symbol=identifier[7-exponent];
#ifdef CONFIG_ASSERT
assert(m_mapping.count(symbol)>0);
#endif
uint64_t value=m_mapping[symbol];
int loopIterations=exponent;
while(loopIterations--){
value*=10;
}
rightPartValue+=value;
}
returnValue+=rightPartValue;
uint64_t leftPartValue=0;
for(int exponent=0;exponent<3;exponent++){
char symbol=identifier[2-exponent];
#ifdef CONFIG_ASSERT
assert(m_mapping.count(symbol)>0);
#endif
uint64_t value=m_mapping[symbol];
int loopIterations=exponent;
while(loopIterations--){
value*=26;
}
leftPartValue+=value;
}
leftPartValue*=100000;
returnValue+=leftPartValue;
return returnValue;
}
void KeyEncoder::populateMap(){
if(m_mapping.size()>0){ //____----___---___--__----__---___-----_
return;
}
int value=0;
m_mapping['0']=value++;
m_mapping['1']=value++;
m_mapping['2']=value++;
m_mapping['3']=value++;
m_mapping['4']=value++;
m_mapping['5']=value++;
m_mapping['6']=value++;
m_mapping['7']=value++;
m_mapping['8']=value++;
m_mapping['9']=value++;
value=0;
m_mapping['A']=value++;
m_mapping['B']=value++;
m_mapping['C']=value++;
m_mapping['D']=value++;
m_mapping['E']=value++;
m_mapping['F']=value++;
m_mapping['G']=value++;
m_mapping['H']=value++;
m_mapping['I']=value++;
m_mapping['J']=value++;
m_mapping['K']=value++;
m_mapping['L']=value++;
m_mapping['M']=value++;
m_mapping['N']=value++;
m_mapping['O']=value++;
m_mapping['P']=value++;
m_mapping['Q']=value++;
m_mapping['R']=value++;
m_mapping['S']=value++;
m_mapping['T']=value++;
m_mapping['U']=value++;
m_mapping['V']=value++;
m_mapping['W']=value++;
m_mapping['X']=value++;
m_mapping['Y']=value++;
m_mapping['Z']=value++;
}
/* GO:0050662 */
GeneOntologyIdentifier KeyEncoder::encodeGeneOntologyHandle(const char*identifier){
populateMap();
#ifdef CONFIG_ASSERT
assert(m_mapping.size()>0);
#endif
uint32_t value=0;
int start=3;
int length=7;
int base=10;
int total=start+length;
int actualLength=strlen(identifier);
if(actualLength!=total){
cout<<"Error: can not encode GO handle "<<identifier<<endl;
return 0;
}
#ifdef CONFIG_ASSERT
assert((int)strlen(identifier)== (start+length));
#endif
for(int i=0;i<length;i++){
char symbol=identifier[total-1-i];
#ifdef CONFIG_ASSERT
if(m_mapping.count(symbol)==0){
cout<<"Error: <input>"<<identifier<<"</input>"<<" symbol is "<<symbol<<endl;
}
assert(m_mapping.count(symbol)>0);
#endif
uint32_t localValue=m_mapping[symbol];
int iterations=i;
while(iterations--){
localValue*=base;
}
value+=localValue;
}
#ifdef DEBUG_GO_ENCODING
cout<<"[goEncode] input= "<<identifier<<" output= "<<value<<endl;
#endif
return value;
}
|
