-
Notifications
You must be signed in to change notification settings - Fork 19
/
LargeInt2.hpp
204 lines (168 loc) · 8.87 KB
/
LargeInt2.hpp
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
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
/*****************************************************************************
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 INRIA
* Authors: R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file LargeInt<2>.hpp
* \date 01/03/2013
* \author edrezen
* \brief Integer class relying on native u_int64_t type
*/
/********************************************************************************/
#if INT128_FOUND == 1
/********************************************************************************/
u_int64_t revcomp64 (const u_int64_t& x, size_t sizeKmer)
{
u_int64_t res = x;
unsigned char* kmerrev = (unsigned char *) (&(res));
unsigned char* kmer = (unsigned char *) (&(x));
for (size_t i=0; i<8; ++i) { kmerrev[8-1-i] = revcomp_4NT [kmer[i]]; }
return (res >> (2*( 32 - sizeKmer))) ;
}
template<> class LargeInt<2>
{
public:
/** Constructor.
* \param[in] c : initial value of the large integer. */
LargeInt<2>(const __uint128_t& c=0) noexcept { value[0] = c; }
LargeInt<2>(const std::string& kmer) noexcept : LargeInt<2>(0) {
int sizeKmer = kmer.size();
for (int i = 0; i < sizeKmer; i++) {
operator<<=(2);
value[0] += std::find(bin2NT.begin(), bin2NT.end(), kmer[i]) - bin2NT.begin();
}
}
template <typename T>
LargeInt<2>(const T& a, const T& b) noexcept : LargeInt<2>(0) {
for(T i = a; i < b; ++i) {
operator<<=(2);
value[0] += std::find(bin2NT.begin(), bin2NT.end(), *i) - bin2NT.begin();
}
}
u_int64_t getVal () const { return *value; }
static const char* getName () { return "LargeInt<2>"; }
static const size_t getSize () { return 8*sizeof(__uint128_t); }
LargeInt<2> operator+ (const LargeInt<2>& other) const { return value[0] + other.value[0]; }
LargeInt<2> operator- (const LargeInt<2>& other) const { return value[0] - other.value[0]; }
LargeInt<2> operator| (const LargeInt<2>& other) const { return value[0] | other.value[0]; }
LargeInt<2> operator* (const int& coeff) const { return value[0] * coeff; }
LargeInt<2> operator/ (const u_int32_t& divisor) const { return value[0] / divisor; }
u_int32_t operator% (const u_int32_t& divisor) const { return value[0] % divisor; }
LargeInt<2> operator^ (const LargeInt<2>& other) const { return value[0] ^ other.value[0]; }
LargeInt<2> operator& (const LargeInt<2>& other) const { return value[0] & other.value[0]; }
LargeInt<2> operator& (const char& other) const { return value[0] & other; }
LargeInt<2> operator~ () const { return ~value[0]; }
LargeInt<2> operator<< (const int& coeff) const { return value[0] << coeff; }
LargeInt<2> operator>> (const int& coeff) const { return value[0] >> coeff; }
bool operator!= (const LargeInt<2>& c) const { return value[0] != c.value[0]; }
bool operator== (const LargeInt<2>& c) const { return value[0] == c.value[0]; }
bool operator< (const LargeInt<2>& c) const { return value[0] < c.value[0]; }
bool operator<= (const LargeInt<2>& c) const { return value[0] <= c.value[0]; }
LargeInt<2>& operator+= (const LargeInt<2>& other) { value[0] += other.value[0]; return *this; }
LargeInt<2>& operator^= (const LargeInt<2>& other) { value[0] ^= other.value[0]; return *this; }
LargeInt<2>& operator<<= (const int& coeff) { value[0] <<= coeff; return *this; }
LargeInt<2>& operator>>= (const int& coeff) { value[0] >>= coeff; return *this; }
u_int8_t operator[] (size_t idx) const { return (value[0] >> (2*idx)) & 3; }
uint8_t Codon(size_t idx) const { return (value[0] >> (2*idx)) & 63; }
/** Output stream overload. NOTE: for easier process, dump the value in hexadecimal.
* \param[in] os : the output stream
* \param[in] in : the integer value to be output.
* \return the output stream.
*/
friend std::ostream & operator<<(std::ostream & os, const LargeInt<2> & in)
{
__uint128_t x = in.value[0];
u_int64_t high_nucl = (u_int64_t) (x>>64);
u_int64_t low_nucl = (u_int64_t)(x&((((__uint128_t)1)<<64)-1));
if (high_nucl == 0) { os << std::hex << low_nucl << std::dec; }
else { os << std::hex << high_nucl << "." << low_nucl << std::dec; }
return os;
}
/********************************************************************************/
/** Print corresponding kmer in ASCII
* \param[in] sizeKmer : kmer size (def=32).
*/
std::string toString (size_t sizeKmer) const
{
std::string seq(sizeKmer,'A');
for (size_t i=0; i<sizeKmer; i++) { seq[sizeKmer-i-1] = bin2NT [(*this)[i]]; }
return seq;
}
u_int64_t oahash() const {
return oahash64((u_int64_t)(value[0]>>64)) ^ oahash64 ((u_int64_t)(value[0]&((((__uint128_t)1)<<64)-1)));
}
/********************************************************************************/
template<typename Map>
static LargeInt<2> polynom (const char* data, size_t size, Map fct)
{
LargeInt<2> res (0);
for (size_t i=0; i<size; ++i) { res.value[0] = res.value[0] * 4 + fct(data[i]); }
return res;
}
u_int64_t* getPointer() { return reinterpret_cast<u_int64_t*>(value); }
const u_int64_t* getPointer() const { return reinterpret_cast<const u_int64_t*>(value); }
private:
friend LargeInt<2> revcomp (const LargeInt<2>& i, size_t sizeKmer);
__uint128_t value[1];
};
/********************************************************************************/
inline LargeInt<2> revcomp (const LargeInt<2>& in, size_t sizeKmer)
{
// ---64bits-- ---64bits--
// original kmer: [__high_nucl__|__low_nucl___]
//
// ex: [ AC | .......TG ]
//
//revcomp: [ CA | .......GT ]
// \_low_nucl__/\high_nucl/
const __uint128_t& x = in.value[0];
u_int64_t high_nucl = (u_int64_t)(x>>64);
int nb_high_nucl = sizeKmer>32?sizeKmer - 32:0;
__uint128_t revcomp_high_nucl = revcomp64 (high_nucl, nb_high_nucl);
if (sizeKmer<=32) revcomp_high_nucl = 0; // srsly dunno why this is needed. gcc bug? u_int64_t x ---> (x>>64) != 0
u_int64_t low_nucl = (u_int64_t)(x&((((__uint128_t)1)<<64)-1));
int nb_low_nucl = sizeKmer>32?32:sizeKmer;
__uint128_t revcomp_low_nucl = revcomp64 (low_nucl, nb_low_nucl);
return (revcomp_low_nucl<<(2*nb_high_nucl)) + revcomp_high_nucl;
}
/********************************************************************************/
#endif //INT128_FOUND
/********************************************************************************/