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
|
/*===========================================================================
*
* 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<1>.hpp
* \date 01/03/2013
* \author edrezen
* \brief Integer class relying on native u_int64_t type
*/
template<> class LargeInt<1>
{
public:
/** Constructor.
* \param[in] c : initial value of the large integer. */
LargeInt<1>(const u_int64_t& c=0) noexcept { value[0] = c; }
LargeInt<1>(const std::string& kmer) noexcept : LargeInt<1>(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<1>(const T& a, const T& b) noexcept : LargeInt<1>(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<1>"; }
static const size_t getSize () { return 8*sizeof(u_int64_t); }
LargeInt<1> operator+ (const LargeInt<1>& other) const { return value[0] + other.value[0]; }
LargeInt<1> operator- (const LargeInt<1>& other) const { return value[0] - other.value[0]; }
LargeInt<1> operator| (const LargeInt<1>& other) const { return value[0] | other.value[0]; }
LargeInt<1> operator* (const int& coeff) const { return value[0] * coeff; }
LargeInt<1> 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<1> operator^ (const LargeInt<1>& other) const { return value[0] ^ other.value[0]; }
LargeInt<1> operator& (const LargeInt<1>& other) const { return value[0] & other.value[0]; }
LargeInt<1> operator& (const char& other) const { return value[0] & other; }
LargeInt<1> operator~ () const { return ~value[0]; }
LargeInt<1> operator<< (const int& coeff) const { return value[0] << coeff; }
LargeInt<1> operator>> (const int& coeff) const { return value[0] >> coeff; }
bool operator!= (const LargeInt<1>& c) const { return value[0] != c.value[0]; }
bool operator== (const LargeInt<1>& c) const { return value[0] == c.value[0]; }
bool operator< (const LargeInt<1>& c) const { return value[0] < c.value[0]; }
bool operator<= (const LargeInt<1>& c) const { return value[0] <= c.value[0]; }
LargeInt<1>& operator+= (const LargeInt<1>& other) { value[0] += other.value[0]; return *this; }
LargeInt<1>& operator^= (const LargeInt<1>& other) { value[0] ^= other.value[0]; return *this; }
LargeInt<1>& operator<<= (const int& coeff) { value[0] <<= coeff; return *this; }
LargeInt<1>& operator>>= (const int& coeff) { value[0] >>= coeff; return *this; }
u_int8_t operator[] (size_t idx) const { return (value[0] >> (2*idx)) & 3; }
/********************************************************************************/
friend std::ostream & operator<<(std::ostream & s, const LargeInt<1> & l)
{
s << std::hex << l.value[0] << std::dec; return s;
}
/********************************************************************************/
/** Print corresponding kmer in ASCII
* \param[in] sizeKmer : kmer size (def=32).
*/
std::string toString (size_t sizeKmer) const
{
int i;
u_int64_t temp = value[0];
std::string seq(sizeKmer,'A');
for (i=sizeKmer-1; i>=0; i--)
{
seq[i] = bin2NT[ temp&3 ];
temp = temp>>2;
}
return seq;
}
u_int64_t oahash() const {
return oahash64(value[0]);
}
/********************************************************************************/
inline static u_int64_t revcomp64 (const u_int64_t& x, size_t sizeKmer)
{
u_int64_t res = x;
// OLD VERSION (with lookup table)
// 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]]; }
res = ((res>> 2 & 0x3333333333333333) | (res & 0x3333333333333333) << 2);
res = ((res>> 4 & 0x0F0F0F0F0F0F0F0F) | (res & 0x0F0F0F0F0F0F0F0F) << 4);
res = ((res>> 8 & 0x00FF00FF00FF00FF) | (res & 0x00FF00FF00FF00FF) << 8);
res = ((res>>16 & 0x0000FFFF0000FFFF) | (res & 0x0000FFFF0000FFFF) << 16);
res = ((res>>32 & 0x00000000FFFFFFFF) | (res & 0x00000000FFFFFFFF) << 32);
res = res ^ 0xAAAAAAAAAAAAAAAA;
return (res >> (2*(32-sizeKmer))) ;
}
/********************************************************************************/
template<typename Map>
static LargeInt<1> polynom (const char* data, size_t size, Map fct)
{
LargeInt<1> res (0);
for (size_t i=0; i<size; ++i) { res.value[0] = 4 * res.value[0] + fct(data[i]); }
return res;
}
u_int64_t* getPointer() { return value; }
const u_int64_t* getPointer() const { return value; }
private:
friend LargeInt<1> revcomp (const LargeInt<1>& i, size_t sizeKmer);
u_int64_t value[1];
};
/********************************************************************************/
inline LargeInt<1> revcomp (const LargeInt<1>& x, size_t sizeKmer)
{
return LargeInt<1>::revcomp64 (x.value[0], sizeKmer);
}
|
