/usr/include/jellyfish/mer_heap.hpp is in libjellyfish-2.0-dev 2.1.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | /* This file is part of Jellyfish.
Jellyfish 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, either version 3 of the License, or
(at your option) any later version.
Jellyfish 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 should have received a copy of the GNU General Public License
along with Jellyfish. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __JELLYFISH_HEAP_HPP__
#define __JELLYFISH_HEAP_HPP__
#include <stdint.h>
#include <algorithm>
namespace jellyfish { namespace mer_heap {
template<typename Key, typename Iterator>
struct heap_item {
Key key_;
uint64_t val_;
uint64_t pos_;
Iterator* it_;
heap_item() : it_(0) { }
heap_item(Iterator& iter) : key_(iter.key()), val_(iter.val()), pos_(iter.pos()), it_(&iter) { }
bool operator>(const heap_item& other) const {
if(pos_ == other.pos_)
return key_ > other.key_;
return pos_ > other.pos_;
}
};
// STL make_heap creates a max heap. We want a min heap, so
// we use the > operator
template<typename Key, typename Iterator>
struct heap_item_comp {
bool operator()(const heap_item<Key, Iterator>* i1, const heap_item<Key, Iterator>* i2) {
return *i1 > *i2;
}
};
template<typename Key, typename Iterator>
class heap {
heap_item<Key, Iterator>* storage_; // Storage of the elements
heap_item<Key, Iterator>** elts_; // Pointers to storage. Create a heap of pointers
size_t capacity_; // Actual capacity
size_t h_; // Head pointer
heap_item_comp<Key, Iterator> comp_;
public:
typedef const heap_item<Key, Iterator> *const_item_t;
heap() : storage_(0), elts_(0), capacity_(0), h_(0) { }
explicit heap(size_t capacity) { initialize(capacity); }
~heap() {
delete[] storage_;
delete[] elts_;
}
void initialize(size_t capacity) {
capacity_ = capacity;
h_ = 0;
storage_ = new heap_item<Key, Iterator>[capacity_];
elts_ = new heap_item<Key, Iterator>*[capacity_];
for(size_t h1 = 0; h1 < capacity_; ++h1)
elts_[h1] = &storage_[h1];
}
void fill(Iterator &it) {
for(h_ = 0; h_ < capacity_; ++h_) {
if(!it.next())
break;
storage_[h_] = it;
elts_[h_] = &storage_[h_];
}
std::make_heap(elts_, elts_ + h_, comp_);
}
// template<typename ForwardIterator>
// void fill(ForwardIterator first, ForwardIterator last) {
// h_ = 0;
// while(h_ < capacity_ && first != last) {
// if(!first->next())
// break;
// storage_[h_].initialize(*first++);
// elts_[h_] = &storage_[h_];
// h_++;
// }
// std::make_heap(elts_, elts_ + h_, compare);
// }
bool is_empty() const { return h_ == 0; }
bool is_not_empty() const { return h_ > 0; }
size_t size() const { return h_; }
size_t capacity() const { return capacity_; }
// The following 3 should only be used after fill has been called
const_item_t head() const { return elts_[0]; }
void pop() { std::pop_heap(elts_, elts_ + h_--, comp_); }
void push(Iterator &item) {
*elts_[h_] = item;
std::push_heap(elts_, elts_ + ++h_, comp_);
}
};
} } // namespace jellyfish { namespace mer_heap {
#endif // __HEAP_HPP__
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