106 lines
2.8 KiB
C++
106 lines
2.8 KiB
C++
/*
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* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
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*
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* This file is part of HISAT 2.
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*
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* HISAT 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* HISAT 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#ifndef __HISAT2_BIT_PACKED_ARRAY_H
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#define __HISAT2_BIT_PACKED_ARRAY_H
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#include <iostream>
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#include <fstream>
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#include <limits>
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#include <map>
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#include "assert_helpers.h"
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#include "word_io.h"
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#include "mem_ids.h"
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#include "ds.h"
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using namespace std;
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class BitPackedArray {
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public:
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BitPackedArray () {}
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~BitPackedArray();
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/**
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* Return true iff there are no items
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* @return
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*/
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inline bool empty() const { return cur_ == 0; }
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inline size_t size() const { return cur_; }
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TIndexOffU get(size_t idx) const;
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inline TIndexOffU operator[](size_t i) const { return get(i); }
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void pushBack(TIndexOffU val);
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void init(size_t max_value);
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void reset();
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void writeFile(const char *filename);
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void writeFile(const string& filename);
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void writeFile(ofstream &fp);
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void readFile(const char *filename);
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void readFile(const string& filename);
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void readFile(ifstream &fp);
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void dump() const;
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size_t getMemUsage() const;
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private:
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void init_by_log2(size_t ceil_log2);
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void put(size_t index, TIndexOffU val);
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inline uint64_t bitToMask(size_t bit) const
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{
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return (uint64_t) ((1ULL << bit) - 1);
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}
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TIndexOffU getItem(uint64_t *block, size_t idx, size_t offset) const;
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void setItem(uint64_t *block, size_t idx, size_t offset, TIndexOffU val);
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pair<size_t, size_t> indexToAddress(size_t index) const;
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pair<size_t, size_t> columnToPosition(size_t col) const;
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void expand(size_t count = 1);
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void allocSize(size_t sz);
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void allocItems(size_t count);
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private:
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size_t item_bit_size_; // item bit size(e.g. 33bit)
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size_t elm_bit_size_; // 64bit
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size_t items_per_block_bit_;
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size_t items_per_block_bit_mask_;
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size_t items_per_block_; // number of items in block
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size_t cur_; // current item count
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size_t sz_; // maximum item count
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size_t block_size_; // block size in byte
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// List of packed array
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EList<uint64_t *> blocks_;
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};
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#endif //__HISAT2_BIT_PACKED_ARRAY_H
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