Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
b9081de
commit 70c021d
Showing
32 changed files
with
2,800 additions
and
1,027 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| // | ||
| // TREES - | ||
| // A TRait-based Eco-Evolutionary Simulation tool | ||
| // Copyright (C) 2017 Jörgen Ripa | ||
| // | ||
| // 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, 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 General Public License for more details. | ||
| // | ||
| // You should have received a copy of the GNU General Public License | ||
| // along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| // | ||
| // Contact: jorgen.ripa@biol.lu.se | ||
| // | ||
|
|
||
| #include <cassert> | ||
|
|
||
| #include "bit_vector.h" | ||
|
|
||
| bit_vector::bit_vector() { // default constructor | ||
| current_int = 0; | ||
| next_position = 0; | ||
| } | ||
|
|
||
| void bit_vector::reserve(size_type bit_count) { | ||
| size_type int_count = bit_count/(sizeof(store_type)*8) + 1; | ||
| std::vector<store_type>:: reserve(int_count); | ||
| } | ||
|
|
||
| void bit_vector::push_back(bool bit) { | ||
| if (bit) { | ||
| store_type mask = store_type(1)<<next_position; | ||
| current_int |= mask; | ||
| } | ||
| next_position++; | ||
| if (next_position==sizeof(store_type)*8) { | ||
| std::vector<store_type>::push_back(current_int); // store in base class | ||
| current_int = 0; | ||
| next_position = 0; | ||
| } | ||
| } | ||
|
|
||
| bit_vector::size_type bit_vector::get_total_bit_count() { | ||
| return size()*sizeof(store_type)*8 + next_position; | ||
| } | ||
|
|
||
| bit_vector::size_type bit_vector::get_total_byte_count() { | ||
| return size()*sizeof(store_type); | ||
| } | ||
|
|
||
| void bit_vector::write_to_file(oSimfile& osf) { | ||
| // Write size of bitstream, followed by the bits themselves | ||
| osf.write<uint32_t>((uint32_t)get_total_bit_count()); | ||
| osf.write<uint32_t>((uint32_t)sizeof(store_type)); | ||
| if(size()>0) { | ||
| osf.writeArray<store_type>(&at(0), (int)size()); | ||
| } | ||
| if (next_position>0) { | ||
| osf.write<store_type>(current_int); | ||
| } | ||
| } | ||
|
|
||
| void bit_vector::read_from_file(iSimfile &isf) { | ||
| clear(); | ||
| uint32_t total_bits = isf.read<uint32_t>(); | ||
| uint32_t chunk_size = isf.read<uint32_t>(); // size of sore_type (in bytes) | ||
| assert(chunk_size==sizeof(store_type)); | ||
| uint32_t total_bytes = total_bits / (sizeof(store_type)*8); | ||
| next_position = total_bits % (sizeof(store_type)*8); // rest bits | ||
| if(total_bytes>0) { | ||
| isf.readArray<store_type>(*this, total_bytes); | ||
| } | ||
| if (next_position>0) { | ||
| current_int = isf.read<store_type>(); | ||
| } else { | ||
| current_int = 0; | ||
| } | ||
| } | ||
|
|
||
| bool bit_vector::get_bit(size_type bit_pos) { | ||
| size_type int_pos = bit_pos/(sizeof(store_type)*8); | ||
| store_type the_int; | ||
| if (int_pos<size()) { | ||
| the_int = at(int_pos); | ||
| } else { | ||
| the_int = current_int; | ||
| } | ||
| int bit = bit_pos % (sizeof(store_type)*8); | ||
| return (the_int & store_type(1)<<bit)>0; | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| // | ||
| // TREES - | ||
| // A TRait-based Eco-Evolutionary Simulation tool | ||
| // Copyright (C) 2017 Jörgen Ripa | ||
| // | ||
| // 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, 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 General Public License for more details. | ||
| // | ||
| // You should have received a copy of the GNU General Public License | ||
| // along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| // | ||
| // Contact: jorgen.ripa@biol.lu.se | ||
| // | ||
|
|
||
| #ifndef bit_vector_hpp | ||
| #define bit_vector_hpp | ||
|
|
||
| #include <stdio.h> | ||
| #include <vector> | ||
| #include <cstdint> | ||
| #include "simfile.h" | ||
|
|
||
| typedef uint64_t store_type; | ||
|
|
||
| class bit_vector : protected std::vector<store_type> { | ||
| protected: | ||
| store_type current_int; | ||
| int next_position; | ||
|
|
||
| public: | ||
| bit_vector(); // default constructor | ||
| void reserve(size_type bit_count); | ||
| void push_back(bool bit); | ||
| size_type get_total_bit_count(); | ||
| size_type get_total_byte_count(); | ||
| void write_to_file(oSimfile& osf); | ||
| void read_from_file(iSimfile& isf); | ||
| bool get_bit(size_type i); | ||
| }; | ||
| #endif /* bit_vector_hpp */ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.