File: allocator_chunkpool.h

package info (click to toggle)
seqan2 2.4.0%2Bdfsg-17
  • links: PTS, VCS
  • area: main
  • in suites: sid
  • size: 224,224 kB
  • sloc: cpp: 256,886; ansic: 91,672; python: 8,330; sh: 995; xml: 570; makefile: 255; awk: 51; javascript: 21
file content (245 lines) | stat: -rw-r--r-- 9,587 bytes parent folder | download | duplicates (6)
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
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
// ==========================================================================
// Allocator that pools one or more consecutive memory blocks of a specific
// size.
// ==========================================================================

#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_
#define SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_

#include <seqan/basic/allocator_interface.h>

namespace seqan {

// ============================================================================
// Forwards
// ============================================================================

// ============================================================================
// Tags, Classes, Enums
// ============================================================================

template <
    size_t SIZE,
    size_t MAX_COUNT = 26,
    typename TParentAllocator = Allocator<SimpleAlloc<Default> > >
struct ChunkPool;

template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator>
struct Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >
{
    enum
    {
        STORAGE_SIZE_1 = 0x1000UL,
        STORAGE_SIZE_2 = SIZE * MAX_COUNT * 8,
        STORAGE_SIZE_UPPER = (STORAGE_SIZE_1 > STORAGE_SIZE_2) ? STORAGE_SIZE_1 : STORAGE_SIZE_2,
        ITEMS_PER_STORAGE = STORAGE_SIZE_UPPER / SIZE,
        STORAGE_SIZE = ITEMS_PER_STORAGE * SIZE,

        STORAGE_SIZE_MIN = SIZE * MAX_COUNT //minimal storage size
    };

    char * data_recycled_blocks [MAX_COUNT];
    char * data_current_begin;
    char * data_current_end;
    char * data_current_free;
    Holder<TParentAllocator, Tristate> data_parent_allocator;

    Allocator()
    {
        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
        data_current_end = data_current_free = 0;
        //dont need to initialize data_current_begin
    }

    Allocator(size_t reserve_item_count)
    {
        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));

        size_t storage_size = (reserve_item_count * SIZE > STORAGE_SIZE_MIN) ? reserve_item_count * SIZE : STORAGE_SIZE_MIN;
        allocate( parentAllocator( *this ), data_current_begin, storage_size );
        data_current_end = data_current_begin + storage_size;
        data_current_free = data_current_begin;
    }

    Allocator(TParentAllocator & parent_alloc)
    {
        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
        data_current_end = data_current_free = 0;
        //dont need to initialize data_current_begin

        setValue(data_parent_allocator, parent_alloc);
    }

    Allocator(size_t reserve_item_count, TParentAllocator & parent_alloc)
    {
        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));

        setValue(data_parent_allocator, parent_alloc);

        size_t storage_size = (reserve_item_count * SIZE > STORAGE_SIZE_MIN) ? reserve_item_count * SIZE : STORAGE_SIZE_MIN;
        allocate( parentAllocator( *this ), data_current_begin, storage_size );
        data_current_end = data_current_begin + storage_size;
        data_current_free = data_current_begin;
    }

    //Dummy copy
    Allocator(Allocator const &)
    {
        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
        data_current_end = data_current_free = 0;
        //dont need to initialize data_current_begin
    }
    inline Allocator &
    operator=(Allocator const &)
    {
        clear(*this);
        return *this;
    }

    ~Allocator()
    {
        clear(*this);
    }
};

// ============================================================================
// Metafunctions
// ============================================================================

// ============================================================================
// Functions
// ============================================================================

// ----------------------------------------------------------------------------
// Function parentAllocator()
// ----------------------------------------------------------------------------

template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator>
inline TParentAllocator &
parentAllocator(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me)
{
    return value(me.data_parent_allocator);
}

// ----------------------------------------------------------------------------
// Function clear()
// ----------------------------------------------------------------------------

template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator>
void
clear(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me)
{
    std::memset(me.data_recycled_blocks, 0, sizeof(me.data_recycled_blocks));
    me.data_current_end = me.data_current_free = 0;

    clear(parentAllocator(me));
}

// ----------------------------------------------------------------------------
// Function allocate()
// ----------------------------------------------------------------------------

template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
inline void
allocate(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me,
         TValue * & data,
         TSize count,
         Tag<TUsage> const tag_)
{
    SEQAN_ASSERT_GT(count, static_cast<TSize>(0));

    typedef Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > TAllocator;

    char * ptr;

    if ((sizeof(TValue) != SIZE) || ((size_t) count > MAX_COUNT))
    {//no blocking
        return allocate(parentAllocator(me), data, count, tag_);
    }

    size_t bytes_needed = count * SIZE;
    if (me.data_recycled_blocks[count - 1])
    {//use recycled
        ptr = me.data_recycled_blocks[count - 1];
        me.data_recycled_blocks[count - 1] = * reinterpret_cast<char **>(ptr);
    }
    else
    {//use new
        ptr = me.data_current_free;
        if (ptr + bytes_needed > me.data_current_end)
        {//not enough free space in current storage: allocate new
            size_t rest_block_number = (me.data_current_end - me.data_current_free) / SIZE;
            if (ptr && rest_block_number)
            {//link rest to recycle list
                *reinterpret_cast<char **>(ptr) = me.data_recycled_blocks[rest_block_number - 1];
                me.data_recycled_blocks[rest_block_number - 1] = reinterpret_cast<char *>(ptr);
            }

            allocate(parentAllocator(me), ptr, (size_t) TAllocator::STORAGE_SIZE, tag_);
            me.data_current_begin = ptr;
            me.data_current_end = ptr + TAllocator::STORAGE_SIZE;
        }
        me.data_current_free = ptr + bytes_needed;
    }

    data = reinterpret_cast<TValue *>(ptr);
}

// ----------------------------------------------------------------------------
// Function deallocate()
// ----------------------------------------------------------------------------

template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
inline void
deallocate(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me,
           TValue * data,
           TSize count,
           Tag<TUsage> const tag_)
{
    SEQAN_ASSERT_GT(count, 0);

    if ((sizeof(TValue) != SIZE) || (static_cast<size_t>(count) > MAX_COUNT))
    {//no blocking
        return deallocate(parentAllocator(me), data, count, tag_);
    }

    //link in recycling list
    *reinterpret_cast<char **>(data) = me.data_recycled_blocks[count - 1];
    me.data_recycled_blocks[count - 1] = reinterpret_cast<char *>(data);
}

}  // namespace seqan

#endif  // SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_