Nemo  2.3.56
Simulate forward-in-time genetic evolution in a spatially explicit, individual-based stochastic simulator
BinaryStorageBuffer Class Reference

A class to store any kind of data in a char buffer before unloading it in a binary data file. More...

#include <binarystoragebuffer.h>

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Public Member Functions

 BinaryStorageBuffer ()
 
 ~BinaryStorageBuffer ()
 
char * getBuffer () const
 
off_t getBuffLength () const
 
off_t getTotByteRecorded () const
 
unsigned int getBytesOut () const
 
void clear ()
 
void emptyBuffer ()
 
void store (void *stream, unsigned int nb_bytes)
 
void set_buff (BinaryDataSaver *owner)
 
void set_buff (void *zone, size_t length)
 
void extend_buff ()
 
void read (void *out, unsigned int nb_bytes)
 
void BSBread (void *out, unsigned int nb_bytes)
 

Private Attributes

char * _buff
 
unsigned int _num_buckets
 
off_t _len
 
off_t _bytes_in
 
off_t _bytes_out
 
off_t _tot_bytes_in
 
BinaryDataSaver_myDataSaver
 

Detailed Description

A class to store any kind of data in a char buffer before unloading it in a binary data file.

Constructor & Destructor Documentation

◆ BinaryStorageBuffer()

BinaryStorageBuffer::BinaryStorageBuffer ( )
inline
55 : _buff(NULL),_len(0),_bytes_in(0),_bytes_out(0),
off_t _tot_bytes_in
Definition: binarystoragebuffer.h:49
unsigned int _num_buckets
Definition: binarystoragebuffer.h:48
char * _buff
Definition: binarystoragebuffer.h:47
off_t _len
Definition: binarystoragebuffer.h:49
BinaryDataSaver * _myDataSaver
Definition: binarystoragebuffer.h:51
off_t _bytes_out
Definition: binarystoragebuffer.h:49
off_t _bytes_in
Definition: binarystoragebuffer.h:49

◆ ~BinaryStorageBuffer()

BinaryStorageBuffer::~BinaryStorageBuffer ( )
inline
57{if(_buff != NULL) delete[]_buff;}

References _buff.

Member Function Documentation

◆ BSBread()

void BinaryStorageBuffer::BSBread ( void *  out,
unsigned int  nb_bytes 
)
inline
180 { read(out,nb_bytes); }
void read(void *out, unsigned int nb_bytes)
Definition: binarystoragebuffer.h:162

References read().

Referenced by BinaryDataLoader::extractPop().

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◆ clear()

void BinaryStorageBuffer::clear ( )
inline
64 {
65 if(_buff != NULL) delete [] _buff;
66 _buff = NULL;
69 }

References _buff, _bytes_in, _bytes_out, _len, _num_buckets, and _tot_bytes_in.

Referenced by BinaryDataLoader::clear(), and BinaryDataSaver::printOffsetTable().

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◆ emptyBuffer()

void BinaryStorageBuffer::emptyBuffer ( )
inline
72 {
73 memset(_buff,'\0',_len);
75 }

References _buff, _bytes_in, _bytes_out, and _len.

Referenced by BinaryDataSaver::printData().

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◆ extend_buff()

void BinaryStorageBuffer::extend_buff ( )
inline
134 {
135#ifdef _DEBUG_
136 std::cout<<"BinaryStorageBuffer::extend_buff"<<std::flush;
137#endif
138
139 char *old_buff, *new_buff;
140
141 old_buff = _buff;
142
143 new_buff = new char[_len + MAX_BUFF];
144
145 if(new_buff == NULL) fatal("BinaryStorageBuffer::extend_buff::memory exhausted !!\n");
146
147 memcpy(new_buff,_buff,_len);
148
149 _buff = new_buff;
150
151 _len += MAX_BUFF;
152
153 delete [] old_buff;
154
155#ifdef _DEBUG_
156 std::cout<<"["<<_len<<" B]"<<std::endl;
157#endif
158 }
#define MAX_BUFF
Definition: binarystoragebuffer.h:36
void fatal(const char *str,...)
Definition: output.cc:96

References _buff, _len, fatal(), and MAX_BUFF.

Referenced by store().

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◆ getBuffer()

char * BinaryStorageBuffer::getBuffer ( ) const
inline
59{return _buff;}

References _buff.

Referenced by BinaryDataSaver::printData(), and BinaryDataSaver::printOffsetTable().

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◆ getBuffLength()

off_t BinaryStorageBuffer::getBuffLength ( ) const
inline
60{return _bytes_in;}

References _bytes_in.

Referenced by BinaryDataSaver::FHwrite(), BinaryDataSaver::printData(), BinaryDataSaver::printOffsetTable(), and BinaryDataSaver::storeData().

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◆ getBytesOut()

unsigned int BinaryStorageBuffer::getBytesOut ( ) const
inline
62{return _bytes_out;}

References _bytes_out.

Referenced by Metapop::retrieve_data().

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◆ getTotByteRecorded()

off_t BinaryStorageBuffer::getTotByteRecorded ( ) const
inline
61{return _tot_bytes_in;}

References _tot_bytes_in.

Referenced by Metapop::store_data().

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◆ read()

void BinaryStorageBuffer::read ( void *  out,
unsigned int  nb_bytes 
)
inline
163 {
164
165 if(((_bytes_out + nb_bytes) > _bytes_in) )
166 fatal("BinaryStorageBuffer::read::attempt to read beyond buffer length (asked %i bytes)\n",nb_bytes);
167 else {
168 char *tab = (char*)out;
169 if(nb_bytes == 1) {
170 (*tab) = _buff[_bytes_out];
171 } else {
172 for(unsigned int i = 0; i < nb_bytes; ++i)
173 tab[i] = _buff[_bytes_out + i];
174 }
175 }
176 _bytes_out += nb_bytes;
177 }

References _buff, _bytes_in, _bytes_out, and fatal().

Referenced by BSBread(), Individual::retrieve_data(), Metapop::retrieve_data(), TProtoBDMI::retrieve_data(), TT_BDMI::retrieve_data(), TTDeletMutations_bitstring::retrieve_data(), TProtoDeletMutations_bitstring::retrieve_data(), TTDispersal::retrieve_data(), TProtoDispersal::retrieve_data(), TTNeutralGenes::retrieve_data(), TProtoNeutralGenes::retrieve_data(), TTQuanti::retrieve_data(), TProtoQuanti::retrieve_data(), and TTWolbachia::retrieve_data().

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◆ set_buff() [1/2]

void BinaryStorageBuffer::set_buff ( BinaryDataSaver owner)
inline
84 {
85#ifdef _DEBUG_
86 std::cout<<"BinaryStorageBuffer::set_buff";
87#endif
88
89 _myDataSaver = owner;
90
91 if(_buff != NULL) delete [] _buff;
92
93 _buff = new char[MAX_BUFF];
94
95 if(_buff == NULL) fatal("BinaryStorageBuffer::set_buff::memory exhausted !!\n");
96
97 _len = MAX_BUFF;
98
99 _bytes_in = 0;
100
101 _num_buckets = 0;
102
103 _tot_bytes_in = 0L;
104
105 memset(_buff,'\0',MAX_BUFF);
106
107#ifdef _DEBUG_
108 std::cout<<"[ok]"<<std::endl;
109#endif
110 }

References _buff, _bytes_in, _len, _myDataSaver, _num_buckets, _tot_bytes_in, fatal(), and MAX_BUFF.

Referenced by BinaryDataSaver::execute(), and BinaryDataLoader::extractPop().

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◆ set_buff() [2/2]

void BinaryStorageBuffer::set_buff ( void *  zone,
size_t  length 
)
inline
115 {
116 if(_buff != NULL) delete [] _buff;
117
118 _buff = new char [length];
119
120 memcpy(_buff, zone, length);
121
122 _bytes_in = _len = length ;
123
125
126 _bytes_out = 0;
127
128 _num_buckets = 0;
129 }

References _buff, _bytes_in, _bytes_out, _len, _num_buckets, and _tot_bytes_in.

◆ store()

void BinaryStorageBuffer::store ( void *  stream,
unsigned int  nb_bytes 
)
17{
18
19 while( !((_bytes_in + nb_bytes) < _len) ) extend_buff();
20
21 if(nb_bytes == 1) {
22
23 _buff[_bytes_in] = *(char*)stream;
24
25 } else {
26
27 char *tab = (char*)stream;
28
29 for(unsigned int i = 0; i < nb_bytes; i++)
30 _buff[_bytes_in + i] = tab[i];
31 }
32
33 _bytes_in += nb_bytes;
34
35 _tot_bytes_in += nb_bytes;
36
37 if(_bytes_in > MAX_BUCKET) {
38
39 // cout<<"\n BinaryStorageBuffer::store::bucket "<<_num_buckets<<" is full, emptying\n";
40
41 // tell the binary data saver to empty to bucket to file
43
44 // cout<<"wrote "<<_tot_bytes_in<<"B so far\n";
45
47
48 _bytes_in = 0;
49 }
50}
#define MAX_BUCKET
Definition: binarystoragebuffer.h:38
void printData()
Definition: binarydatasaver.cc:368
void extend_buff()
Definition: binarystoragebuffer.h:133

References _buff, _bytes_in, _len, _myDataSaver, _num_buckets, _tot_bytes_in, extend_buff(), MAX_BUCKET, and BinaryDataSaver::printData().

Referenced by BinaryDataSaver::printOffsetTable(), Individual::store_data(), Metapop::store_data(), TProtoBDMI::store_data(), TT_BDMI::store_data(), TTDeletMutations_bitstring::store_data(), TProtoDeletMutations_bitstring::store_data(), TTDispersal::store_data(), TProtoDispersal::store_data(), TTNeutralGenes::store_data(), TProtoNeutralGenes::store_data(), TTQuanti::store_data(), TProtoQuanti::store_data(), TTWolbachia::store_data(), and BinaryDataSaver::storeData().

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Member Data Documentation

◆ _buff

char* BinaryStorageBuffer::_buff
private

◆ _bytes_in

off_t BinaryStorageBuffer::_bytes_in
private

◆ _bytes_out

off_t BinaryStorageBuffer::_bytes_out
private

◆ _len

off_t BinaryStorageBuffer::_len
private

◆ _myDataSaver

BinaryDataSaver* BinaryStorageBuffer::_myDataSaver
private

Referenced by set_buff(), and store().

◆ _num_buckets

unsigned int BinaryStorageBuffer::_num_buckets
private

Referenced by clear(), set_buff(), and store().

◆ _tot_bytes_in

off_t BinaryStorageBuffer::_tot_bytes_in
private

The documentation for this class was generated from the following files:

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