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>

Collaboration diagram for BinaryStorageBuffer:

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	set_buff (size_t length)
off_t	set_buff_from_file (int FD, 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

                        : _buff(NULL),_len(0),_bytes_in(0),_bytes_out(0),
                          _num_buckets(0), _tot_bytes_in(0L), _myDataSaver(0) {}

~BinaryStorageBuffer()

BinaryStorageBuffer::~BinaryStorageBuffer ( )

inline

{if(_buff != NULL) delete[]_buff;}

References _buff.

Member Function Documentation

BSBread()

void BinaryStorageBuffer::BSBread ( void *  out, unsigned int  nb_bytes  )

inline

  { read(out,nb_bytes); }

References read().

Referenced by BinaryDataLoader::extractPop().

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clear()

void BinaryStorageBuffer::clear ( )

inline

  {
    if(_buff != NULL) delete [] _buff;
    _buff = NULL;
    _len = _bytes_in = _bytes_out = 0;
    _num_buckets = 0; _tot_bytes_in = 0L;
  }

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

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

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emptyBuffer()

void BinaryStorageBuffer::emptyBuffer ( )

inline

  {
    memset(_buff,'\0',_len);
    _bytes_in = _bytes_out = 0;
  }

References _buff, _bytes_in, _bytes_out, and _len.

Referenced by BinaryDataSaver::printData().

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extend_buff()

void BinaryStorageBuffer::extend_buff ( )

inline

  {
#ifdef _DEBUG_
        std::cout<<"BinaryStorageBuffer::extend_buff"<<std::flush;
#endif
        
        char *old_buff, *new_buff;
        
        old_buff = _buff;
        
        new_buff = new char[_len + MAX_BUFF];
        
        if(new_buff == NULL) fatal("BinaryStorageBuffer::extend_buff::memory exhausted !!\n");
        
        memcpy(new_buff,_buff,_len);
        
        _buff = new_buff;
        
        _len += MAX_BUFF;
        
        delete [] old_buff;
        
#ifdef _DEBUG_
        std::cout<<"["<<_len<<" B]"<<std::endl;
#endif
  }

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

Referenced by store().

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getBuffer()

char* BinaryStorageBuffer::getBuffer ( ) const

inline

{return _buff;}

References _buff.

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

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getBuffLength()

off_t BinaryStorageBuffer::getBuffLength ( ) const

inline

{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

{return _bytes_out;} 

References _bytes_out.

Referenced by Metapop::retrieve_data().

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getTotByteRecorded()

off_t BinaryStorageBuffer::getTotByteRecorded ( ) const

inline

{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

  {
    
        if(((_bytes_out + nb_bytes) > _bytes_in) ) 
          fatal("BinaryStorageBuffer::read::attempt to read beyond buffer length (asked %i bytes)\n",nb_bytes);
        else {
          char *tab = (char*)out;
          if(nb_bytes == 1) {
        (*tab) = _buff[_bytes_out];
          } else {
        for(unsigned int i = 0; i < nb_bytes; ++i)
          tab[i] = _buff[_bytes_out + i];
          }
        }
        _bytes_out += nb_bytes;
  }

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_byte::retrieve_data(), TProtoNeutralGenes::retrieve_data(), TTNeutralGenes_bitstring::retrieve_data(), TTQuanti_continuous::retrieve_data(), TTQuanti_diallelic::retrieve_data(), TProtoQuanti::retrieve_data(), TTQuanti_diallelic_bitstring::retrieve_data(), and TTWolbachia::retrieve_data().

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set_buff() [1/3]

void BinaryStorageBuffer::set_buff ( BinaryDataSaver *  owner )

inline

  {
#ifdef _DEBUG_
        std::cout<<"BinaryStorageBuffer::set_buff";
#endif
        
        _myDataSaver = owner;
 
        if(_buff != NULL) delete [] _buff;
        
        _buff = new char[MAX_BUFF];
        
        if(_buff == NULL) fatal("BinaryStorageBuffer::set_buff::memory exhausted !!\n");
        
        _len = MAX_BUFF;
 
        _bytes_in = 0;
 
        _num_buckets = 0;
 
        _tot_bytes_in = 0L;
 
        memset(_buff,'\0',MAX_BUFF);
        
#ifdef _DEBUG_
    std::cout<<"[ok]"<<std::endl;
#endif
  }

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() [2/3]

void BinaryStorageBuffer::set_buff ( size_t  length )

inline

  {
    if(_buff != NULL) delete [] _buff;
 
    _buff = new char [length];
 
    memset(_buff,'\0', length);
 
    _bytes_in = _len = length ;
 
    _tot_bytes_in += _bytes_in;
 
    _bytes_out = 0;
 
    _num_buckets = 0;
  }

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

set_buff() [3/3]

void BinaryStorageBuffer::set_buff ( void *  zone, size_t  length  )

inline

  {
    if(_buff != NULL) delete [] _buff;
    
    _buff = new char [length];
    
    memcpy(_buff, zone, length);
    
    _bytes_in = _len = length ;
    
    _tot_bytes_in += _bytes_in;
 
    _bytes_out = 0;
 
    _num_buckets = 0;
  }

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

set_buff_from_file()

off_t BinaryStorageBuffer::set_buff_from_file ( int  FD, size_t  length  )

inline

  {
    if(_buff != NULL) delete [] _buff;
 
    _buff = new char [length];
 
    _len = length;
 
    off_t rout = -1; // , rcount = 0;
//    off_t rest = length;
 
    //@TODO need to find a solution for the call to read, replace with fread ?
 
//    while(rest != 0 && rout != 0) {
//
//      if( (rout = read(FD, &_buff[rcount], rest)) == -1)
//        fatal("Binary file appears corrupted:\n >>>> error while reading data: %s (reading in %li bytes, read %li so far)\n", strerror(errno), rest, rout);
//
//      rcount += rout;
//
//      rest -= rout;
//
//#ifdef _DEBUG_
//      message("BinaryStorageBuffer::set_buff_from_file:read %i bytes from file\n", rout);
//#endif
//    }
 
    _bytes_in = rout;
 
    _tot_bytes_in += _bytes_in;
 
    _bytes_out = 0;
 
    _num_buckets = 0;
 
    return rout;
  }

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

store()

void BinaryStorageBuffer::store	(	void *	stream,
		unsigned int	nb_bytes
	)

{
 
  while( !((_bytes_in + nb_bytes) < _len) ) extend_buff();
 
  if(nb_bytes == 1) {
 
    _buff[_bytes_in] = *(char*)stream;
 
  } else {
 
    char *tab = (char*)stream;
 
    for(unsigned int i = 0; i < nb_bytes; i++)
      _buff[_bytes_in + i] = tab[i];
  }
 
  _bytes_in += nb_bytes;
 
  _tot_bytes_in += nb_bytes;
 
  if(_bytes_in > MAX_BUCKET) {
 
    //      cout<<"\n BinaryStorageBuffer::store::bucket "<<_num_buckets<<" is full, emptying\n";
 
    // tell the binary data saver to empty to bucket to file
    _myDataSaver->printData();
 
    //      cout<<"wrote "<<_tot_bytes_in<<"B so far\n";
 
    _num_buckets++;
 
    _bytes_in = 0;
  }
}

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_byte::store_data(), TProtoNeutralGenes::store_data(), TTNeutralGenes_bitstring::store_data(), TTQuanti_continuous::store_data(), TTQuanti_diallelic::store_data(), TProtoQuanti::store_data(), TTQuanti_diallelic_bitstring::store_data(), TTWolbachia::store_data(), and BinaryDataSaver::storeData().

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Member Data Documentation

_buff

char* BinaryStorageBuffer::_buff

private

Referenced by clear(), emptyBuffer(), extend_buff(), getBuffer(), read(), set_buff(), set_buff_from_file(), store(), and ~BinaryStorageBuffer().

_bytes_in

off_t BinaryStorageBuffer::_bytes_in

private

Referenced by clear(), emptyBuffer(), getBuffLength(), read(), set_buff(), set_buff_from_file(), and store().

_bytes_out

off_t BinaryStorageBuffer::_bytes_out

private

Referenced by clear(), emptyBuffer(), getBytesOut(), read(), set_buff(), and set_buff_from_file().

_len

off_t BinaryStorageBuffer::_len

private

Referenced by clear(), emptyBuffer(), extend_buff(), set_buff(), set_buff_from_file(), and store().

_myDataSaver

BinaryDataSaver* BinaryStorageBuffer::_myDataSaver

private

Referenced by set_buff(), and store().

_num_buckets

unsigned int BinaryStorageBuffer::_num_buckets

private

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

_tot_bytes_in

off_t BinaryStorageBuffer::_tot_bytes_in

private

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

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

• binarystoragebuffer.h
• binarystoragebuffer.cc