SocketOutputBufferTemplate(
::libmaus::network::SocketBase * rdst,
int const rtag,
uint64_t const bufsize)
: dst(rdst), tag(rtag), B(bufsize), pa(B.get()), pc(pa), pe(pa+B.getN())
{
}
/**
* constructor
*
* @param rW output writer
* @param bufsize size of buffer
* @param rmetaid meta information for each written block
**/
MetaOutputBuffer8(
::libmaus::aio::AsynchronousWriter & rW,
uint64_t const bufsize,
uint64_t const rmetaid)
: B(bufsize), pa(B.get()), pc(pa), pe(pa+B.getN()), W(rW), metaid(rmetaid)
{
}
static void writeArray(::libmaus::autoarray::AutoArray<data_type> const & A,
std::string const & outputfilename)
{
this_type out(outputfilename,64*1024);
for ( uint64_t i = 0; i < A.getN(); ++i )
out.put(A[i]);
out.flush();
}
void putTerm(uint64_t num)
{
uint8_t * p = termbuf.get() + termbuf.getN();
for ( unsigned int i = 0; i < expo; ++i )
{
*(--p) = (num % base) + 1;
num /= base;
}
assert ( p == termbuf.get() );
for ( unsigned int i = 0; i < expo; ++i )
put( *(p++) );
}
SynchronousOutputBuffer8Posix(std::string const & rfilename, uint64_t const bufsize, bool truncate = true)
: filename(rfilename), B(bufsize), pa(B.get()), pc(pa), pe(pa+B.getN()), ptr(0)
{
if ( truncate )
{
int const tres = ::truncate(filename.c_str(),0);
if ( tres )
{
::libmaus::exception::LibMausException se;
se.getStream() << "SynchronousOutputBuffer8Posix::SynchronousOutputBuffer8Posix(): truncate() failed: " << strerror(errno) << std::endl;
se.finish();
throw se;
}
}
}
SynchronousGenericOutputPosix(
std::string const & rfilename,
uint64_t const bufsize,
bool const truncate,
uint64_t const offset,
bool const rmetasync = true
)
: filename(rfilename), dirname(::libmaus::util::ArgInfo::getDirName(filename)), metasync(rmetasync),
B(bufsize), pa(B.get()), pc(pa), pe(pa+B.getN()),
fd ( -1 ),
totalwrittenbytes(0), totalwrittenwords(0)
{
while ( (fd = ::open(filename.c_str(), truncate ? (O_WRONLY|O_TRUNC|O_CREAT) : O_WRONLY , 0755 )) < 0 )
{
switch ( errno )
{
case EINTR:
{
std::cerr << "Restarting open() system call interupted by signal." << std::endl;
break;
}
default:
{
::libmaus::exception::LibMausException se;
se.getStream() << "Failed to open file "<< filename <<" in SynchronousGenericOutputPosix: " <<
strerror(errno);
se.finish();
throw se;
}
}
}
if ( lseek ( fd, offset, SEEK_SET) == static_cast<off_t>(-1) )
{
close(fd);
::libmaus::exception::LibMausException se;
se.getStream() << "Failed to seek " << filename << " in SynchronousGenericOutputPosix: " <<
strerror(errno);
se.finish();
throw se;
}
#if 0
std::cerr << "File " << filename << " opened for output in "
<< ::libmaus::util::Demangle::demangle<this_type>() << std::endl;
#endif
}
bool getNextTriple(TripleEdge & triple)
{
if ( ! curbufleft )
{
istr.read ( reinterpret_cast<char *>(B.get()), B.getN() * sizeof(TripleEdge) );
if ( istr.gcount() == 0 )
return false;
assert ( istr.gcount() % sizeof(TripleEdge) == 0 );
curbufleft = istr.gcount() / sizeof(TripleEdge);
assert ( curbufleft );
curtrip = B.get();
}
triple = *(curtrip++);
curbufleft -= 1;
return true;
}
FileBunchLRU ( std::vector < std::string > const & rfilenames, uint64_t rlrusize = 1024)
: LRU(rlrusize), lrusize(rlrusize), filenames ( rfilenames ), mapping(filenames.size()), rmapping(lrusize), files(lrusize)
{
std::fill ( mapping.get(), mapping.get() + mapping.getN(), lrusize );
}
SynchronousOutputBuffer8(std::string const & rfilename, uint64_t const bufsize, bool truncate = true)
: filename(rfilename), B(bufsize), pa(B.get()), pc(pa), pe(pa+B.getN())
{
if ( truncate )
{
std::ofstream ostr(filename.c_str(), std::ios::binary);
ostr.flush();
}
}