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/*==========================================================================
SeqAn - The Library for Sequence Analysis
http://www.seqan.de
============================================================================
Copyright (C) 2007
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
This library 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
Lesser General Public License for more details.
============================================================================
$Id: chunk_collector.h 4615 2009-07-25 07:09:21Z doering@PCPOOL.MI.FU-BERLIN.DE $
==========================================================================*/
#ifndef SEQAN_HEADER_CHUNK_COLLECTOR_H
#define SEQAN_HEADER_CHUNK_COLLECTOR_H
namespace SEQAN_NAMESPACE_MAIN
{
//////////////////////////////////////////////////////////////////////////////
/**
.Internal._ChunkCollector:
..cat:Classes
..summary:Reads piecewise from stream, collects pieces (chunks) in a vector.
..signature:_ChunkCollector<Host>
..param.Host:Type of host object that is used as allocator.
*/
//////////////////////////////////////////////////////////////////////////////
template <typename T>
struct ChunkLength
{
enum { VALUE = 1024 };
};
//////////////////////////////////////////////////////////////////////////////
// _StreamChunkCollector class: collects content of a stream in chunks
//////////////////////////////////////////////////////////////////////////////
template <typename THost>
class _ChunkCollector
{
public:
THost * data_host;
typename Size<THost>::Type data_length;
typedef ::std::vector<typename Value<THost>::Type *, ToStdAllocator<THost, typename Value<THost>::Type *> > Chunk_Holder;
Chunk_Holder data_chunks;
public:
static int const CHUNK_LENGTH = ChunkLength<_ChunkCollector>::VALUE;
public:
_ChunkCollector(THost & _host):
data_host(& _host),
data_length(0),
data_chunks(typename Chunk_Holder::allocator_type(_host))
{
}
~_ChunkCollector()
{
clear(*this);
}
};
template <typename THost>
inline void
clear(_ChunkCollector<THost> & me)
{
typedef _ChunkCollector<THost> TChunkCollector;
typedef typename TChunkCollector::Chunk_Holder Chunk_Holder;
typename Chunk_Holder::iterator it = me.data_chunks.begin();
typename Chunk_Holder::iterator it_end = me.data_chunks.end();
for (; it != it_end; ++it)
{
deallocate(me.data_host, *it, TChunkCollector::CHUNK_LENGTH);
}
me.data_chunks.clear();
me.data_length = 0;
}
template <typename THost>
inline typename Size<THost>::Type
length(_ChunkCollector<THost> const & me)
{
return me.data_length;
}
template <typename THost>
inline void
_setLength(_ChunkCollector<THost> & me, typename Size<THost>::Type new_length)
{
me.data_length = new_length;
}
template <typename THost>
inline int
chunkCount(_ChunkCollector<THost> const & me)
{
return me.data_chunks.size();
}
template <typename THost>
inline typename Value<THost>::Type *
getChunk(_ChunkCollector<THost> const & me, int chunk_number)
{
return me.data_chunks[chunk_number];
}
template <typename THost>
inline typename Value<THost>::Type *
createChunk(_ChunkCollector<THost> & me)
{
typedef _ChunkCollector<THost> TChunkCollector;
typename Value<THost>::Type * new_chunk;
allocate(me.data_host, new_chunk, TChunkCollector::CHUNK_LENGTH);
me.data_chunks.push_back(new_chunk);
return new_chunk;
}
//////////////////////////////////////////////////////////////////////////////
template <typename THost>
struct Host<_ChunkCollector<THost> >
{
typedef THost Type;
};
template <typename THost>
struct Host<_ChunkCollector<THost> const >
{
typedef THost Type;
};
//////////////////////////////////////////////////////////////////////////////
template <typename THost>
struct Value<_ChunkCollector<THost> >
{
typedef typename Value<THost>::Type Type;
};
template <typename THost>
struct Value<_ChunkCollector<THost> const >
{
typedef typename Value<THost>::Type Type;
};
//////////////////////////////////////////////////////////////////////////////
template <typename THost>
struct GetValue<_ChunkCollector<THost> >
{
typedef typename GetValue<THost>::Type Type;
};
template <typename THost>
struct GetValue<_ChunkCollector<THost> const >
{
typedef typename GetValue<THost>::Type Type;
};
//////////////////////////////////////////////////////////////////////////////
template <typename THost>
struct Size<_ChunkCollector<THost> >
{
typedef typename Size<THost>::Type Type;
};
template <typename THost>
struct Size<_ChunkCollector<THost> const >
{
typedef typename Size<THost>::Type Type;
};
//////////////////////////////////////////////////////////////////////////////
struct _Assign_Stream_2_ChunkCollector
{
template <typename THost, typename TSource>
static inline void
assign_(_ChunkCollector<THost> & target,
TSource & source)
{
clear(target);
while (!_streamEOF(source))
{
typename Value<THost>::Type * chunk = createChunk(target);
typename Size<THost>::Type count = _streamRead(chunk, source, ChunkLength< _ChunkCollector<THost> >::VALUE);
_setLength(target, length(target) + count);
}
}
template <typename THost, typename TSource>
static inline void
assign_(_ChunkCollector<THost> & target,
TSource & source,
typename Size< _ChunkCollector<THost> >::Type limit)
{
clear(target);
while (!_streamEOF(source))
{
typename Value<THost>::Type * chunk = createChunk(target);
typename Size<THost>::Type count = _streamRead(chunk, source, ChunkLength< _ChunkCollector<THost> >::VALUE);
_setLength(target, length(target) + count);
if (length(target) >= limit)
{
_setLength(target, limit);
break;
}
}
}
};
//////////////////////////////////////////////////////////////////////////////
template <typename THost, typename TSource>
inline void
assign(_ChunkCollector<THost> & target,
TSource & source)
{
_Assign_Stream_2_ChunkCollector::assign_(target, source);
}
template <typename THost, typename TSource>
inline void
assign(_ChunkCollector<THost> & target,
TSource const & source)
{
_Assign_Stream_2_ChunkCollector::assign_(target, source);
}
template <typename THost, typename TSource, typename TSize>
inline void
assign(_ChunkCollector<THost> & target,
TSource & source,
TSize limit)
{
_Assign_Stream_2_ChunkCollector::assign_(target, source, limit);
}
template <typename THost, typename TSource, typename TSize>
inline void
assign(_ChunkCollector<THost> & target,
TSource const & source,
TSize limit)
{
_Assign_Stream_2_ChunkCollector::assign_(target, source, limit);
}
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
template <typename TExpand>
struct _Assign_ChunkCollector_2_String
{
template <typename TTarget, typename TSource>
static void assign_(
TTarget & target,
TSource & source)
{
typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), TExpand());
int i_end = chunkCount(source);
typename Value<TTarget>::Type * pos = begin(target);
for (int i = 0; i < i_end; ++i)
{
bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
typename Value<TSource>::Type * chunk = getChunk(source, i);
arrayConstructCopy(chunk, chunk + chunk_length, pos);
if (is_last_chunk) break;
pos += chunk_length;
}
}
template <typename TTarget, typename TSource>
static void assign_(
TTarget & target,
TSource & source,
typename Size<TTarget>::Type limit)
{
typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), limit, TExpand());
int i_end = chunkCount(source);
typename Value<TTarget>::Type * pos = begin(target);
for (int i = 0; i < i_end; ++i)
{
bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
typename Value<TSource>::Type * chunk = getChunk(source, i);
arrayConstructCopy(chunk, chunk + chunk_length, pos);
if (is_last_chunk) break;
pos += chunk_length;
}
}
};
//////////////////////////////////////////////////////////////////////////////
template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
inline void
assign(String<TTargetValue, TTargetSpec> & target,
_ChunkCollector<TSourceHost> const & source,
Tag<TExpand> const tag)
{
_Assign_ChunkCollector_2_String<Tag<TExpand> const>::assign_(target, source);
}
template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
inline void
assign(String<TTargetValue, TTargetSpec> & target,
_ChunkCollector<TSourceHost> const & source,
typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
Tag<TExpand> const tag)
{
_Assign_ChunkCollector_2_String<Tag<TExpand> const>::assign_(target, source, limit);
}
//////////////////////////////////////////////////////////////////////////////
template <typename TExpand>
struct _Append_ChunkCollector_2_String
{
template <typename TTarget, typename TSource>
static void append_(
TTarget & target,
TSource & source)
{
typedef typename Size<TTarget>::Type TSize;
TSize target_length_old = length(target);
TSize part_length = _clearSpace(target, length(source), target_length_old, target_length_old, TExpand());
int i_end = chunkCount(source);
typename Value<TTarget>::Type * pos = begin(target) + target_length_old; //begin(target) was possibly changed by _clearSpace
for (int i = 0; i < i_end; ++i)
{
bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : (TSize) ChunkLength<TSource>::VALUE;
typename Value<TSource>::Type * chunk = getChunk(source, i);
arrayConstructCopy(chunk, chunk + chunk_length, pos);
if (is_last_chunk) break;
pos += chunk_length;
}
}
template <typename TTarget, typename TSource>
static void append_(
TTarget & target,
TSource & source,
typename Size<TTarget>::Type limit)
{
typedef typename Size<TTarget>::Type TSize;
TSize target_length_old = length(target);
TSize part_length = _clearSpace(target, length(source), target_length_old, target_length_old, limit, TExpand());
int i_end = chunkCount(source);
typename Value<TTarget>::Type * pos = begin(target) + target_length_old; //begin(target) was possibly changed by _clearSpace
for (int i = 0; i < i_end; ++i)
{
bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : (TSize) ChunkLength<TSource>::VALUE;
typename Value<TSource>::Type * chunk = getChunk(source, i);
arrayConstructCopy(chunk, chunk + chunk_length, pos);
if (is_last_chunk) break;
pos += chunk_length;
}
}
};
//////////////////////////////////////////////////////////////////////////////
template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
inline void
append(String<TTargetValue, TTargetSpec> & target,
_ChunkCollector<TSourceHost> const & source,
Tag<TExpand> const )
{
_Append_ChunkCollector_2_String<Tag<TExpand> const>::append_(target, source);
}
template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
inline void
append(String<TTargetValue, TTargetSpec> & target,
_ChunkCollector<TSourceHost> const & source,
typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
Tag<TExpand> const )
{
_Append_ChunkCollector_2_String<Tag<TExpand> const>::append_(target, source, limit);
}
//////////////////////////////////////////////////////////////////////////////
template <typename TExpand>
struct _Replace_ChunkCollector_2_String
{
template <typename TTarget, typename TSource>
static void replace_(
TTarget & target,
typename Size<TTarget>::Type pos_begin,
typename Size<TTarget>::Type pos_end,
TSource & source)
{
typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, TExpand());
int i_end = chunkCount(source);
typename Value<TTarget>::Type * pos = begin(target) + pos_begin;
for (int i = 0; i < i_end; ++i)
{
bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
typename Value<TSource>::Type * chunk = getChunk(source, i);
arrayConstructCopy(chunk, chunk + chunk_length, pos);
if (is_last_chunk) break;
pos += chunk_length;
}
}
template <typename TTarget, typename TSource>
static void replace_(
TTarget & target,
typename Size<TTarget>::Type pos_begin,
typename Size<TTarget>::Type pos_end,
TSource & source,
typename Size<TTarget>::Type limit)
{
typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, limit, TExpand());
int i_end = chunkCount(source);
typename Value<TTarget>::Type * pos = begin(target) + pos_begin;
for (int i = 0; i < i_end; ++i)
{
bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
typename Value<TSource>::Type * chunk = getChunk(source, i);
arrayConstructCopy(chunk, chunk + chunk_length, pos);
if (is_last_chunk) break;
pos += chunk_length;
}
}
};
//////////////////////////////////////////////////////////////////////////////
template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
inline void
replace(String<TTargetValue, TTargetSpec> & target,
typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
_ChunkCollector<TSourceHost> const & source,
Tag<TExpand> const tag)
{
_Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
}
template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
inline void
replace(String<TTargetValue, TTargetSpec> & target,
typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
_ChunkCollector<TSourceHost> const & source,
typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
Tag<TExpand> const tag)
{
_Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
}
//////////////////////////////////////////////////////////////////////////////
template <typename TTargetValue, typename TSourceHost, typename TExpand>
inline void
replace(TTargetValue * target,
size_t pos_begin,
size_t pos_end,
_ChunkCollector<TSourceHost> const & source,
Tag<TExpand> const tag)
{
_Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
}
template <typename TTargetValue, typename TSourceHost, typename TExpand>
inline void
replace(TTargetValue * target,
size_t pos_begin,
size_t pos_end,
_ChunkCollector<TSourceHost> const & source,
size_t limit,
Tag<TExpand> const tag)
{
_Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
}
//____________________________________________________________________________
/*
template <typename TTargetValue, typename TSourceHost, typename TExpand>
inline void
replace(TTargetValue * target,
size_t pos_begin,
size_t pos_end,
_ChunkCollector<TSourceHost> const & source,
Tag<TExpand> const tag)
{
_Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
}
template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
inline void
replace(String<TTargetValue, TTargetSpec> & target,
typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
_ChunkCollector<TSourceHost> const & source,
typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
Tag<TExpand> const tag)
{
_Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
}
*/
//////////////////////////////////////////////////////////////////////////////
} //namespace SEQAN_NAMESPACE_MAIN
#endif //#ifndef SEQAN_HEADER_...
|