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/*******************************************************************************
* $Id: ParallelMemHash.h,v 1.23 2004/03/01 02:40:08 darling Exp $
* This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
* This file is licensed under the GPL.
* Please see the file called COPYING for licensing details.
* **************
******************************************************************************/
#ifndef _ParallelMemHash_h_
#define _ParallelMemHash_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#ifdef _OPENMP
#include "libMUSCLE/threadstorage.h"
#include <omp.h>
#include "libMems/MemHash.h"
namespace mems {
/**
* ParallelMemHash implements an algorithm for finding exact matches of a certain minimal
* length in several sequences.
*/
class ParallelMemHash : public MemHash {
public:
ParallelMemHash();
ParallelMemHash(const ParallelMemHash& mh);
ParallelMemHash& operator=( const ParallelMemHash& mh );
virtual ParallelMemHash* Clone() const;
/**
* Finds (in parallel) all matches in the sequences contained by "match_list"
* The resulting list of matches is stored within "match_list"
*/
virtual void FindMatches( MatchList& match_list );
protected:
virtual MatchHashEntry* AddHashEntry(MatchHashEntry& mhe);
virtual void MergeTable();
TLS< std::vector< std::vector<MatchHashEntry*> > > thread_mem_table;
};
}
#else // _OPENMP
namespace mems {
/**
* When built without OpenMP, the ParallelMemHash is just a stub wrapper around MemHash
*/
class ParallelMemHash : public MemHash {
public:
ParallelMemHash() : MemHash();
ParallelMemHash(const ParallelMemHash& mh) : MemHash(mh);
ParallelMemHash& operator=( const ParallelMemHash& mh ) : MemHash::operator=(mh){ return *this; }
virtual ParallelMemHash* Clone() const{ return new ParallelMemHash(*this); }
};
}
#endif // _OPENMP
#endif //_ParallelMemHash_h_
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