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/*******************************************************************************
* $Id: Match.h,v 1.10 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 _RepeatMatch_h_
#define _RepeatMatch_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnClone.h"
#include <iostream>
#include <vector>
#include <set>
#include "libMems/MatchHashEntry.h"
namespace mems {
/**
* The Match class stores the location of an <b>equal size</b> (inexact or exactly)
* matching region
* between several sequences. There are numerous functions in this
* class which can be used to compare and manipulate this match.
*/
class RepeatMatch : public MatchHashEntry {
public:
RepeatMatch();
RepeatMatch( const uint32 seq_count, const gnSeqI mersize, const MemType m_type = seed );
RepeatMatch(const RepeatMatch& mhe);
~RepeatMatch();
void FromSeq( uint32 match_id, uint32 seq_id );
uint32 SeqId( uint32 match_id );
protected:
std::vector<uint32> m_seq_id;
private:
};
std::ostream& operator<<(std::ostream& os, const RepeatMatch& mhe); //write to source.
} // namespace mems
#endif // _RepeatMatch_h_
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