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/*******************************************************************************
* $Id: RepeatHash.h,v 1.8 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 _RepeatHash_h_
#define _RepeatHash_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libMems/MemHash.h"
namespace mems {
/**
* Finds repeats within a single sequence.
* This class extends the functionality of MemHash to search for repetitive
* matches within a single sequence.
*/
class RepeatHash : public MemHash{
public:
virtual RepeatHash* Clone() const;
virtual boolean CreateMatches();
protected:
virtual boolean EnumerateMatches( IdmerList& match_list );
virtual boolean HashMatch(IdmerList& match_list);
virtual SortedMerList* GetSar(uint32 sarI) const;
};
inline
SortedMerList* RepeatHash::GetSar(uint32 sarI) const{
return sar_table[0];
}
inline
bool idmer_greaterthan(idmer& a_v, idmer& m_v){
return (a_v.mer < m_v.mer);// ? true : false;
};
inline
bool idmer_position_lessthan(idmer& a_v, idmer& m_v){
return (a_v.position < m_v.position);// ? true : false;
};
}
#endif //_RepeatHash_h_
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